Mercurial > repos > iuc > isoformswitchanalyzer

annotate isoformswitchanalyzer.xml @ 5:69fa05891f9d draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
author iuc
date Fri, 02 Jun 2023 10:26:51 +0000
parents 8575def9219d
children
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bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
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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
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2 <description>statistical identification of isoform switching</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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6 <expand macro='xrefs'/>
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7 <expand macro='requirements'/>
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8 <stdio>
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9 <regex match="Execution halted"
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10 source="both"
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11 level="fatal"
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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12 description="Execution halted." />
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13 <regex match="Error in"
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14 source="both"
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15 level="fatal"
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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
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17 <regex match="Fatal error"
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18 source="both"
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19 level="fatal"
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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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
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21 </stdio>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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22 <command><![CDATA[
5
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
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23 #set $conditions = list()
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24 #set $sampleIDs = list()
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
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25 #set $replicates = list()
0
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26 #if $functionMode.selector == 'data_import'
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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27 #if $functionMode.transcriptome.is_of_type("fasta.gz"):
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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28 ln -s '${functionMode.transcriptome}' './transcriptome.fasta.gz' &&
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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29 #set $transcriptome = './transcriptome.fasta.gz'
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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30 #else
1
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31 ln -s '${functionMode.transcriptome}' './transcriptome.fasta' &&
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bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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32 #set $transcriptome = './transcriptome.fasta'
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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33 #end if
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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34 #if $functionMode.genomeAnnotation.is_of_type("gtf.gz"):
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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35 ln -s '${functionMode.genomeAnnotation}' './annotation.gtf.gz' &&
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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36 #set $annotation = './annotation.gtf.gz'
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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37 #else
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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38 ln -s '${functionMode.genomeAnnotation}' './annotation.gtf' &&
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39 #set $annotation = './annotation.gtf'
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40 #end if
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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41 mkdir -p 'input_files' &&
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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42 #if $functionMode.countFiles != 'disabled':
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43 mkdir -p "count_files/factor1/" &&
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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44 mkdir -p "count_files/factor2/" &&
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45 #end if
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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46 #if $functionMode.tool_source.selector == 'stringtie'
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47 #set $filename = 't_data.ctab'
2
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48 #if $functionMode.tool_source.novoisoforms.selector == 'novel'
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49 #if $functionMode.tool_source.novoisoforms.stringtieAnnotation.is_of_type("gtf.gz"):
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50 ln -s '${$functionMode.tool_source.novoisoforms.stringtieAnnotation}' './stringtie_annotation.gtf.gz' &&
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51 #set $stringtie_annotation = './stringtie_annotation.gtf.gz'
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52 #else
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53 ln -s '${$functionMode.tool_source.novoisoforms.stringtieAnnotation}' './stringtie_annotation.gtf' &&
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54 #set $stringtie_annotation = './stringtie_annotation.gtf'
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55 #end if
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56 #end if
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57 #else if $functionMode.tool_source.selector == 'salmon'
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58 #set $filename = 'quant.sf'
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59 #else
5
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60 #set $filename = 'abundance.tsv'
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61 #end if
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62
5
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63 #for $index in range(len($functionMode.tool_source.first_factor.trans_counts)):
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
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64 $conditions.append($functionMode.tool_source.first_factor.factorLevel)
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65 $sampleIDs.append(str($functionMode.tool_source.first_factor.factorLevel) + str($index))
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
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66 $replicates.append($index)
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67 mkdir './input_files/${functionMode.tool_source.first_factor.factorLevel}${index}/' &&
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
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68 ln -s $functionMode.tool_source.first_factor.trans_counts[$index] './input_files/${functionMode.tool_source.first_factor.factorLevel}${index}/${filename}' &&
0
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69 #end for
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70
5
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71 #for $index in range(len($functionMode.tool_source.second_factor.trans_counts)):
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
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72 $conditions.append($functionMode.tool_source.second_factor.factorLevel)
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73 $sampleIDs.append(str($functionMode.tool_source.second_factor.factorLevel) + str($index))
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
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74 $replicates.append($index)
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75 mkdir './input_files/${functionMode.tool_source.second_factor.factorLevel}${index}/' &&
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
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76 ln -s $functionMode.tool_source.second_factor.trans_counts[$index] './input_files/${functionMode.tool_source.second_factor.factorLevel}${index}/${filename}' &&
