Mercurial > repos > iuc > isoformswitchanalyzer

annotate isoformswitchanalyzer.xml @ 6:293ed243039c draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
author iuc
date Wed, 14 Jan 2026 09:30:17 +0000
parents 69fa05891f9d
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1 <tool id="isoformswitchanalyzer" name="IsoformSwitchAnalyzeR" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
2 <description>statistical identification of isoform switching</description>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
3 <macros>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
4 <import>macros.xml</import>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
5 </macros>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
6 <expand macro='xrefs'/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
7 <expand macro='requirements'/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
8 <stdio>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
9 <regex match="Execution halted"
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
10 source="both"
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
11 level="fatal"
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
12 description="Execution halted." />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
13 <regex match="Error in"
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
14 source="both"
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
15 level="fatal"
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
16 description="An undefined error occurred, please check your input carefully and contact your administrator." />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
17 <regex match="Fatal error"
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
18 source="both"
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
19 level="fatal"
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
20 description="An undefined error occurred, please check your input carefully and contact your administrator." />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
21 </stdio>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
22 <command><![CDATA[
5
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
23 #set $conditions = list()
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
24 #set $sampleIDs = list()
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
25 #set $replicates = list()
0
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
26 #if $functionMode.selector == 'data_import'
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
27 #if $functionMode.transcriptome.is_of_type("fasta.gz"):
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
28 ln -s '${functionMode.transcriptome}' './transcriptome.fasta.gz' &&
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
29 #set $transcriptome = './transcriptome.fasta.gz'
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
30 #else
1
5ae218cee629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7d278967f9c8d2c6ce0a8f83be2c444822746bbf
iuc
parents: 0
diff changeset
31 ln -s '${functionMode.transcriptome}' './transcriptome.fasta' &&
0
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
32 #set $transcriptome = './transcriptome.fasta'
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
33 #end if
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
34 #if $functionMode.genomeAnnotation.is_of_type("gtf.gz"):
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
35 ln -s '${functionMode.genomeAnnotation}' './annotation.gtf.gz' &&
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
36 #set $annotation = './annotation.gtf.gz'
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
37 #else
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
38 ln -s '${functionMode.genomeAnnotation}' './annotation.gtf' &&
1
5ae218cee629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7d278967f9c8d2c6ce0a8f83be2c444822746bbf
iuc
parents: 0
diff changeset
39 #set $annotation = './annotation.gtf'
0
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
40 #end if
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
41 mkdir -p 'input_files' &&
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
42 #if $functionMode.countFiles != 'disabled':
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
43 mkdir -p "count_files/factor1/" &&
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
44 mkdir -p "count_files/factor2/" &&
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
45 #end if
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
46 #if $functionMode.tool_source.selector == 'stringtie'
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
47 #set $filename = 't_data.ctab'
2
db30020fee5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a
iuc
parents: 1
diff changeset
48 #if $functionMode.tool_source.novoisoforms.selector == 'novel'
db30020fee5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a
iuc
parents: 1
diff changeset
49 #if $functionMode.tool_source.novoisoforms.stringtieAnnotation.is_of_type("gtf.gz"):
db30020fee5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a
iuc
parents: 1
diff changeset
50 ln -s '${$functionMode.tool_source.novoisoforms.stringtieAnnotation}' './stringtie_annotation.gtf.gz' &&
db30020fee5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a
iuc
parents: 1
diff changeset
51 #set $stringtie_annotation = './stringtie_annotation.gtf.gz'
db30020fee5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a
iuc
parents: 1
diff changeset
52 #else
db30020fee5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a
iuc
parents: 1
diff changeset
53 ln -s '${$functionMode.tool_source.novoisoforms.stringtieAnnotation}' './stringtie_annotation.gtf' &&
db30020fee5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a
iuc
parents: 1
diff changeset
54 #set $stringtie_annotation = './stringtie_annotation.gtf'
db30020fee5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a
iuc
parents: 1
diff changeset
55 #end if
db30020fee5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a
iuc
parents: 1
diff changeset
56 #end if
5
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
57 #else if $functionMode.tool_source.selector == 'salmon'
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
58 #set $filename = 'quant.sf'
0
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
59 #else
5
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
60 #set $filename = 'abundance.tsv'
0
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
61 #end if
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
62
6
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
63 ## read cofactor repeats and generate cofactor_map dictionary
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
64 ## cofactor_map structure: {file_path: {cofactor_name: cofactor_level_name, ...}, ...}
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
65 #set $cofactor_map = {}
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
66 #set $cofactor_names = []
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
67 #for $cofactor_item in $functionMode.tool_source.cofactor:
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
68 #set $cofactor_name = str($cofactor_item.cofactor_name)
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
69 $cofactor_names.append($cofactor_name)
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
70 #for $level_item in $cofactor_item.cofactor_level:
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
71 #set $level_name = str($level_item.cofactor_level_name)
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
72 #for $level_file in $level_item.cofactor_level_files:
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
73 #set $file_path = str($level_file)
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
74 #if $file_path not in $cofactor_map:
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
75 #set $cofactor_map[$file_path] = {}
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
76 #end if
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
77 #set $cofactor_map[$file_path][$cofactor_name] = $level_name
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
78 #end for
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
79 #end for
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
80 #end for
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
81
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
82 ## create file_to_sample_map dictionary
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
83 #set $file_to_sample_map = {}
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
84
5
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
85 #for $index in range(len($functionMode.tool_source.first_factor.trans_counts)):
6
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
86 #set $sampleID = str($functionMode.tool_source.first_factor.factorLevel) + str($index)
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
87 #set $trans_file = $functionMode.tool_source.first_factor.trans_counts[$index]
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
88 #set $file_to_sample_map[$sampleID] = str($trans_file)
5
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
89 $conditions.append($functionMode.tool_source.first_factor.factorLevel)
6
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
90 $sampleIDs.append($sampleID)
5
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
91 $replicates.append($index)
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
92 mkdir './input_files/${functionMode.tool_source.first_factor.factorLevel}${index}/' &&
6
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
93 ln -s $trans_file './input_files/${functionMode.tool_source.first_factor.factorLevel}${index}/${filename}' &&
0
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
94 #end for
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
95
5
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
96 #for $index in range(len($functionMode.tool_source.second_factor.trans_counts)):
6
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
97 #set $sampleID = str($functionMode.tool_source.second_factor.factorLevel) + str($index)
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
98 #set $trans_file = $functionMode.tool_source.second_factor.trans_counts[$index]
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
99 #set $file_to_sample_map[$sampleID] = str($trans_file)
5
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
100 $conditions.append($functionMode.tool_source.second_factor.factorLevel)
6
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
101 $sampleIDs.append($sampleID)
5
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
102 $replicates.append($index)
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
103 mkdir './input_files/${functionMode.tool_source.second_factor.factorLevel}${index}/' &&
6
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
104 ln -s $trans_file './input_files/${functionMode.tool_source.second_factor.factorLevel}${index}/${filename}' &&
0
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
105 #end for
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
106
6
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
107
0
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
108 Rscript '${__tool_directory__}/IsoformSwitchAnalyzeR.R'
5
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
109 #for $i, $condition in enumerate($conditions)
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
110 --condition $condition
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
111 --sampleID $sampleIDs[$i]
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
112 --replicate $replicates[$i]
6
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
113 #set $sample_file = $file_to_sample_map[$sampleIDs[$i]]
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
114 #if $sample_file in $cofactor_map
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
115 #set $cofactor_values = []
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
116 #for $cofactor_name in $cofactor_names:
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
117 #if $cofactor_name in $cofactor_map[$sample_file]
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
118 #set $cofactor_value = $cofactor_map[$sample_file][$cofactor_name]
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
119 #silent $cofactor_values.append(str($cofactor_value))
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
120 #end if
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
121 #end for
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
122 --cofactors $(','.join($cofactor_values))
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
123 #end if
5
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
124 #end for
6
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
125 #if len($cofactor_names) > 0
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
126 --cofactorNames $(','.join($cofactor_names))
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
127 #end if
5
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
128 $functionMode.pairedSamples
0
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
129 --modeSelector $functionMode.selector
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
130 --parentDir './input_files'
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
131 --annotation $annotation
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
132 --transcriptome $transcriptome
2
db30020fee5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a
iuc
parents: 1
diff changeset
133 $functionMode.removeNonConvensionalChr
0
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
134 --toolSource $functionMode.tool_source.selector
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
135 #if $functionMode.tool_source.selector == 'stringtie'
2
db30020fee5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a
iuc
parents: 1
diff changeset
136 #if $functionMode.tool_source.novoisoforms.selector == 'novel'
db30020fee5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a
iuc
parents: 1
diff changeset
137 --stringtieAnnotation $stringtie_annotation
db30020fee5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a
iuc
parents: 1
diff changeset
138 #end if
0
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
139 --readLength $functionMode.tool_source.averageSize
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
140 $functionMode.tool_source.fixStringTieAnnotationProblem
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
141 #end if
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
142 --countFiles $functionMode.countFiles
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
143 #else if $functionMode.selector == 'first_step'
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
144 Rscript '${__tool_directory__}/IsoformSwitchAnalyzeR.R'
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
145 --modeSelector $functionMode.selector
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
146 --rObject $functionMode.robject
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
147 --alpha $functionMode.alpha
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
148 --dIFcutoff $functionMode.dIFcutoff
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
149 $functionMode.onlySigIsoforms
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
150 $functionMode.filterForConsequences
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
151 --geneExpressionCutoff $functionMode.prefilter.geneExpressionCutoff
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
152 --isoformExpressionCutoff $functionMode.prefilter.isoformExpressionCutoff
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
153 --IFcutoff $functionMode.prefilter.IFcutoff
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
154 $functionMode.prefilter.removeSingleIsformGenes
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
155 $functionMode.prefilter.keepIsoformInAllConditions
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
156 $functionMode.dexseq.correctForConfoundingFactors
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
157 $functionMode.dexseq.overwriteIFvalues
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
158 $functionMode.dexseq.reduceToSwitchingGenes
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
159 $functionMode.dexseq.reduceFurtherToGenesWithConsequencePotential
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
160 $functionMode.dexseq.keepIsoformInAllConditions
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
161 --minORFlength $functionMode.novel_isoform.minORFlength
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
162 --orfMethod $functionMode.novel_isoform.orfMethod
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
163 --PTCDistance $functionMode.novel_isoform.PTCDistance
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
164 $functionMode.extract_sequence.removeShortAAseq
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
165 $functionMode.extract_sequence.removeLongAAseq
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
166 $functionMode.extract_sequence.removeORFwithStop
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
167 $functionMode.extract_sequence.onlySwitchingGenes
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
168 #else
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
169 #if $functionMode.protein_domains.selector == 'enabled'
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
170 mkdir -p './pfam_files' &&
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
171 #for $index,$filename in enumerate($functionMode.protein_domains.analyzePFAM)
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
172 ln -s $filename './pfam_files/dataset${index}.txt' &&
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
173 #end for
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
174 #end if
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
175 #if $functionMode.signal_peptides.selector == 'enabled'
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
176 mkdir -p './signalp_files' &&
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
177 #for $index,$filename in enumerate($functionMode.signal_peptides.analyzeSignalP)
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
178 ln -s $filename './signalp_files/dataset${index}.txt' &&
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
179 #end for
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
180 #end if
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
181 #if $functionMode.disordered_regions.selector == 'netsurfp'
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
182 mkdir -p './netsurf_files' &&
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
183 #for $index,$filename in enumerate($functionMode.disordered_regions.analyzeNetSurfP2)
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
184 ln -s $filename './netsurf_files/dataset${index}.txt' &&
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
185 #end for
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
186 #end if
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
187 Rscript '${__tool_directory__}/IsoformSwitchAnalyzeR.R'
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
188 --modeSelector $functionMode.selector
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
189 --rObject $functionMode.robject
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
190 --analysisMode $functionMode.analysis_mode.selector
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
191 --alpha $functionMode.analysis_mode.alpha
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
192 --dIFcutoff $functionMode.analysis_mode.dIFcutoff
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
193 #if $functionMode.analysis_mode.selector == 'top'
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
194 --genesToPlot $functionMode.analysis_mode.n
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
195 $functionMode.analysis_mode.advanced_options.filterForConsequences
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
196 $functionMode.analysis_mode.advanced_options.sortByQvals
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
197 $functionMode.analysis_mode.advanced_options.onlySigIsoforms
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
198 $functionMode.analysis_mode.advanced_options.onlySwitchingGenes
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
199 $functionMode.analysis_mode.advanced_options.countGenes
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
200 $functionMode.analysis_mode.advanced_options.asFractionTotal
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
201 $functionMode.analysis_mode.advanced_options.plotGenes
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
202 $functionMode.analysis_mode.advanced_options.simplifyLocation
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
203 $functionMode.analysis_mode.advanced_options.removeEmptyConsequences
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
204 $functionMode.analysis_mode.advanced_options.removeEmptyConsequences
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
205 #else
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
206 --gene $functionMode.analysis_mode.gene
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
207 --IFcutoff $functionMode.analysis_mode.advanced_options.IFcutoff
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
208 $functionMode.analysis_mode.advanced_options.rescaleTranscripts
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
209 $functionMode.analysis_mode.advanced_options.reverseMinus
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
210 $functionMode.analysis_mode.advanced_options.addErrorbars
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
211 $functionMode.analysis_mode.advanced_options.onlySwitchingGenes
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
212 #end if
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
213 #if $functionMode.coding_potential.selector == 'cpat'
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
214 --pathToCPATresultFile $functionMode.coding_potential.analyzeCPAT
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
215 --codingCutoff $functionMode.coding_potential.codingCutoff
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
216 #else if $functionMode.coding_potential.selector == 'cpc2'
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
217 --pathToCPC2resultFile $functionMode.coding_potential.analyzeCPC2
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
218 $functionMode.coding_potential.removeNoncodingORFs
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
219 --codingCutoff $functionMode.coding_potential.codingCutoff
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
220 #end if
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
221 #if $functionMode.protein_domains.selector == 'enabled'
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
222 --pathToPFAMresultFile './pfam_files'
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
223 #end if
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
224 #if $functionMode.signal_peptides.selector == 'enabled'
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
225 --pathToSignalPresultFile './signalp_files'
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
226 --minSignalPeptideProbability $functionMode.signal_peptides.minSignalPeptideProbability
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
227 #end if
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
228 #if $functionMode.disordered_regions.selector == 'netsurfp'
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
229 --pathToNetSurfP2resultFile './netsurf_files'
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
230 --smoothingWindowSize $functionMode.disordered_regions.smoothingWindowSize
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
231 --probabilityCutoff $functionMode.disordered_regions.probabilityCutoff
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
232 --minIdrSize $functionMode.disordered_regions.minIdrSize
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
233 #else if $functionMode.disordered_regions.selector == 'iupred2a'
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
234 --pathToIUPred2AresultFile $functionMode.disordered_regions.AanalyzeIUPred2A
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
235 --smoothingWindowSize $functionMode.disordered_regions.smoothingWindowSize
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
236 --probabilityCutoff $functionMode.disordered_regions.probabilityCutoff
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
237 --minIdrSize $functionMode.disordered_regions.minIdrSize
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
238 $functionMode.disordered_regions.annotateBindingSites
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
239 --minIdrBindingSize $functionMode.disordered_regions.minIdrBindingSize
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
240 --minIdrBindingOverlapFrac $functionMode.disordered_regions.minIdrBindingOverlapFrac
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
241 #end if
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
242 --ntCutoff $functionMode.analyzeSwitchConsequences.ntCutoff
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
243 #if $functionMode.analyzeSwitchConsequences.ntFracCutoff
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
244 --ntFracCutoff $functionMode.analyzeSwitchConsequences.ntFracCutoff
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
245 #end if
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
246 --ntJCsimCutoff $functionMode.analyzeSwitchConsequences.ntJCsimCutoff
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
247 --AaCutoff $functionMode.analyzeSwitchConsequences.AaCutoff
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
248 --AaFracCutoff $functionMode.analyzeSwitchConsequences.AaFracCutoff
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
249 --AaJCsimCutoff $functionMode.analyzeSwitchConsequences.AaJCsimCutoff
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
250 $functionMode.analyzeSwitchConsequences.removeNonConseqSwitches
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
251 #if $functionMode.analysis_mode.selector == 'top'
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
252 && mkdir -p './pdf_outputs/'
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
253 && mv *pdf './pdf_outputs/'
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
254 && mv *_vs_* gene_plots
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
255 #end if
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
256 #end if
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
257 ]]></command>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
258 <inputs>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
259 <conditional name="functionMode">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
260 <param name="selector" type="select" label="Tool function mode"
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
261 help="The first step of a IsoformSwitchAnalyzeR workflow is to import and integrate the isoform quantification
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
262 with its basic annotation. Once you have all the relevant data imported into R (IsoformSwitchAnalyzeR will
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
263 also help you with that), the workflow for identification and analysis of isoform switches with functional
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
264 consequences can be divided into two parts.">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
265 <option value="data_import">Import data</option>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
266 <option value="first_step">Analysis part one: Extract isoform switches and their sequences</option>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
267 <option value="second_step">Analysis part two: Plot all isoform switches and their annotation</option>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
268 </param>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
269 <when value="data_import">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
270 <conditional name="tool_source">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
271 <param name="selector" type="select" label="Quantification data source" help="IsoformSwitchAnalyzeR has different functions for importing data from different sources.">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
272 <option value="stringtie">StringTie</option>
5
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
273 <option value="salmon">Salmon</option>
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
274 <option value="kallisto">Kallisto</option>
0
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
275 </param>
5
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
276 <when value="salmon">
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
277 <expand macro="macro_inputs"/>
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
278 </when>
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
279 <when value="kallisto">
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
280 <expand macro="macro_inputs"/>
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
281 </when>
0
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
282 <when value="stringtie">
5
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
283 <expand macro="macro_inputs"/>
0
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
284 <param name="averageSize" type="integer" min="0" value="150" label="Average read length" help="Must be the number of base pairs sequenced. e.g. if the data
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
285 quantified is 75 bp paired ends the the user should supply readLength=75" />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
286 <param argument="fixStringTieAnnotationProblem" type="boolean" truevalue="--fixStringTieAnnotationProblem" falsevalue="" checked="true"
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
287 label="Fix StringTie annotation problem" help="This option will automatically try and correct some of the annoation problems created when
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
288 doing transcript assembly (unassigned transcripts and merged genes)" />
2
db30020fee5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a
iuc
parents: 1
diff changeset
289 <conditional name="novoisoforms">
4
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
290 <param name="selector" type="select" label="Analysis mode">
2
db30020fee5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a
iuc
parents: 1
diff changeset
291 <option value="novel">Include novel isoforms in analysis</option>
db30020fee5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a
iuc
parents: 1
diff changeset
292 <option value="reference">Reference-only analysis</option>
db30020fee5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a
iuc
parents: 1
diff changeset
293 </param>
db30020fee5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a
iuc
parents: 1
diff changeset
294 <when value="novel">
db30020fee5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a
iuc
parents: 1
diff changeset
295 <param name="stringtieAnnotation" type="data" format="gtf,gtf.gz" label="Annotation generated by StringTie merge"
db30020fee5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a
iuc
parents: 1
diff changeset
296 help="The merged GTF is used to recalculate expression estimates using the merged, novel transcripts." />
db30020fee5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a
iuc
parents: 1
diff changeset
297 </when>
db30020fee5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a
iuc
parents: 1
diff changeset
298 <when value="reference"/>
db30020fee5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a
iuc
parents: 1
diff changeset
299 </conditional>
0
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
300 </when>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
301 </conditional>
2
db30020fee5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a
iuc
parents: 1
diff changeset
302 <param name="genomeAnnotation" type="data" format="gtf,gtf.gz" label="Genome annotation"
0
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
303 help="It is used to integrate the coding sequence (CDS) regions from in the GTF file as the ORF regions used by IsoformSwitchAnalyzeR." />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
304 <param name="transcriptome" type="data" format="fasta,fasta.gz" label="Transcriptome"
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
305 help="Please note this different from a fasta file with the sequences of the entire genome." />
2
db30020fee5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a
iuc
parents: 1
diff changeset
306 <param argument="removeNonConvensionalChr" type="boolean" truevalue="--removeNonConvensionalChr" falsevalue="" checked="false"
db30020fee5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a
iuc
parents: 1
diff changeset
307 label="Remove non-conventional chromosomes" help="These regions are typically used to annotate regions that cannot be associated to a specific region." />
5
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
308 <param argument="pairedSamples" type="boolean" truevalue="--pairedSamples" falsevalue="" checked="false" label="Paired samples between factors" help="Samples
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
309 from different factors belong to the same individual (e.g. samples from same patient from health and cancerous tissues or different parts from the same plant)" />
0
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
310 <param name="countFiles" type="select" label="Generate count matrix files" help="If IsoformSwitchAnalyzeR is used for fixing Stringtie annotation
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
311 problem, it can generate count files for analyzing differential expression with DESeq2 (when selecting collection) or CEMiTool (when secting the expression matrix format).">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
312 <option value="disabled">Disabled</option>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
313 <option value="collection">Collection of count files</option>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
314 <option value="matrix">Expression matrix</option>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
315 </param>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
316 </when>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
317
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