0
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77 #end for
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78
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79 Rscript '${__tool_directory__}/IsoformSwitchAnalyzeR.R'
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80 #for $i, $condition in enumerate($conditions)
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81 --condition $condition
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82 --sampleID $sampleIDs[$i]
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83 --replicate $replicates[$i]
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84 #end for
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
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diff changeset
85 $functionMode.pairedSamples
0
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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diff changeset
86 --modeSelector $functionMode.selector
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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diff changeset
87 --parentDir './input_files'
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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88 --annotation $annotation
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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diff changeset
89 --transcriptome $transcriptome
2
db30020fee5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a
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parents: 1
diff changeset
90 $functionMode.removeNonConvensionalChr
0
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
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91 --toolSource $functionMode.tool_source.selector
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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92 #if $functionMode.tool_source.selector == 'stringtie'
2
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93 #if $functionMode.tool_source.novoisoforms.selector == 'novel'
db30020fee5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a
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parents: 1
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94 --stringtieAnnotation $stringtie_annotation
db30020fee5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a
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95 #end if
0
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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96 --readLength $functionMode.tool_source.averageSize
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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97 $functionMode.tool_source.fixStringTieAnnotationProblem
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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98 #end if
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
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diff changeset
99 --countFiles $functionMode.countFiles
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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100 #else if $functionMode.selector == 'first_step'
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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101 Rscript '${__tool_directory__}/IsoformSwitchAnalyzeR.R'
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102 --modeSelector $functionMode.selector
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103 --rObject $functionMode.robject
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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104 --alpha $functionMode.alpha
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
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105 --dIFcutoff $functionMode.dIFcutoff
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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106 $functionMode.onlySigIsoforms
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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107 $functionMode.filterForConsequences
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108 --geneExpressionCutoff $functionMode.prefilter.geneExpressionCutoff
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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109 --isoformExpressionCutoff $functionMode.prefilter.isoformExpressionCutoff
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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110 --IFcutoff $functionMode.prefilter.IFcutoff
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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111 $functionMode.prefilter.removeSingleIsformGenes
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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112 $functionMode.prefilter.keepIsoformInAllConditions
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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113 $functionMode.dexseq.correctForConfoundingFactors
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114 $functionMode.dexseq.overwriteIFvalues
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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115 $functionMode.dexseq.reduceToSwitchingGenes
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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116 $functionMode.dexseq.reduceFurtherToGenesWithConsequencePotential
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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117 $functionMode.dexseq.keepIsoformInAllConditions
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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118 --minORFlength $functionMode.novel_isoform.minORFlength
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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119 --orfMethod $functionMode.novel_isoform.orfMethod
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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120 --PTCDistance $functionMode.novel_isoform.PTCDistance
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
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121 $functionMode.extract_sequence.removeShortAAseq
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
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122 $functionMode.extract_sequence.removeLongAAseq
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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123 $functionMode.extract_sequence.removeORFwithStop
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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124 $functionMode.extract_sequence.onlySwitchingGenes
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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125 #else
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126 #if $functionMode.protein_domains.selector == 'enabled'
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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127 mkdir -p './pfam_files' &&
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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128 #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
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129 ln -s $filename './pfam_files/dataset${index}.txt' &&
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130 #end for
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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131 #end if
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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132 #if $functionMode.signal_peptides.selector == 'enabled'
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133 mkdir -p './signalp_files' &&
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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134 #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
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135 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
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136 #end for
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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diff changeset
137 #end if
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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138 #if $functionMode.disordered_regions.selector == 'netsurfp'
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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139 mkdir -p './netsurf_files' &&
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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140 #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
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141 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