318 <!--WRAPPER FIRST STEP SECTION-->
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
319
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
320 <when value="first_step">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
321 <param name="robject" type="data" format="rdata" label="IsoformSwitchAnalyzeR R object" help="It is generated when running the analysis part 1." />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
322 <expand macro="macro_alpha_difcutoff"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
323 <expand macro="macro_onlysigisoforms1"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
324 <param argument="filterForConsequences" type="boolean" truevalue="--filterForConsequences" falsevalue="" checked="false"
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
325 label="Filter for consquences" help="Filter for genes with functional consequences. The output will then be the number of significant genes
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
326 and isoforms originating from genes with predicted consequences" />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
327 <section name="prefilter" title="Pre-filter parameters" help="SwitchAnalyzeR will remove genes/isoforms with the aim of allowing faster
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
328 processing time as well as more trustworthy results.">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
329 <param argument="geneExpressionCutoff" type="float" min="0" value="1" label="Gene expression cutoff" help="The expression cutoff (most
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
330 likely in TPM/RPKM/FPKM) which the average expression in BOTH condisions must be higher than." />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
331 <param argument="isoformExpressionCutoff" type="float" min="0" value="0" label="Isoform expresion cutoff" help="The expression cutoff (most
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
332 likely in RPKM/FPKM) which isoforms must be expressed more than, in at least one conditions of a comparison. Default is 0 (which removes
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
333 completely unused isoforms)." />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
334 <expand macro="macro_ifcutoff" value="0.01" help="The cutoff on isoform usage (measured as Isoform Fraction) which isoforms must be used more
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
335 than in at least one conditions of a comparison" />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
336 <param argument="removeSingleIsformGenes" type="boolean" truevalue="--removeSingleIsformGenes" falsevalue="" checked="true" label="Remove single isoform genes"
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
337 help="Only keep genes containing more than one isoform (in any comparison, after the other filters have been applied)" />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
338 <expand macro="macro_keeisoforminall" checked="false"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
339 </section>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
340 <section name="dexseq" title="DEXseq parameters" help="DEXSeq is used to test isoforms (isoform resolution) for differential isoform usage.">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
341 <param argument="correctForConfoundingFactors" type="boolean" truevalue="--correctForConfoundingFactors" falsevalue="" checked="true" label="Correct for confounding factors"
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
342 help="A logic indicating whether IsoformSwitchAnalyzeR to use limma to correct for any confounding effects (e.g. batch effects) as indicated in the
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
343 design matrix (as additional columns (apart from the two default columns)) " />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
344 <param argument="overwriteIFvalues" type="boolean" truevalue="--overwriteIFvalues" falsevalue="" checked="true" label="Overwrite IF values" help="It indicates
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
345 whether to overwrite the IF and dIF stored in the switchAnalyzeRlist with the corrected IF and dIF values - if no confounding effects are
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
346 present in the design matrix this will not change anything" />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
347 <param argument="reduceToSwitchingGenes" type="boolean" truevalue="--reduceToSwitchingGenes" falsevalue="" checked="true" label="Reduce to switch genes" help="Reduced to the
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
348 genes which contains at least one isoform significantly differential used (as indicated by the alpha and dIFcutoff parameters" />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
349 <param argument="reduceFurtherToGenesWithConsequencePotential" type="boolean" truevalue="--reduceFurtherToGenesWithConsequencePotential" falsevalue="" checked="false"
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
350 label="Reduce to genes with consequence potential" help="This argument is a more strict version of reduceToSwitchingGenes
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
351 as it not only requires that at least one isoform is significantly differential used (as indicated by the alpha and dIFcutoff parameters) but also that there is an isoform
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
352 with the opposite effect size (e.g. used less if the first isoform is used more). The minimum effect size of the opposing isoform usage is also controlled by dIFcutoff.
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
353 The existence of such an opposing isoform means a switch pair can be formed" />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
354 <expand macro="macro_keeisoforminall" checked="true"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
355 </section>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
356 <section name="novel_isoform" title="Novel isoform analysis parameters" help="For the subset of isoforms not already annotated with ORFs this
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
357 function predicts the most likely Open Reading Frame (ORF) and the NMD sensitivity. This function is made to help annotate
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
358 isoforms if you have performed (guided) de-novo isoform reconstruction (isoform deconvolution).">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
359 <param argument="minORFlength" type="integer" min="0" value="100" label="Minimum ORF length" help="The minimum size (in nucleotides) an
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
360 ORF must be to be considered (and reported). Default is 100 nucleotides, which around 97.5% of Gencode coding isoforms in both human and mouse have." />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
361 <param argument="orfMethod" type="select" label="ORF identification method" help="More information in the help section">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
362 <option value="longest.AnnotatedWhenPossible">Longest and annotated when possible</option>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
363 <option value="longest">Longest</option>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
364 <option value="mostUpstream">Most upstream</option>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
365 <option value="longestAnnotated">Longest annotated</option>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
366 <option value="mostUpstreamAnnoated">Most upstream annotated</option>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
367 </param>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
368 <param argument="PTCDistance" type="integer" min="0" value="50" label="Maximal allowed premature termination codon-distance" help="The minimum
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
369 distance (number of nucleotides) from the STOP codon to the final exon-exon junction. If the distance from the STOP to the final exon-exon
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
370 junction is larger than this the isoform to be marked as NMD-sensitive. " />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
371 </section>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
372 <section name="extract_sequence" title="Sequence extraction parameters" help="switchAnalyzeR will extracts the nucleotide (NT) sequence of transcripts by
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
373 extracting and concatenating the sequences of a reference genome corresponding to the genomic coordinates of the isoforms. ">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
374 <expand macro="macro_onlyswitching"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
375 <param argument="removeShortAAseq" type="boolean" truevalue="--removeShortAAseq" falsevalue="" checked="true" label="Remove short aminoacid sequences" help="This
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
376 option exist to allows for easier usage of the Pfam and SignalP web servers which both currently have restrictions on allowed sequence lengths. If
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
377 enabled AA sequences are filtered to be > 5 AA. This will only affect the sequences written to the FASTA file not the sequences added to the switchAnalyzeRlist" />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
378 <param argument="removeLongAAseq" type="boolean" truevalue="--removeLongAAseq" falsevalue="" checked="false" label="Remove long aminoacid sequences" help="A
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
379 logical indicating whether to removesequences based on their length. This option exist to allows for easier usage of the Pfam and SignalP web servers
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
380 which both currently have restrictions on allowed sequence lengths. If enabled AA sequences are filtered to be smaller 1000 AA. This will only affect the
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
381 sequences written to the fasta file (if writeToFile=TRUE) not the sequences added to the switchAnalyzeRlist. " />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
382 <param argument="removeORFwithStop" type="boolean" truevalue="--removeORFwithStop" falsevalue="" checked="true" label="Remove ORFs containint STOP codons" help="ORFs
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
383 containing stop codons, defined as * when the ORF nucleotide sequences is translated to the amino acid sequence, should be A) removed from the ORF
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
384 annotation in the switchAnalyzeRlist and B) removed from the sequences added to the switchAnalyzeRlist and/or written to FASTA files. This is only
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
385 necessary if you are analyzing quantified known annotated data where you supplied a GTF file to the import function" />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
386 </section>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
387 <param name="outputs_first" type="select" display="checkboxes" multiple="true" label="Outputs selector">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
388 <option value="nt" selected="true">Nucleotide sequences</option>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
389 <option value="aa" selected="true">Aminoacid sequences</option>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
390 <option value="summary" selected="true">Gene switch summary</option>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
391 </param>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
392 </when>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
393
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
394 <!-- WRAPPER SECOND STEP SECTION-->
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
395
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
396 <when value="second_step">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
397 <param name="robject" type="data" format="rdata" label="IsoformSwitchAnalyzeR R object" help="It is generated when running the analysis part 2." />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
398 <conditional name="analysis_mode">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
399 <param name="selector" type="select" label="Analysis mode" help="This selector allows so specify if you want to analyze a specific gene or
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
400 the (top) switching genes/isoforms ">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
401 <option value="top" selected="true">Full analysis</option>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
402 <option value="single">Analyze specific gene</option>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
403 </param>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
404 <when value="top">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
405 <expand macro="macro_alpha_difcutoff"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
406 <param argument="n" type="integer" min="1" value="10" label="Number of top switching features (genes/isoforms) to plot"
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
407 help="This parameters allows to specify the number of top genes/isoforms to plot"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
408 <section name="advanced_options" title="Full analysis advanced options">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
409 <param argument="filterForConsequences" type="boolean" truevalue="--filterForConsequences" falsevalue="" checked="false" label="Filter genes with functional consequences"
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
410 help="The output will then be the number of significant genes and isoforms originating from genes with predicted consequences"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
411 <param argument="sortByQvals" type="boolean" truevalue="--sortByQvals" falsevalue="" checked="true" label="Sorting mode" help="A logic indicating
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
412 whether to the top n features are sorted by decreasing significance (increasing q-values) (if enabled) or decreasing switch size
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
413 (absolute dIF, which are still significant as defined by alpha) (if disabled). The dIF values for genes are considered as the total
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
414 change within the gene calculated as sum(abs(dIF)) for each gene" />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
415 <expand macro="macro_onlysigisoforms2"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
416 <expand macro="macro_onlyswitching"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
417 <param argument="countGenes" type="boolean" truevalue="--countGenes" falsevalue="" checked="true" label="Number genes or isoform switches counts" help="This parameter indicates
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
418 whether it is the number of genes (if enabled) or isoform switches (if disabled) which primary result in gain/loss that are counted" />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
419 <param argument="asFractionTotal" type="boolean" truevalue="--asFractionTotal" falsevalue="" checked="false" label="Summary as numbers of as fraction" help="The consequences/splicing events
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
420 should be summarized calculated as numbers (if disabled) or as a fraction of the total number of switches/genes" />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
421 <param argument="plotGenes" type="boolean" truevalue="--plotGenes" falsevalue="" checked="false" label="Plot number/fraction of genes or isoforms" help="Plot the number/fraction of genes with
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
422 (if enabled) or isoforms (if disabled) involved with isoform switches with functional consequences (both filtered via alpha and dIFcutoff)" />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
423 <param argument="simplifyLocation" type="boolean" truevalue="--simplifyLocation" falsevalue="" checked="true" label="Simplify location" help="Simplify the switches involved in changes
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
424 in subcellular localizations (due the the hundreds of possible combinations)" />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
425 <param argument="removeEmptyConsequences" type="boolean" truevalue="--removeEmptyConsequences" falsevalue="" checked="false" label="Remove empty consequences" help="Remove consequenses analyzed
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
426 but where no differences was found (those showing zero in the plot)" />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
427 <param argument="analysisOppositeConsequence" type="boolean" truevalue="--analysisOppositeConsequence" falsevalue="" checked="false"
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
428 label="Analysis opposite consequences in enrichment analysis" help="Reverse the analysis meaning if 'Domain gains' are analyze will case the analysis to be performed on 'Domain loss'.