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142 #end for
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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143 #end if
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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144 Rscript '${__tool_directory__}/IsoformSwitchAnalyzeR.R'
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145 --modeSelector $functionMode.selector
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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146 --rObject $functionMode.robject
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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147 --analysisMode $functionMode.analysis_mode.selector
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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148 --alpha $functionMode.analysis_mode.alpha
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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149 --dIFcutoff $functionMode.analysis_mode.dIFcutoff
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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150 #if $functionMode.analysis_mode.selector == 'top'
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151 --genesToPlot $functionMode.analysis_mode.n
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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152 $functionMode.analysis_mode.advanced_options.filterForConsequences
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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153 $functionMode.analysis_mode.advanced_options.sortByQvals
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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154 $functionMode.analysis_mode.advanced_options.onlySigIsoforms
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
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155 $functionMode.analysis_mode.advanced_options.onlySwitchingGenes
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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156 $functionMode.analysis_mode.advanced_options.countGenes
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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157 $functionMode.analysis_mode.advanced_options.asFractionTotal
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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158 $functionMode.analysis_mode.advanced_options.plotGenes
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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159 $functionMode.analysis_mode.advanced_options.simplifyLocation
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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160 $functionMode.analysis_mode.advanced_options.removeEmptyConsequences
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
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161 $functionMode.analysis_mode.advanced_options.removeEmptyConsequences
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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162 #else
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163 --gene $functionMode.analysis_mode.gene
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
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164 --IFcutoff $functionMode.analysis_mode.advanced_options.IFcutoff
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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165 $functionMode.analysis_mode.advanced_options.rescaleTranscripts
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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166 $functionMode.analysis_mode.advanced_options.reverseMinus
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
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167 $functionMode.analysis_mode.advanced_options.addErrorbars
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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168 $functionMode.analysis_mode.advanced_options.onlySwitchingGenes
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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169 #end if
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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170 #if $functionMode.coding_potential.selector == 'cpat'
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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171 --pathToCPATresultFile $functionMode.coding_potential.analyzeCPAT
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
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172 --codingCutoff $functionMode.coding_potential.codingCutoff
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173 #else if $functionMode.coding_potential.selector == 'cpc2'
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174 --pathToCPC2resultFile $functionMode.coding_potential.analyzeCPC2
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175 $functionMode.coding_potential.removeNoncodingORFs
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176 --codingCutoff $functionMode.coding_potential.codingCutoff
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177 #end if
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178 #if $functionMode.protein_domains.selector == 'enabled'
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179 --pathToPFAMresultFile './pfam_files'
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180 #end if
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181 #if $functionMode.signal_peptides.selector == 'enabled'
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182 --pathToSignalPresultFile './signalp_files'
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183 --minSignalPeptideProbability $functionMode.signal_peptides.minSignalPeptideProbability
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184 #end if
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185 #if $functionMode.disordered_regions.selector == 'netsurfp'
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186 --pathToNetSurfP2resultFile './netsurf_files'
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187 --smoothingWindowSize $functionMode.disordered_regions.smoothingWindowSize
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188 --probabilityCutoff $functionMode.disordered_regions.probabilityCutoff
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189 --minIdrSize $functionMode.disordered_regions.minIdrSize
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190 #else if $functionMode.disordered_regions.selector == 'iupred2a'
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191 --pathToIUPred2AresultFile $functionMode.disordered_regions.AanalyzeIUPred2A
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192 --smoothingWindowSize $functionMode.disordered_regions.smoothingWindowSize
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193 --probabilityCutoff $functionMode.disordered_regions.probabilityCutoff
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194 --minIdrSize $functionMode.disordered_regions.minIdrSize
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195 $functionMode.disordered_regions.annotateBindingSites
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196 --minIdrBindingSize $functionMode.disordered_regions.minIdrBindingSize
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197 --minIdrBindingOverlapFrac $functionMode.disordered_regions.minIdrBindingOverlapFrac
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198 #end if
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199 --ntCutoff $functionMode.analyzeSwitchConsequences.ntCutoff
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200 #if $functionMode.analyzeSwitchConsequences.ntFracCutoff
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201 --ntFracCutoff $functionMode.analyzeSwitchConsequences.ntFracCutoff
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202 #end if
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203 --ntJCsimCutoff $functionMode.analyzeSwitchConsequences.ntJCsimCutoff
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204 --AaCutoff $functionMode.analyzeSwitchConsequences.AaCutoff
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205 --AaFracCutoff $functionMode.analyzeSwitchConsequences.AaFracCutoff
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206 --AaJCsimCutoff $functionMode.analyzeSwitchConsequences.AaJCsimCutoff
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207 $functionMode.analyzeSwitchConsequences.removeNonConseqSwitches
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208 #if $functionMode.analysis_mode.selector == 'top'
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209 && mkdir -p './pdf_outputs/'
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210 && mv *pdf './pdf_outputs/'