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
429 The main effect is for the visual appearance of plot which will be mirrored (around the 0.5 fraction)" />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
430 </section>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
431 </when>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
432 <when value="single">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
433 <param argument="gene" type="text" value="" label="Gene name" help="Either the gene_id or the gene name of the gene to plot">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
434 <sanitizer invalid_char="">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
435 <valid initial="string.letters,string.digits">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
436 <add value="_" />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
437 <add value="-" />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
438 </valid>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
439 </sanitizer>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
440 <validator type="regex">[0-9a-zA-Z_-]+</validator>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
441 </param>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
442 <expand macro="macro_alpha_difcutoff"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
443 <section name="advanced_options" title="Single gene mode advanced options">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
444 <expand macro="macro_ifcutoff" value="0.05" help="The cutoff used for the minimum contribution to gene expression (in at least one
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
445 condition) for an isoforms must have to be plotted (measured as Isoform Fraction (IF) values)" />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
446 <param argument="rescaleTranscripts" type="boolean" truevalue="--rescaleTranscripts" falsevalue="" checked="true" label="Rescale transcripts"
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
447 help="All the isoforms should be resealed to the square root of their original sizes. This feature is implemented because
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
448 introns usually are much larger than exons making it difficult to see structural changes. This is very useful for structural
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
449 visualization but the scaling might distort actual intron and exon sizes" />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
450 <param argument="reverseMinus" type="boolean" truevalue="--reverseMinus" falsevalue="" checked="true" label="Isoforms on minus strand
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
451 should be inverted" help="Isoforms on minus strand should be inverted so they are visualized as going from left to right
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
452 instead of right to left" />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
453 <param argument="addErrorbars" type="boolean" truevalue="--addErrorbars" falsevalue="" checked="true" label="Add error bars" help="Error
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
454 bars should be added to the expression plots to show uncertainty in estimates" />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
455 <expand macro="macro_onlyswitching"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
456 </section>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
457 </when>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
458 </conditional>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
459 <conditional name="coding_potential">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
460 <param name="selector" type="select" label="Include prediction of coding potential information"
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
461 help="Integrate in the analysis de output from CPAT or CPC2.">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
462 <option value="disabled">Disabled</option>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
463 <option value="cpat">CPAT</option>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
464 <option value="cpc2">CPC2</option>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
465 </param>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
466 <when value="disabled"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
467 <when value="cpat">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
468 <param argument="analyzeCPAT" type="data" format="txt" label="CPAT result file"
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
469 help=" Use default parameters and the nucleotide fasta file (_nt.fasta). If the webserver was used, download the tab-delimited
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
470 result file (available at the bottom of the result page). If a stand-alone version was used, just supply the path to the result file" />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
471 <param argument="codingCutoff" type="float" min="0" max="1" value="0.725" label="Coding cutoff" help="cutoff used by CPAT for distinguishing between
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
472 coding and non-coding transcripts. The cutoff is dependent on species analyzed. IsoformSwitchAnalyzerR developers suggest that the optimal cutoff
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
473 for overlapping coding and noncoding isoforms are 0.725 for human and 0.721 for mouse. However the suggested cutoffs from the CPAT develpers
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
474 derived by comparing known genes to random non-coding regions of the genome is 0.364 for human and 0.44 for mouse" />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
475 </when>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
476 <when value="cpc2">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
477 <param argument="analyzeCPC2" type="data" format="txt" label="CPC2 result file"
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
478 help="Use default parameters and if required select the most similar species. If the webserver (batch submission) was used,
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
479 download the tab-delimited result file (via the “Download the result” button). If a stand-alone version was just just supply the path to the result file" />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
480 <param argument="removeNoncodingORFs" type="boolean" truevalue="--removeNoncodingORFs" falsevalue="" checked="false" label="Remove non-coding ORFs" help="Remove ORF information
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
481 from the isoforms which the CPC2 analysis classifies as non-coding. This can be particular useful if the isoform (and ORF) was predicted de-novo but is not
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
482 recommended if ORFs was imported from a GTF file" />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
483 <param argument="codingCutoff" type="float" min="0" max="1" value="0.5" label="Coding cutoff" help="Numeric indicating the cutoff used by CPC2 for distinguishing
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
484 between coding and non-coding transcripts. The cutoff appears to be species independent." />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
485 </when>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
486 </conditional>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
487 <conditional name="protein_domains">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
488 <param name="selector" type="select" label="Include Pfam information" help="Pfam is a database of protein families that includes their annotations and multiple sequence
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
489 alignments generated using hidden Markov models.">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
490 <option value="disabled">Disabled</option>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
491 <option value="enabled">Enabled</option>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
492 </param>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
493 <when value="disabled"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
494 <when value="enabled">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
495 <param argument="analyzePFAM" type="data" format="txt" multiple="true" optional="true" label="Include Pfam results (sequence analysis of protein domains)" help="Use default
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
496 parameters and the amino acid fasta file (_AA.fasta). If the webserver is used you need to copy/paste the result part of the mail you receive into an empty plain text
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
497 document (notepad, sublimetext, TextEdit or similar (not Word)) and save that to a plain text (txt) file. The path to that file should be supplied. If a stand-alone
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
498 version was used, just supply the path to the result file" />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
499 </when>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
500 </conditional>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
501 <conditional name="signal_peptides">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
502 <param name="selector" type="select" label="Include SignalP results" help="Integration of the result of SignalP (external sequence analysis of signal peptides)">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
503 <option value="disabled">Disabled</option>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
504 <option value="enabled">Enabled</option>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
505 </param>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
506 <when value="disabled"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
507 <when value="enabled">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
508 <param argument="analyzeSignalP" type="data" format="txt" multiple="true" optional="true" label="SignalP" help="Use the amino acid fasta file (_AA.fasta). If using the webserver SignalP
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
509 should be run with the parameter 'Short output (no figures)' under 'Output format' and one should select the appropriate 'Organism group'. When
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
510 using a stand-alone version SignalP should be run with the '-f summary' option. If using the webserver the results can be downloaded using the
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
511 'Downloads' button in the top-right corner where the user should select 'Prediction summary' and supply the path to the resulting file to the
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
512 'pathToSignalPresultFile' argument. If a stand-alone version was just supply the path to the summary result file." />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
513 <param argument="minSignalPeptideProbability" type="float" min="0" max="1" value="0.5" label="Minimum probability for calling a signal peptide"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
514 </when>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
515 </conditional>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
516
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
517 <conditional name="disordered_regions">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
518 <param name="selector" type="select" label="Include prediction of intrinsically disordered Regions (IDR) information"
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
519 help="Integrate in the analysis de output from IUPred2A or NetSurfP-2">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
520 <option value="disabled">Disabled</option>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
521 <option value="iupred2a">IUPred2A</option>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
522 <option value="netsurfp">NetSurfP-2</option>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
523 </param>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
524 <when value="disabled"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
525 <when value="iupred2a">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
526 <param argument="AanalyzeIUPred2A" type="data" format="txt,gz" label="IUPred2A result file" help="Can be gziped. If
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
527 multiple result files were created (multiple web-server runs) just supply all of them." />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
528 <expand macro="macro_disordered_regions"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
529 <param argument="annotateBindingSites" type="boolean" truevalue="--annotateBindingSites" falsevalue="" checked="true" label="Annotate binding sites"
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
530 help="Integrate the ANCHOR2 prediction of Intrinsically Disordered Binding Regions (IDBRs)" />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
531 <param argument="minIdrBindingSize" type="integer" min="0" value="15" label="Minimum IDBR binding size" help="How long a stretch of
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
532 binding site the region part of the Intrinsically Disordered Binding Regions (IDBR)" />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
533 <param argument="minIdrBindingOverlapFrac" type="float" min="0" value="0.8" label="Minimum fraction of a predicted IDBR" help="Minimum
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
534 fraction of a predicted IDBR must also be within a IDR before the IDR is considered as a an IDR with a binding region" />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
535 </when>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
536 <when value="netsurfp">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
537 <param argument="analyzeNetSurfP2" type="data" format="txt,gz" multiple="true" label="NetSurfP-2 result file" help="Can be gziped. If
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
538 multiple result files were created (multiple web-server runs) just supply all of them." />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
539 <expand macro="macro_disordered_regions"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
540 </when>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
541 </conditional>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
542 <section name="analyzeSwitchConsequences" title="Analyze switch consequences parameters">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
543 <param argument="ntCutoff" type="integer" min="0" value="50" label="Nucleotide length cutoff" help="The length difference (in nucleotides) a
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
544 comparison must be larger than for reporting differences" />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
545 <param argument="ntFracCutoff" type="float" min="0" max="1" optional="true" label="Nucleotide length fraction cutoff" help="The cutoff in length
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
546 difference, measured as a fraction of the length of the downregulated isoform, a comparison must be larger than for
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
547 reporting differences. For example does 0.05 mean the upregulated isoform must be 5% longer/shorter before it is reported. " />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
548 <param argument="ntJCsimCutoff" type="float" min="0" max="1" value="0.8" label="Cutoff on Jaccard similarity between the overlap of two nucloetide sequences" help=" If the
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
549 measured JCsim is smaller than this cutoff the sequences are considered different and reported as such" />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
550 <param argument="AaCutoff" type="integer" min="0" value="10" label="Aminoacid lenght cutoff" help="Length difference (in AA) a comparison must be larger
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
551 than for reporting differences when evaluating ’ORF_seq_similarity’, primarily implemented to avoid differences in very short AA sequences being
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
552 classified as different" />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
553 <param argument="AaFracCutoff" type="float" min="0" max="1" value="0.5" label="Aminoacid length fraction cutoff" help="Cutoff of length difference of
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
554 the protein domain or IDR. The difference is measured as a fraction of the longest region, a comparison must be larger than before reporting it" />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
555 <param argument="AaJCsimCutoff" type="float" min="0" max="1" value="0.9" label="Cutoff between the overlap of two aminoacid sequences" help="If the
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
556 measured JCsim is smaller than this cutoff the sequences are considered different and reported as such" />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
557 <param argument="removeNonConseqSwitches" type="boolean" truevalue="--removeNonConseqSwitches" falsevalue="" checked="true" label="Remove the comparison of isoforms
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
558 where no consequences were found" />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
559 </section>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
560 </when>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
561 </conditional>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
562 </inputs>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
563 <outputs>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
564 <collection name="collection_counts_factor1" type="list" label="${tool.name} on ${on_string}: gene counts factor1">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
565 <discover_datasets pattern="__designation_and_ext__" format="tabular" directory="count_files/factor1" />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
566 <filter>functionMode['selector'] == 'data_import'</filter>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
567 <filter>functionMode['countFiles'] == 'collection'</filter>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
568 </collection>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
569 <collection name="collection_counts_factor2" type="list" label="${tool.name} on ${on_string}: gene counts factor2">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
570 <discover_datasets pattern="__designation_and_ext__" format="tabular" directory="count_files/factor2" />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
571 <filter>functionMode['selector'] == 'data_import'</filter>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
572 <filter>functionMode['countFiles'] == 'collection'</filter>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
573 </collection>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
574 <data name="matrix_counts" format="tabular" from_work_dir="count_files/matrix.tabular" label="${tool.name} on ${on_string}: gene counts matrix">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
575 <filter>functionMode['selector'] == 'data_import'</filter>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
576 <filter>functionMode['countFiles'] == 'matrix'</filter>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
577 </data>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
578 <data name="sample_annotation" format="tabular" from_work_dir="count_files/samples.tabular" label="${tool.name} on ${on_string}: samples annotation">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
579 <filter>functionMode['selector'] == 'data_import'</filter>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
580 <filter>functionMode['countFiles'] == 'matrix'</filter>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
581 </data>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
582 <data name="switchList" format="rdata" from_work_dir="SwitchList.Rda" label="${tool.name} on ${on_string}: SwitchList (RData)"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
583 <data name="isoformAA" format="fasta" from_work_dir="isoformSwitchAnalyzeR_isoform_AA.fasta" label="${tool.name} on ${on_string}: aminoacid sequences">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
584 <filter>functionMode['selector'] == 'first_step'</filter>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
585 <filter>functionMode['outputs_first'] and 'aa' in functionMode['outputs_first']</filter>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
586 </data>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
587 <data name="isoformNT" format="fasta" from_work_dir="isoformSwitchAnalyzeR_isoform_nt.fasta" label="${tool.name} on ${on_string}: nucleotide sequences">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
588 <filter>functionMode['selector'] == 'first_step'</filter>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
589 <filter>functionMode['outputs_first'] and 'nt' in functionMode['outputs_first']</filter>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
590 </data>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
591 <data name="switchSummary" format="tabular" from_work_dir="switchSummary.tsv" label="${tool.name} on ${on_string}: summary">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
592 <filter>functionMode['selector'] == 'first_step'</filter>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
593 <filter>functionMode['outputs_first'] and 'summary' in functionMode['outputs_first']</filter>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
594 </data>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
595 <collection name="plots_summary" type="list" label="${tool.name} on ${on_string}: genome wide plots">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
596 <discover_datasets pattern="__designation_and_ext__" format="pdf" directory="pdf_outputs" />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
597 <filter>functionMode['selector'] == 'second_step'</filter>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
598 <filter>functionMode['analysis_mode']['selector'] == 'top'</filter>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
599 </collection>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
600 <collection name="genes_consequences" type="list" label="${tool.name} on ${on_string}: isoform switches with predicted functional consequences plots">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
601 <discover_datasets pattern="__designation_and_ext__" format="pdf" directory="gene_plots/with_consequences" />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
602 <filter>functionMode['selector'] == 'second_step'</filter>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
603 <filter>functionMode['analysis_mode']['selector'] == 'top'</filter>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
604 </collection>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
605 <collection name="genes_wo_consequences" type="list" label="${tool.name} on ${on_string}: isoform switches without predicted functional consequences plots">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
606 <discover_datasets pattern="__designation_and_ext__" format="pdf" directory="gene_plots/without_consequences" />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
607 <filter>functionMode['selector'] == 'second_step'</filter>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
608 <filter>functionMode['analysis_mode']['selector'] == 'top'</filter>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
609 </collection>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
610 <data name="mostSwitching" format="tabular" from_work_dir="mostSwitchingGene.tsv" label="${tool.name} on ${on_string}: switching gene/isoforms">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
611 <filter>functionMode['selector'] == 'second_step'</filter>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
612 <filter>functionMode['analysis_mode']['selector'] == 'top'</filter>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
613 </data>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
614 <data name="consequencesSummary" format="tabular" from_work_dir="consequencesSummary.tsv" label="${tool.name} on ${on_string}: consequences summary">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
615 <filter>functionMode['selector'] == 'second_step'</filter>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
616 <filter>functionMode['analysis_mode']['selector'] == 'top'</filter>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
617 </data>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
618 <data name="consequencesEnrichment" format="tabular" from_work_dir="consequencesEnrichment.tsv" label="${tool.name} on ${on_string}: consequences enrichment">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
619 <filter>functionMode['selector'] == 'second_step'</filter>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
620 <filter>functionMode['analysis_mode']['selector'] == 'top'</filter>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
621 </data>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
622 <data name="splicingSummary" format="tabular" from_work_dir="splicingSummary.tsv" label="${tool.name} on ${on_string}: splicing summary">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
623 <filter>functionMode['selector'] == 'second_step'</filter>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
624 <filter>functionMode['analysis_mode']['selector'] == 'top'</filter>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
625 </data>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
626 <data name="splicingEnrichment" format="tabular" from_work_dir="splicingEnrichment.tsv" label="${tool.name} on ${on_string}: splicing enrichment">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
627 <filter>functionMode['selector'] == 'second_step'</filter>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
628 <filter>functionMode['analysis_mode']['selector'] == 'top'</filter>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
629 </data>
4
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
630 <data name="splicing_fulldata" format="tabular" from_work_dir="switchSplicing_fulldata.tsv" label="${tool.name} on ${on_string}: alternative splicing full data">
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
631 <filter>functionMode['selector'] == 'second_step'</filter>
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
632 <filter>functionMode['analysis_mode']['selector'] == 'top'</filter>
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
633 </data>
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
634 <data name="consequences_fulldata" format="tabular" from_work_dir="switchConsequence_fulldata.tsv" label="${tool.name} on ${on_string}: funcional consequences full data">
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
635 <filter>functionMode['selector'] == 'second_step'</filter>
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
636 <filter>functionMode['analysis_mode']['selector'] == 'top'</filter>
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
637 </data>
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
638 <data name="isoformFeatures" format="tabular" from_work_dir="IsoformFeatures.tsv" label="${tool.name} on ${on_string}: isoform features">
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
639 <filter>functionMode['selector'] == 'second_step'</filter>
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
640 <filter>functionMode['analysis_mode']['selector'] == 'top'</filter>
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
641 </data>
0
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
642 <data name="single_gene" format="pdf" from_work_dir="single_gene.pdf" label="${tool.name} on ${on_string}: single gene analysis">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
643 <filter>functionMode['selector'] == 'second_step'</filter>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
644 <filter>functionMode['analysis_mode']['selector'] == 'single'</filter>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
645 </data>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
646 </outputs>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
647 <tests>
5
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
648 <!-- Test 01: Data import mode-->
0
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
649 <test expect_num_outputs="1">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
650 <conditional name="functionMode">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
651 <param name="selector" value="data_import"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
652 <param name="genomeAnnotation" value="annotation_salmon.gtf.gz"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
653 <param name="transcriptome" value="transcriptome.fasta.gz"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
654 <param name="countFiles" value="disabled"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
655 <conditional name="tool_source">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
656 <param name="selector" value="salmon"/>
5
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
657 <section name="first_factor">
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
658 <param name="factorLevel" value="health"/>
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
659 <param name="trans_counts" value="salmon_cond1_rep1.sf,salmon_cond1_rep2.sf"/>
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
660 </section>
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
661 <section name="second_factor">
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
662 <param name="factorLevel" value="cancer"/>
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
663 <param name="trans_counts" value="salmon_cond2_rep1.sf,salmon_cond2_rep2.sf"/>
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
664 </section>
0
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
665 </conditional>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
666 </conditional>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
667 <output name="switchList" file="test01.RData" ftype="rdata" compare="sim_size" delta="100"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
668 </test>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
669 <!-- Test 02: Data import mode generate expression matrix-->
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
670 <test expect_num_outputs="3">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
671 <conditional name="functionMode">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
672 <param name="selector" value="data_import"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
673 <param name="genomeAnnotation" value="annotation_salmon.gtf.gz"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
674 <param name="transcriptome" value="transcriptome.fasta.gz"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
675 <param name="countFiles" value="matrix"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
676 <conditional name="tool_source">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
677 <param name="selector" value="salmon"/>
5
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
678 <section name="first_factor">
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
679 <param name="factorLevel" value="health"/>
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
680 <param name="trans_counts" value="salmon_cond1_rep1.sf,salmon_cond1_rep2.sf"/>
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
681 </section>
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
682 <section name="second_factor">
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
683 <param name="factorLevel" value="cancer"/>
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
684 <param name="trans_counts" value="salmon_cond2_rep1.sf,salmon_cond2_rep2.sf"/>
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
685 </section>
0
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
686 </conditional>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
687 </conditional>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
688 <output name="switchList" ftype="rdata">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
689 <assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
690 <has_size value="652170" delta="300"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
691 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
692 </output>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
693 <output name="matrix_counts" file="test02_counts.tabular" ftype="tabular" lines_diff="6"/>
6
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
694 <output name="sample_annotation">
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
695 <assert_contents>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
696 <has_text_matching expression="sampleID\s+condition"/>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
697 <has_text_matching expression="health0\s+health"/>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
698 <has_text_matching expression="health1\s+health"/>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
699 <has_text_matching expression="cancer0\s+cancer"/>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
700 <has_text_matching expression="cancer1\s+cancer"/>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
701 </assert_contents>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
702 </output>
0
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
703 </test>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
704 <!-- Test 03: Data import mode generate collection count files-->
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
705 <test expect_num_outputs="3">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
706 <conditional name="functionMode">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
707 <param name="selector" value="data_import"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
708 <param name="genomeAnnotation" value="annotation_salmon.gtf.gz"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
709 <param name="transcriptome" value="transcriptome.fasta.gz"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
710 <param name="countFiles" value="collection"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
711 <conditional name="tool_source">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
712 <param name="selector" value="salmon"/>
5
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
713 <section name="first_factor">
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
714 <param name="factorLevel" value="health"/>
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
715 <param name="trans_counts" value="salmon_cond1_rep1.sf,salmon_cond1_rep2.sf"/>
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
716 </section>
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
717 <section name="second_factor">
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
718 <param name="factorLevel" value="cancer"/>
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
719 <param name="trans_counts" value="salmon_cond2_rep1.sf,salmon_cond2_rep2.sf"/>
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