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211 && mv *_vs_* gene_plots
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212 #end if
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213 #end if
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214 ]]></command>
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215 <inputs>
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216 <conditional name="functionMode">
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217 <param name="selector" type="select" label="Tool function mode"
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218 help="The first step of a IsoformSwitchAnalyzeR workflow is to import and integrate the isoform quantification
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219 with its basic annotation. Once you have all the relevant data imported into R (IsoformSwitchAnalyzeR will
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220 also help you with that), the workflow for identification and analysis of isoform switches with functional
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221 consequences can be divided into two parts.">
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222 <option value="data_import">Import data</option>
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223 <option value="first_step">Analysis part one: Extract isoform switches and their sequences</option>
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224 <option value="second_step">Analysis part two: Plot all isoform switches and their annotation</option>
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225 </param>
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226 <when value="data_import">
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227 <conditional name="tool_source">
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228 <param name="selector" type="select" label="Quantification data source" help="IsoformSwitchAnalyzeR has different functions for importing data from different sources.">
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229 <option value="stringtie">StringTie</option>
5
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230 <option value="salmon">Salmon</option>
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231 <option value="kallisto">Kallisto</option>
0
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232 </param>
5
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233 <when value="salmon">
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234 <expand macro="macro_inputs"/>
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235 </when>
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236 <when value="kallisto">
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237 <expand macro="macro_inputs"/>
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238 </when>
0
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239 <when value="stringtie">
5
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240 <expand macro="macro_inputs"/>
0
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241 <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
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242 quantified is 75 bp paired ends the the user should supply readLength=75" />
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243 <param argument="fixStringTieAnnotationProblem" type="boolean" truevalue="--fixStringTieAnnotationProblem" falsevalue="" checked="true"
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244 label="Fix StringTie annotation problem" help="This option will automatically try and correct some of the annoation problems created when
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245 doing transcript assembly (unassigned transcripts and merged genes)" />
2
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246 <conditional name="novoisoforms">
4
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247 <param name="selector" type="select" label="Analysis mode">
2
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248 <option value="novel">Include novel isoforms in analysis</option>
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249 <option value="reference">Reference-only analysis</option>
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250 </param>
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251 <when value="novel">
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252 <param name="stringtieAnnotation" type="data" format="gtf,gtf.gz" label="Annotation generated by StringTie merge"
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253 help="The merged GTF is used to recalculate expression estimates using the merged, novel transcripts." />
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254 </when>
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255 <when value="reference"/>
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256 </conditional>
0
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257 </when>
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258 </conditional>
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259 <param name="genomeAnnotation" type="data" format="gtf,gtf.gz" label="Genome annotation"
0
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260 help="It is used to integrate the coding sequence (CDS) regions from in the GTF file as the ORF regions used by IsoformSwitchAnalyzeR." />
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261 <param name="transcriptome" type="data" format="fasta,fasta.gz" label="Transcriptome"
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262 help="Please note this different from a fasta file with the sequences of the entire genome." />
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263 <param argument="removeNonConvensionalChr" type="boolean" truevalue="--removeNonConvensionalChr" falsevalue="" checked="false"
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264 label="Remove non-conventional chromosomes" help="These regions are typically used to annotate regions that cannot be associated to a specific region." />
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265 <param argument="pairedSamples" type="boolean" truevalue="--pairedSamples" falsevalue="" checked="false" label="Paired samples between factors" help="Samples
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266 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)" />
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267 <param name="countFiles" type="select" label="Generate count matrix files" help="If IsoformSwitchAnalyzeR is used for fixing Stringtie annotation
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268 problem, it can generate count files for analyzing differential expression with DESeq2 (when selecting collection) or CEMiTool (when secting the expression matrix format).">
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269 <option value="disabled">Disabled</option>
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270 <option value="collection">Collection of count files</option>
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271 <option value="matrix">Expression matrix</option>
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272 </param>
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273 </when>
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274
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275 <!--WRAPPER FIRST STEP SECTION-->
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276
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277 <when value="first_step">
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278 <param name="robject" type="data" format="rdata" label="IsoformSwitchAnalyzeR R object" help="It is generated when running the analysis part 1." />
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279 <expand macro="macro_alpha_difcutoff"/>
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280 <expand macro="macro_onlysigisoforms1"/>
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281 <param argument="filterForConsequences" type="boolean" truevalue="--filterForConsequences" falsevalue="" checked="false"
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282 label="Filter for consquences" help="Filter for genes with functional consequences. The output will then be the number of significant genes
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283 and isoforms originating from genes with predicted consequences" />
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284 <section name="prefilter" title="Pre-filter parameters" help="SwitchAnalyzeR will remove genes/isoforms with the aim of allowing faster
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285 processing time as well as more trustworthy results.">
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286 <param argument="geneExpressionCutoff" type="float" min="0" value="1" label="Gene expression cutoff" help="The expression cutoff (most