720 </section>
0
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
721 </conditional>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
722 </conditional>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
723 <output name="switchList" ftype="rdata">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
724 <assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
725 <has_size value="652170" delta="300"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
726 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
727 </output>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
728 <output_collection name="collection_counts_factor1" type="list" count="2">
5
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
729 <element name="health0_dataset" file="test03_health_counts.tabular" ftype="tabular" lines_diff="6"/>
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
730
0
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
731 </output_collection>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
732 <output_collection name="collection_counts_factor2" type="list" count="2">
5
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
733 <element name="cancer0_dataset" file="test03_cancer_counts.tabular" ftype="tabular" lines_diff="6"/>
0
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
734 </output_collection>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
735 </test>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
736 <!-- Test 04: Extract isoform switches all outputs-->
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
737 <test expect_num_outputs="4">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
738 <conditional name="functionMode">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
739 <param name="selector" value="first_step"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
740 <param name="robject" value="test01.RData"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
741 <param name="alpha" value="0.05"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
742 <param name="dIFcutoff" value="0.1"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
743 <param name="onlySigIsoforms" value="false"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
744 <param name="filterForConsequences" value="false"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
745 <param name="outputs_first" value="nt,aa,summary"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
746 <section name="prefilter">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
747 <param name="geneExpressionCutoff" value="1"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
748 <param name="isoformExpressionCutoff" value="0"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
749 <param name="IFcutoff" value="0.01"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
750 <param name="removeSingleIsformGenes" value="true"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
751 <param name="keepIsoformInAllConditions" value="false"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
752 </section>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
753 <section name="dexseq">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
754 <param name="correctForConfoundingFactors" value="true"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
755 <param name="overwriteIFvalues" value="true"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
756 <param name="reduceToSwitchingGenes" value="true"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
757 <param name="reduceFurtherToGenesWithConsequencePotential" value="false"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
758 <param name="keepIsoformInAllConditions" value="true"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
759 </section>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
760 <section name="novel_isoform">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
761 <param name="minORFlength" value="100"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
762 <param name="orfMethod" value="longest.AnnotatedWhenPossible"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
763 <param name="PTCDistance" value="50"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
764 </section>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
765 <section name="extract_sequence">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
766 <param name="onlySwitchingGenes" value="true"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
767 <param name="removeShortAAseq" value="true"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
768 <param name="removeLongAAseq" value="false"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
769 <param name="removeORFwithStop" value="true"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
770 </section>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
771 </conditional>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
772 <output name="switchList" file="test04.RData" ftype="rdata" compare="sim_size" delta="100"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
773 <output name="isoformAA" ftype="fasta">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
774 <assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
775 <has_size value="138275" delta="300"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
776 <has_text text=">TCONS_00000007"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
777 <has_text text="MLLPPGSLSRPRTFSSQPLQT"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
778 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
779 </output>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
780 <output name="isoformNT" ftype="fasta">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
781 <assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
782 <has_size value="780375" delta="300"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
783 <has_text text=">TCONS_00000007"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
784 <has_text text="GGGTCTCCCTCTGTTGTCCAAGGC"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
785 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
786 </output>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
787 <output name="switchSummary" file="test04_summary.tabular" ftype="tabular"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
788 </test>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
789 <!-- Test 05: Extract isoform switches alternative parameters-->
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
790 <test expect_num_outputs="1">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
791 <conditional name="functionMode">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
792 <param name="selector" value="first_step"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
793 <param name="robject" value="test01.RData"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
794 <param name="outputs_first" value=""/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
795 <section name="dexseq">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
796 <param name="correctForConfoundingFactors" value="true"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
797 <param name="overwriteIFvalues" value="true"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
798 <param name="reduceToSwitchingGenes" value="true"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
799 <param name="reduceFurtherToGenesWithConsequencePotential" value="true"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
800 <param name="keepIsoformInAllConditions" value="true"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
801 </section>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
802 <section name="novel_isoform">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
803 <param name="orfMethod" value="mostUpstream"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
804 </section>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
805 </conditional>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
806 <output name="switchList" ftype="rdata">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
807 <assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
808 <has_size value="500518" delta="300"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
809 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
810 </output>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
811 </test>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
812 <!--Test 06: generate plots and summaries full analsys-->
4
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
813 <test expect_num_outputs="12">
0
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
814 <conditional name="functionMode">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
815 <param name="selector" value="second_step"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
816 <param name="robject" value="test04.RData"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
817 <section name="analyzeSwitchConsequences">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
818 <param name="ntCutoff" value="50"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
819 <param name="ntJCsimCutoff" value="0.8"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
820 <param name="AaCutoff" value="10"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
821 <param name="AaFracCutoff" value="0.5"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
822 <param name="AaJCsimCutoff" value="0.9"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
823 <param name="removeNonConseqSwitches" value="true"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
824 </section>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
825 <conditional name="analysis_mode">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
826 <param name="selector" value="top"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
827 <param name="alpha" value="0.05"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
828 <param name="dIFcutoff" value="0.1"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
829 <param name="n" value="2"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
830 <section name="advanced_options">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
831 <param name="filterForConsequences" value="false"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
832 <param name="sortByQvals" value="true"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
833 <param name="onlySigIsoforms" value="false"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
834 <param name="onlySwitchingGenes" value="true"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
835 <param name="countGenes" value="true"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
836 <param name="asFractionTotal" value="false"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
837 <param name="plotGenes" value="false"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
838 <param name="simplifyLocation" value="true"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
839 <param name="removeEmptyConsequences" value="false"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
840 <param name="analysisOppositeConsequence" value="false"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
841 </section>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
842 </conditional>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
843 </conditional>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
844 <output name="switchList" ftype="rdata">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
845 <assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
846 <has_size value="531580" delta="300"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
847 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
848 </output>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
849 <output_collection name="plots_summary" type="list" count="7">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
850 <element name="consequencesEnrichment" ftype="pdf">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
851 <assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
852 <has_size value="5995" delta="300"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
853 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
854 </element>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
855 <element name="extractConsequencesSummary" ftype="pdf">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
856 <assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
857 <has_size value="5681" delta="300"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
858 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
859 </element>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
860 <element name="splicingEnrichment" ftype="pdf">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
861 <assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
862 <has_size value="6361" delta="300"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
863 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
864 </element>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
865 <element name="splicingGenomewide" ftype="pdf">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
866 <assert_contents>
1
5ae218cee629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7d278967f9c8d2c6ce0a8f83be2c444822746bbf
iuc
parents: 0
diff changeset
867 <has_size value="165752" delta="300"/>
0
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
868 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
869 </element>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
870 <element name="splicingSummary" ftype="pdf">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
871 <assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
872 <has_size value="5990" delta="300"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
873 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
874 </element>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
875 <element name="switchGene" ftype="pdf">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
876 <assert_contents>
1
5ae218cee629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7d278967f9c8d2c6ce0a8f83be2c444822746bbf
iuc
parents: 0
diff changeset
877 <has_size value="18432" delta="300"/>
0
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
878 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
879 </element>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
880 <element name="volcanoPlot" ftype="pdf">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
881 <assert_contents>
1
5ae218cee629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7d278967f9c8d2c6ce0a8f83be2c444822746bbf
iuc
parents: 0
diff changeset
882 <has_size value="20147" delta="300"/>
0
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
883 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
884 </element>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
885 </output_collection>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
886 <output_collection name="genes_consequences" type="list" count="2">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
887 <element name="1_switch_plot_NADK_aka_NADK" ftype="pdf">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
888 <assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
889 <has_size value="8716" delta="300"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
890 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
891 </element>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
892 <element name="2_switch_plot_PRKCZ_aka_PRKCZ" ftype="pdf">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
893 <assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
894 <has_size value="8463" delta="300"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
895 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
896 </element>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
897 </output_collection>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
898 <output_collection name="genes_wo_consequences" type="list" count="2">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
899 <element name="1_switch_plot_CLSTN1_aka_CLSTN1" ftype="pdf">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
900 <assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
901 <has_size value="8039" delta="300"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
902 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
903 </element>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
904 <element name="2_switch_plot_ZBTB40_aka_ZBTB40" ftype="pdf">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
905 <assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
906 <has_size value="7506" delta="300"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
907 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
908 </element>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
909 </output_collection>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
910 <output name="mostSwitching" file="test06_switching.tabular" ftype="tabular" lines_diff="4"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
911 <output name="consequencesSummary" file="test06_consequences_summary.tabular" ftype="tabular" lines_diff="4"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
912 <output name="consequencesEnrichment" file="test06_consequences_enrichment.tabular" ftype="tabular" lines_diff="4"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
913 <output name="splicingSummary" file="test06_splicing_summary.tabular" ftype="tabular" lines_diff="4"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
914 <output name="splicingEnrichment" file="test06_splicing_enrichment.tabular" ftype="tabular" lines_diff="4"/>
4
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
915 <output name="consequences_fulldata" ftype="tabular">
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
916 <assert_contents>
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
917 <has_size value="51508" delta="100"/>
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
918 <has_text text="ORF_genomic"/>
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
919 </assert_contents>
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
920 </output>
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
921 <output name="splicing_fulldata" ftype="tabular">
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
922 <assert_contents>
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
923 <has_size value="46951" delta="100"/>
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
924 <has_text text="ATTS_genomic_start"/>
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
925 </assert_contents>
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
926 </output>
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
927 <output name="isoformFeatures" ftype="tabular">
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
928 <assert_contents>
5
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
929 <has_size value="94888" delta="100"/>
4
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
930 <has_text text="gene_overall_mean"/>
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
931 </assert_contents>
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
932 </output>
0
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
933 </test>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
934 <!--Test 07: generate plots and summaries full analsys all inputs-->
4
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
935 <test expect_num_outputs="12">
0
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
936 <conditional name="functionMode">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
937 <param name="selector" value="second_step"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
938 <param name="robject" value="test04.RData"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
939 <section name="analyzeSwitchConsequences">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
940 <param name="ntCutoff" value="20"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
941 <param name="ntJCsimCutoff" value="0.5"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
942 <param name="AaCutoff" value="10"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
943 <param name="AaFracCutoff" value="0.4"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
944 <param name="AaJCsimCutoff" value="0.8"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
945 <param name="removeNonConseqSwitches" value="false"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
946 </section>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
947 <conditional name="analysis_mode">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
948 <param name="selector" value="top"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
949 <param name="alpha" value="0.05"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
950 <param name="dIFcutoff" value="0.1"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
951 <param name="n" value="2"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
952 <section name="advanced_options">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
953 <param name="filterForConsequences" value="false"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
954 <param name="sortByQvals" value="true"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
955 <param name="onlySigIsoforms" value="false"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
956 <param name="onlySwitchingGenes" value="true"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
957 <param name="countGenes" value="true"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
958 <param name="asFractionTotal" value="false"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
959 <param name="plotGenes" value="false"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
960 <param name="simplifyLocation" value="true"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
961 <param name="removeEmptyConsequences" value="false"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
962 <param name="analysisOppositeConsequence" value="false"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
963 </section>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
964 </conditional>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
965 <conditional name="coding_potential">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
966 <param name="selector" value="cpc2"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
967 <param name="analyzeCPC2" value="cpc2_result.txt"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
968 <param name="removeNoncodingORFs" value="false"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
969 <param name="codingCutoff" value="0.5"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
970 </conditional>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
971 <conditional name="protein_domains">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
972 <param name="selector" value="enabled"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
973 <param name="analyzePFAM" value="pfam_results.txt"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
974 </conditional>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
975 <conditional name="signal_peptides">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
976 <param name="selector" value="enabled"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
977 <param name="analyzeSignalP" value="signalP_results.txt"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
978 <param name="minSignalPeptideProbability" value="0.5"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
979 </conditional>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
980 <conditional name="disordered_regions">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
981 <param name="selector" value="iupred2a"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
982 <param name="AanalyzeIUPred2A" value="iupred2a_result.txt.gz"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
983 <param name="smoothingWindowSize" value="5"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
984 <param name="probabilityCutoff" value="0.5"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
985 <param name="minIdrSize" value="30"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
986 <param name="annotateBindingSites" value="true"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
987 <param name="minIdrBindingSize" value="15"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
988 <param name="minIdrBindingOverlapFrac" value="0.8"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
989 </conditional>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
990 </conditional>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
991 <output name="switchList" ftype="rdata">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
992 <assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
993 <has_size value="542120" delta="300"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
994 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
995 </output>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
996 <output_collection name="plots_summary" type="list" count="7">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
997 <element name="consequencesEnrichment" ftype="pdf">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
998 <assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
999 <has_size value="5995" delta="300"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1000 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1001 </element>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1002 <element name="extractConsequencesSummary" ftype="pdf">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1003 <assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1004 <has_size value="6617" delta="300"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1005 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1006 </element>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1007 <element name="splicingEnrichment" ftype="pdf">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1008 <assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1009 <has_size value="6361" delta="300"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1010 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1011 </element>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1012 <element name="splicingGenomewide" ftype="pdf">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1013 <assert_contents>
1
5ae218cee629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7d278967f9c8d2c6ce0a8f83be2c444822746bbf
iuc
parents: 0
diff changeset
1014 <has_size value="165752" delta="300"/>
0
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1015 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1016 </element>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1017 <element name="splicingSummary" ftype="pdf">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1018 <assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1019 <has_size value="5990" delta="300"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1020 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1021 </element>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1022 <element name="switchGene" ftype="pdf">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1023 <assert_contents>
1
5ae218cee629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7d278967f9c8d2c6ce0a8f83be2c444822746bbf
iuc
parents: 0
diff changeset
1024 <has_size value="18432" delta="300"/>
0
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1025 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1026 </element>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1027 <element name="volcanoPlot" ftype="pdf">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1028 <assert_contents>
1
5ae218cee629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7d278967f9c8d2c6ce0a8f83be2c444822746bbf
iuc
parents: 0
diff changeset
1029 <has_size value="20147" delta="300"/>
0
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1030 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1031 </element>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1032 </output_collection>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1033 <output_collection name="genes_consequences" type="list" count="2">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1034 <element name="1_switch_plot_NADK_aka_NADK" ftype="pdf">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1035 <assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1036 <has_size value="8716" delta="300"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1037 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1038 </element>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1039 <element name="2_switch_plot_PRKCZ_aka_PRKCZ" ftype="pdf">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1040 <assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1041 <has_size value="8463" delta="300"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1042 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1043 </element>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1044 </output_collection>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1045 <output_collection name="genes_wo_consequences" type="list" count="2">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1046 <element name="1_switch_plot_CLSTN1_aka_CLSTN1" ftype="pdf">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1047 <assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1048 <has_size value="8559" delta="300"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1049 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1050 </element>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1051 <element name="2_switch_plot_ZBTB40_aka_ZBTB40" ftype="pdf">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1052 <assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1053 <has_size value="8051" delta="300"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1054 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1055 </element>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1056 </output_collection>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1057 <output name="mostSwitching" ftype="tabular">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1058 <assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1059 <has_size value="4062" delta="50"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1060 <has_text text="RPL11"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1061 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1062 </output>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1063 <output name="consequencesSummary" ftype="tabular">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1064 <assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1065 <has_size value="1192" delta="50"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1066 <has_text text="nrGenesWithConsequences"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1067 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1068 </output>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1069 <output name="consequencesEnrichment" ftype="tabular">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1070 <assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1071 <has_size value="1432" delta="50"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1072 <has_text text="NMD insensitive (paired with NMD sensitive"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1073 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1074 </output>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1075 <output name="splicingSummary" ftype="tabular">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1076 <assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1077 <has_size value="892" delta="50"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1078 <has_text text="MEE in isoform used less"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1079 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1080 </output>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1081 <output name="splicingEnrichment" ftype="tabular">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1082 <assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1083 <has_size value="1157" delta="50"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1084 <has_text text="A5 gain (paired with A5 loss)"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1085 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1086 </output>
4
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
1087 <output name="consequences_fulldata" ftype="tabular">
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
1088 <assert_contents>
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
1089 <has_size value="103581" delta="50"/>
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
1090 <has_text text="signal_peptide_identified"/>
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
1091 </assert_contents>
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
1092 </output>
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
1093 <output name="splicing_fulldata" ftype="tabular">
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
1094 <assert_contents>
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
1095 <has_size value="46951" delta="50"/>
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
1096 <has_text text="ATTS_genomic_start"/>
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
1097 </assert_contents>
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
1098 </output>
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
1099 <output name="isoformFeatures" ftype="tabular">
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
1100 <assert_contents>
5
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
1101 <has_size value="99310" delta="50"/>
4
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
1102 <has_text text="gene_overall_mean"/>
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
1103 </assert_contents>
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
1104 </output>
0
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1105 </test>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1106 <!-- Test 08: analyze single gene-->
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1107 <test expect_num_outputs="2">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1108 <conditional name="functionMode">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1109 <param name="selector" value="second_step"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1110 <param name="robject" value="test04.RData"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1111 <conditional name="analysis_mode">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1112 <param name="selector" value="single"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1113 <param name="gene" value="NADK"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1114 </conditional>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1115 </conditional>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1116 <output name="single_gene" ftype="pdf" file="test08_single_gene.pdf" compare="sim_size"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1117 <output name="switchList" ftype="rdata">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1118 <assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1119 <has_size value="531580" delta="300"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1120 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1121 </output>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1122 </test>