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287 likely in TPM/RPKM/FPKM) which the average expression in BOTH condisions must be higher than." />
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288 <param argument="isoformExpressionCutoff" type="float" min="0" value="0" label="Isoform expresion cutoff" help="The expression cutoff (most
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289 likely in RPKM/FPKM) which isoforms must be expressed more than, in at least one conditions of a comparison. Default is 0 (which removes
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290 completely unused isoforms)." />
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291 <expand macro="macro_ifcutoff" value="0.01" help="The cutoff on isoform usage (measured as Isoform Fraction) which isoforms must be used more
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292 than in at least one conditions of a comparison" />
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293 <param argument="removeSingleIsformGenes" type="boolean" truevalue="--removeSingleIsformGenes" falsevalue="" checked="true" label="Remove single isoform genes"
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294 help="Only keep genes containing more than one isoform (in any comparison, after the other filters have been applied)" />
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295 <expand macro="macro_keeisoforminall" checked="false"/>
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296 </section>
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297 <section name="dexseq" title="DEXseq parameters" help="DEXSeq is used to test isoforms (isoform resolution) for differential isoform usage.">
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298 <param argument="correctForConfoundingFactors" type="boolean" truevalue="--correctForConfoundingFactors" falsevalue="" checked="true" label="Correct for confounding factors"
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299 help="A logic indicating whether IsoformSwitchAnalyzeR to use limma to correct for any confounding effects (e.g. batch effects) as indicated in the
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300 design matrix (as additional columns (apart from the two default columns)) " />
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301 <param argument="overwriteIFvalues" type="boolean" truevalue="--overwriteIFvalues" falsevalue="" checked="true" label="Overwrite IF values" help="It indicates
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302 whether to overwrite the IF and dIF stored in the switchAnalyzeRlist with the corrected IF and dIF values - if no confounding effects are
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303 present in the design matrix this will not change anything" />
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304 <param argument="reduceToSwitchingGenes" type="boolean" truevalue="--reduceToSwitchingGenes" falsevalue="" checked="true" label="Reduce to switch genes" help="Reduced to the
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305 genes which contains at least one isoform significantly differential used (as indicated by the alpha and dIFcutoff parameters" />
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306 <param argument="reduceFurtherToGenesWithConsequencePotential" type="boolean" truevalue="--reduceFurtherToGenesWithConsequencePotential" falsevalue="" checked="false"
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307 label="Reduce to genes with consequence potential" help="This argument is a more strict version of reduceToSwitchingGenes
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308 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
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309 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.
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310 The existence of such an opposing isoform means a switch pair can be formed" />
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311 <expand macro="macro_keeisoforminall" checked="true"/>
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312 </section>
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313 <section name="novel_isoform" title="Novel isoform analysis parameters" help="For the subset of isoforms not already annotated with ORFs this
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314 function predicts the most likely Open Reading Frame (ORF) and the NMD sensitivity. This function is made to help annotate
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315 isoforms if you have performed (guided) de-novo isoform reconstruction (isoform deconvolution).">
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316 <param argument="minORFlength" type="integer" min="0" value="100" label="Minimum ORF length" help="The minimum size (in nucleotides) an
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317 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." />
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318 <param argument="orfMethod" type="select" label="ORF identification method" help="More information in the help section">
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319 <option value="longest.AnnotatedWhenPossible">Longest and annotated when possible</option>
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320 <option value="longest">Longest</option>
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321 <option value="mostUpstream">Most upstream</option>
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322 <option value="longestAnnotated">Longest annotated</option>
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323 <option value="mostUpstreamAnnoated">Most upstream annotated</option>
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324 </param>
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325 <param argument="PTCDistance" type="integer" min="0" value="50" label="Maximal allowed premature termination codon-distance" help="The minimum
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326 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
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327 junction is larger than this the isoform to be marked as NMD-sensitive. " />
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328 </section>
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329 <section name="extract_sequence" title="Sequence extraction parameters" help="switchAnalyzeR will extracts the nucleotide (NT) sequence of transcripts by
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330 extracting and concatenating the sequences of a reference genome corresponding to the genomic coordinates of the isoforms. ">
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331 <expand macro="macro_onlyswitching"/>
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332 <param argument="removeShortAAseq" type="boolean" truevalue="--removeShortAAseq" falsevalue="" checked="true" label="Remove short aminoacid sequences" help="This
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333 option exist to allows for easier usage of the Pfam and SignalP web servers which both currently have restrictions on allowed sequence lengths. If
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334 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" />
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335 <param argument="removeLongAAseq" type="boolean" truevalue="--removeLongAAseq" falsevalue="" checked="false" label="Remove long aminoacid sequences" help="A
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336 logical indicating whether to removesequences based on their length. This option exist to allows for easier usage of the Pfam and SignalP web servers
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337 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
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diff changeset
338 sequences written to the fasta file (if writeToFile=TRUE) not the sequences added to the switchAnalyzeRlist. " />
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339 <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
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340 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
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341 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
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342 necessary if you are analyzing quantified known annotated data where you supplied a GTF file to the import function" />
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343 </section>
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344 <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
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345 <option value="nt" selected="true">Nucleotide sequences</option>
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346 <option value="aa" selected="true">Aminoacid sequences</option>
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347 <option value="summary" selected="true">Gene switch summary</option>
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348 </param>
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349 </when>
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350
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351 <!-- WRAPPER SECOND STEP SECTION-->
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352
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353 <when value="second_step">
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354 <param name="robject" type="data" format="rdata" label="IsoformSwitchAnalyzeR R object" help="It is generated when running the analysis part 2." />
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355 <conditional name="analysis_mode">
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356 <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
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357 the (top) switching genes/isoforms ">
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358 <option value="top" selected="true">Full analysis</option>
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359 <option value="single">Analyze specific gene</option>
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diff changeset
360 </param>
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361 <when value="top">
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362 <expand macro="macro_alpha_difcutoff"/>
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363 <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
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364 help="This parameters allows to specify the number of top genes/isoforms to plot"/>
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365 <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
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366 <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
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367 help="The output will then be the number of significant genes and isoforms originating from genes with predicted consequences"/>
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368 <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
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369 whether to the top n features are sorted by decreasing significance (increasing q-values) (if enabled) or decreasing switch size
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370 (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
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371 change within the gene calculated as sum(abs(dIF)) for each gene" />
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diff changeset
372 <expand macro="macro_onlysigisoforms2"/>
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373 <expand macro="macro_onlyswitching"/>
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374 <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
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375 whether it is the number of genes (if enabled) or isoform switches (if disabled) which primary result in gain/loss that are counted" />
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376 <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
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377 should be summarized calculated as numbers (if disabled) or as a fraction of the total number of switches/genes" />
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378 <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
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diff changeset
379 (if enabled) or isoforms (if disabled) involved with isoform switches with functional consequences (both filtered via alpha and dIFcutoff)" />
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380 <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
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diff changeset
381 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
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diff changeset
382 <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
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diff changeset
383 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
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diff changeset
384 <param argument="analysisOppositeConsequence" type="boolean" truevalue="--analysisOppositeConsequence" falsevalue="" checked="false"
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385 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'.
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386 The main effect is for the visual appearance of plot which will be mirrored (around the 0.5 fraction)" />
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387 </section>
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388 </when>
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389 <when value="single">
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390 <param argument="gene" type="text" value="" label="Gene name" help="Either the gene_id or the gene name of the gene to plot">
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diff changeset
391 <sanitizer invalid_char="">
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392 <valid initial="string.letters,string.digits">
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393 <add value="_" />
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394 <add value="-" />
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395 </valid>
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396 </sanitizer>
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397 <validator type="regex">[0-9a-zA-Z_-]+</validator>
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398 </param>
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399 <expand macro="macro_alpha_difcutoff"/>
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400 <section name="advanced_options" title="Single gene mode advanced options">
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401 <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
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402 condition) for an isoforms must have to be plotted (measured as Isoform Fraction (IF) values)" />
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403 <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
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404 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
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405 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
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406 visualization but the scaling might distort actual intron and exon sizes" />
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407 <param argument="reverseMinus" type="boolean" truevalue="--reverseMinus" falsevalue="" checked="true" label="Isoforms on minus strand
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408 should be inverted" help="Isoforms on minus strand should be inverted so they are visualized as going from left to right
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409 instead of right to left" />
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410 <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
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411 bars should be added to the expression plots to show uncertainty in estimates" />
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412 <expand macro="macro_onlyswitching"/>
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413 </section>
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414 </when>
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415 </conditional>
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416 <conditional name="coding_potential">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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417 <param name="selector" type="select" label="Include prediction of coding potential information"
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diff changeset
418 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
419 <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
420 <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
421 <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
422 </param>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
423 <when value="disabled"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
424 <when value="cpat">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
425 <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