5
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
1123 <!-- Test 09: Kallisto input-->
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
1124 <test expect_num_outputs="1">
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
1125 <conditional name="functionMode">
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
1126 <param name="selector" value="data_import"/>
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
1127 <param name="genomeAnnotation" value="annotation_kallisto.gtf.gz"/>
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
1128 <param name="transcriptome" value="transcriptome_kallisto.fasta.gz"/>
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
1129 <param name="countFiles" value="disabled"/>
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
1130 <conditional name="tool_source">
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
1131 <param name="selector" value="kallisto"/>
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
1132 <section name="first_factor">
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
1133 <param name="factorLevel" value="health"/>
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
1134 <param name="trans_counts" value="kallisto_cond1_rep1.tsv,kallisto_cond1_rep2.tsv"/>
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
1135 </section>
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
1136 <section name="second_factor">
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
1137 <param name="factorLevel" value="cancer"/>
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
1138 <param name="trans_counts" value="kallisto_cond2_rep1.tsv,kallisto_cond2_rep2.tsv"/>
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
1139 </section>
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
1140 </conditional>
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
1141 </conditional>
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
1142 <output name="switchList" file="test09.RData" ftype="rdata" compare="sim_size" delta="100"/>
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
1143 </test>
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
1144 <!-- Test 10: Test paired samples in the experimental design-->
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
1145 <test expect_num_outputs="3">
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
1146 <conditional name="functionMode">
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
1147 <param name="selector" value="data_import"/>
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
1148 <param name="genomeAnnotation" value="annotation_salmon.gtf.gz"/>
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
1149 <param name="transcriptome" value="transcriptome.fasta.gz"/>
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
1150 <param name="pairedSamples" value="true"/>
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
1151 <param name="countFiles" value="matrix"/>
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
1152 <conditional name="tool_source">
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
1153 <param name="selector" value="salmon"/>
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
1154 <section name="first_factor">
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
1155 <param name="factorLevel" value="health"/>
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
1156 <param name="trans_counts" value="salmon_cond1_rep1.sf,salmon_cond1_rep2.sf"/>
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
1157 </section>
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
1158 <section name="second_factor">
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
1159 <param name="factorLevel" value="cancer"/>
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
1160 <param name="trans_counts" value="salmon_cond2_rep1.sf,salmon_cond2_rep2.sf"/>
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
1161 </section>
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
1162 </conditional>
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
1163 </conditional>
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
1164 <output name="switchList" ftype="rdata">
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
1165 <assert_contents>
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
1166 <has_size value="652170" delta="300"/>
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
1167 </assert_contents>
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
1168 </output>
6
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1169 <output name="sample_annotation">
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1170 <assert_contents>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1171 <has_text_matching expression="sampleID\s+condition\s+replicate"/>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1172 <has_text_matching expression="health0\s+health\s+0"/>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1173 <has_text_matching expression="health1\s+health\s+1"/>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1174 <has_text_matching expression="cancer0\s+cancer\s+0"/>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1175 <has_text_matching expression="cancer1\s+cancer\s+1"/>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1176 </assert_contents>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1177 </output>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1178 </test>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1179 <!-- Test 11: Data import mode add cofactor-->
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1180 <test expect_num_outputs="3">
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1181 <conditional name="functionMode">
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1182 <param name="selector" value="data_import"/>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1183 <param name="genomeAnnotation" value="gencode.hg19.chr10_1000.gtf.gz"/>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1184 <param name="transcriptome" value="transcriptome_stringtie.fasta.gz"/>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1185 <param name="countFiles" value="matrix"/>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1186 <conditional name="tool_source">
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1187 <param name="selector" value="stringtie"/>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1188 <conditional name="novoisoforms">
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1189 <param name="selector" value="novel"/>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1190 <param name="stringtieAnnotation" value="annotation_stringtie.gtf.gz"/>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1191 </conditional>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1192 <section name="first_factor">
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1193 <param name="factorLevel" value="EWS-FLI1"/>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1194 <param name="trans_counts" value="ASP14_1.tabular,ASP14_2.tabular,ASP14_3.tabular"/>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1195 </section>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1196 <section name="second_factor">
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1197 <param name="factorLevel" value="no-EWS-FLI1"/>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1198 <param name="trans_counts" value="ASP14_doxycycline_1.tabular,ASP14_doxycycline_2.tabular,ASP14_doxycycline_3.tabular"/>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1199 </section>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1200 <repeat name="cofactor">
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1201 <param name="cofactor_name" value="Batch"/>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1202 <repeat name="cofactor_level">
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1203 <param name="cofactor_level_name" value="batch1"/>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1204 <param name="cofactor_level_files" value="ASP14_1.tabular,ASP14_doxycycline_1.tabular"/>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1205 </repeat>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1206 <repeat name="cofactor_level">
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1207 <param name="cofactor_level_name" value="batch2"/>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1208 <param name="cofactor_level_files" value="ASP14_2.tabular,ASP14_doxycycline_2.tabular"/>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1209 </repeat>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1210 <repeat name="cofactor_level">
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1211 <param name="cofactor_level_name" value="batch3"/>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1212 <param name="cofactor_level_files" value="ASP14_3.tabular,ASP14_doxycycline_3.tabular"/>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1213 </repeat>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1214 </repeat>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1215 <repeat name="cofactor">
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1216 <param name="cofactor_name" value="Age"/>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1217 <repeat name="cofactor_level">
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1218 <param name="cofactor_level_name" value="20"/>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1219 <param name="cofactor_level_files" value="ASP14_1.tabular,ASP14_doxycycline_1.tabular,ASP14_2.tabular"/>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1220 </repeat>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1221 <repeat name="cofactor_level">
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1222 <param name="cofactor_level_name" value="60"/>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1223 <param name="cofactor_level_files" value="ASP14_doxycycline_2.tabular,ASP14_3.tabular,ASP14_doxycycline_3.tabular"/>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1224 </repeat>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1225 </repeat>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1226 </conditional>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1227 </conditional>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1228 <output name="switchList" ftype="rdata">
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1229 <assert_contents>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1230 <has_size value="374542" delta="300"/>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1231 </assert_contents>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1232 </output>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1233 <output name="matrix_counts" file="stringtie_counts.tabular" ftype="tabular" lines_diff="6"/>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1234 <output name="sample_annotation">
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1235 <assert_contents>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1236 <has_text_matching expression="sampleID\s+condition\s+Batch\s+Age"/>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1237 <has_text_matching expression="EWSXFLI10\s+EWSXFLI1\s+batch1\s+20"/>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1238 <has_text_matching expression="EWSXFLI11\s+EWSXFLI1\s+batch2\s+20"/>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1239 <has_text_matching expression="EWSXFLI12\s+EWSXFLI1\s+batch3\s+60"/>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1240 <has_text_matching expression="noXEWSXFLI10\s+noXEWSXFLI1\s+batch1\s+20"/>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1241 <has_text_matching expression="noXEWSXFLI11\s+noXEWSXFLI1\s+batch2\s+60"/>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1242 <has_text_matching expression="noXEWSXFLI12\s+noXEWSXFLI1\s+batch3\s+60"/>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1243 </assert_contents>
293ed243039c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878
iuc
parents: 5
diff changeset
1244 </output>
5
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
1245 </test>
0
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1246 </tests>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1247 <help><![CDATA[
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1248
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1249 .. class:: infomark
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1250
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1251 **Purpose**
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1252
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1253 IsoformSwitchAnalyzeR is an easy-to use-R package that enables statistical identification of isoform switching from RNA-seq derived quantification
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1254 of novel and/or annotated full-length isoforms. IsoformSwitchAnalyzeR facilitates integration of many sources of (predicted) annotation such as Open
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1255 Reading Frame (ORF/CDS), protein domains (via Pfam), signal peptides (via SignalP), Intrinsically Disordered Regions (IDR, via NetSurfP-2 or IUPred2A),
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1256 coding potential (via CPAT or CPC2) and sensitivity to Non-sense Mediated Decay (NMD) and more. The combination of identified isoform switches and
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1257 their annotation enables IsoformSwitchAnalyzeR to predict potential functional consequences of the identified isoform switches — such as loss of
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1258 protein domains — thereby identifying isoform switches of particular interest. Lastly, IsoformSwitchAnalyzeR provides article-ready visualization
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1259 methods for isoform switches for individual genes as well as both summary statistics and visualization of the genome-wide changes/consequences of
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1260 isoform switches, their consequences and the associated alternative splicing.
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1261
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1262 -----
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1263
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1264 .. class:: infomark
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1265
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1266 **Differential isoform expression (DIE) and differential isoform usage (DIU)**
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1267
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1268 Differential isoform expression (DIE) and differential isoform usage (DIU) are related but distinct concepts. DIE assesses the difference of
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1269 absolute expression in isoform level. In contrast, DIU assesses the difference of relative expression in isoform level. For example, if the
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1270 expression of two isoforms of one gene are 10 and 20 in control and 50 and 100 in case, then there is DIE but no DIU because the relative
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1271 expression of the first isoform is 1/3 in both case and control.
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1272
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1273 -----
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1274
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1275 .. class:: infomark
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1276
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1277 **ORF identification methods (novel isoform analysis)**
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1278
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1279 - **Longest**: Identifies the longest ORF in the transcript (after filtering via minORFlength). This approach is similar to what the CPAT tool uses in it is analysis of coding potential.
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1280 - **LongestAnnotated**: Identifies the longest ORF (after filtering via minORFlength) downstream of an annotated translation start site (which are supplied via the cds argument).
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1281 - **Longest.AnnotatedWhenPossible**: A merge between "longestAnnotated" and "longest". For all isoforms where CDS start positions from known isoform overlap, only these CDS starts are considered and the longest ORF is annotated (similar to "longestAnnotated"). All isoforms without any overlapping CDS start sites they will be analysed with the "longest" approach.
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1282 - **MostUpstream**: Identifies the most upstream ORF in the transcript (after filtering via minORFlength).
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1283 - **MostUpstreamAnnoated**: Identifies the ORF (after filtering via minORFlength) downstream of the most upstream overlapping annotated translation start site (supplied via the cds argument).
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1284
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1285 ]]></help>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1286 <expand macro="citations" />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1287 </tool>