426 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
427 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
428 <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
429 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
430 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
431 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
432 </when>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
433 <when value="cpc2">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
434 <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
435 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
436 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
437 <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
438 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
439 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
440 <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
441 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
442 </when>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
443 </conditional>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
444 <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
445 <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
446 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
447 <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
448 <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
449 </param>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
450 <when value="disabled"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
451 <when value="enabled">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
452 <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
453 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
454 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
455 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
456 </when>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
457 </conditional>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
458 <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
459 <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
460 <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
461 <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
462 </param>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
463 <when value="disabled"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
464 <when value="enabled">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
465 <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
466 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
467 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
468 '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
469 '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
470 <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
471 </when>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
472 </conditional>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
473
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
474 <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
475 <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
476 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
477 <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
478 <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
479 <option value="netsurfp">NetSurfP-2</option>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
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parents:
diff changeset
480 </param>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
481 <when value="disabled"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
482 <when value="iupred2a">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
483 <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
484 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
485 <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
486 <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
487 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
488 <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
489 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
490 <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
491 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
492 </when>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
493 <when value="netsurfp">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
494 <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
495 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
496 <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
497 </when>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
498 </conditional>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
499 <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
500 <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
501 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
502 <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
503 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
504 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
505 <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
506 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
507 <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
508 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
509 classified as different" />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
510 <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
511 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
512 <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
513 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
514 <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
515 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
516 </section>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
517 </when>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
518 </conditional>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
519 </inputs>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
520 <outputs>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
521 <collection name="collection_counts_factor1" type="list" label="${tool.name} on ${on_string}: gene counts factor1">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
522 <discover_datasets pattern="__designation_and_ext__" format="tabular" directory="count_files/factor1" />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
523 <filter>functionMode['selector'] == 'data_import'</filter>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
524 <filter>functionMode['countFiles'] == 'collection'</filter>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
525 </collection>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
526 <collection name="collection_counts_factor2" type="list" label="${tool.name} on ${on_string}: gene counts factor2">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
527 <discover_datasets pattern="__designation_and_ext__" format="tabular" directory="count_files/factor2" />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
528 <filter>functionMode['selector'] == 'data_import'</filter>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
529 <filter>functionMode['countFiles'] == 'collection'</filter>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
530 </collection>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
531 <data name="matrix_counts" format="tabular" from_work_dir="count_files/matrix.tabular" label="${tool.name} on ${on_string}: gene counts matrix">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
532 <filter>functionMode['selector'] == 'data_import'</filter>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
533 <filter>functionMode['countFiles'] == 'matrix'</filter>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
534 </data>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
535 <data name="sample_annotation" format="tabular" from_work_dir="count_files/samples.tabular" label="${tool.name} on ${on_string}: samples annotation">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
536 <filter>functionMode['selector'] == 'data_import'</filter>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
537 <filter>functionMode['countFiles'] == 'matrix'</filter>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
538 </data>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
539 <data name="switchList" format="rdata" from_work_dir="SwitchList.Rda" label="${tool.name} on ${on_string}: SwitchList (RData)"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
540 <data name="isoformAA" format="fasta" from_work_dir="isoformSwitchAnalyzeR_isoform_AA.fasta" label="${tool.name} on ${on_string}: aminoacid sequences">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
541 <filter>functionMode['selector'] == 'first_step'</filter>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
542 <filter>functionMode['outputs_first'] and 'aa' in functionMode['outputs_first']</filter>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
543 </data>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
544 <data name="isoformNT" format="fasta" from_work_dir="isoformSwitchAnalyzeR_isoform_nt.fasta" label="${tool.name} on ${on_string}: nucleotide sequences">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
545 <filter>functionMode['selector'] == 'first_step'</filter>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
546 <filter>functionMode['outputs_first'] and 'nt' in functionMode['outputs_first']</filter>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
547 </data>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
548 <data name="switchSummary" format="tabular" from_work_dir="switchSummary.tsv" label="${tool.name} on ${on_string}: summary">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
549 <filter>functionMode['selector'] == 'first_step'</filter>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
550 <filter>functionMode['outputs_first'] and 'summary' in functionMode['outputs_first']</filter>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
551 </data>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
552 <collection name="plots_summary" type="list" label="${tool.name} on ${on_string}: genome wide plots">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
553 <discover_datasets pattern="__designation_and_ext__" format="pdf" directory="pdf_outputs" />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
554 <filter>functionMode['selector'] == 'second_step'</filter>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
555 <filter>functionMode['analysis_mode']['selector'] == 'top'</filter>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
556 </collection>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
557 <collection name="genes_consequences" type="list" label="${tool.name} on ${on_string}: isoform switches with predicted functional consequences plots">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
558 <discover_datasets pattern="__designation_and_ext__" format="pdf" directory="gene_plots/with_consequences" />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
559 <filter>functionMode['selector'] == 'second_step'</filter>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
560 <filter>functionMode['analysis_mode']['selector'] == 'top'</filter>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
561 </collection>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
562 <collection name="genes_wo_consequences" type="list" label="${tool.name} on ${on_string}: isoform switches without predicted functional consequences plots">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
563 <discover_datasets pattern="__designation_and_ext__" format="pdf" directory="gene_plots/without_consequences" />
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
564 <filter>functionMode['selector'] == 'second_step'</filter>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
565 <filter>functionMode['analysis_mode']['selector'] == 'top'</filter>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
566 </collection>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
567 <data name="mostSwitching" format="tabular" from_work_dir="mostSwitchingGene.tsv" label="${tool.name} on ${on_string}: switching gene/isoforms">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
568 <filter>functionMode['selector'] == 'second_step'</filter>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
569 <filter>functionMode['analysis_mode']['selector'] == 'top'</filter>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
570 </data>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
571 <data name="consequencesSummary" format="tabular" from_work_dir="consequencesSummary.tsv" label="${tool.name} on ${on_string}: consequences summary">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
572 <filter>functionMode['selector'] == 'second_step'</filter>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
573 <filter>functionMode['analysis_mode']['selector'] == 'top'</filter>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
574 </data>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
575 <data name="consequencesEnrichment" format="tabular" from_work_dir="consequencesEnrichment.tsv" label="${tool.name} on ${on_string}: consequences enrichment">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
576 <filter>functionMode['selector'] == 'second_step'</filter>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
577 <filter>functionMode['analysis_mode']['selector'] == 'top'</filter>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
578 </data>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
579 <data name="splicingSummary" format="tabular" from_work_dir="splicingSummary.tsv" label="${tool.name} on ${on_string}: splicing summary">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
580 <filter>functionMode['selector'] == 'second_step'</filter>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
581 <filter>functionMode['analysis_mode']['selector'] == 'top'</filter>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
582 </data>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
583 <data name="splicingEnrichment" format="tabular" from_work_dir="splicingEnrichment.tsv" label="${tool.name} on ${on_string}: splicing enrichment">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
584 <filter>functionMode['selector'] == 'second_step'</filter>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
585 <filter>functionMode['analysis_mode']['selector'] == 'top'</filter>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
586 </data>
4
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
587 <data name="splicing_fulldata" format="tabular" from_work_dir="switchSplicing_fulldata.tsv" label="${tool.name} on ${on_string}: alternative splicing full data">
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
588 <filter>functionMode['selector'] == 'second_step'</filter>
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
589 <filter>functionMode['analysis_mode']['selector'] == 'top'</filter>
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
590 </data>
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
591 <data name="consequences_fulldata" format="tabular" from_work_dir="switchConsequence_fulldata.tsv" label="${tool.name} on ${on_string}: funcional consequences full data">
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
592 <filter>functionMode['selector'] == 'second_step'</filter>
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
593 <filter>functionMode['analysis_mode']['selector'] == 'top'</filter>
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
594 </data>
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
595 <data name="isoformFeatures" format="tabular" from_work_dir="IsoformFeatures.tsv" label="${tool.name} on ${on_string}: isoform features">
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
596 <filter>functionMode['selector'] == 'second_step'</filter>
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
597 <filter>functionMode['analysis_mode']['selector'] == 'top'</filter>
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
598 </data>
0
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
599 <data name="single_gene" format="pdf" from_work_dir="single_gene.pdf" label="${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
600 <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
601 <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
602 </data>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
603 </outputs>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
604 <tests>
5
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
605 <!-- 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
606 <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
607 <conditional name="functionMode">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
608 <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
609 <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
610 <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
611 <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
612 <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
613 <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
614 <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
615 <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
616 <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
617 </section>
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
618 <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
619 <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
620 <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
621 </section>
0
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
622 </conditional>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
623 </conditional>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
624 <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
625 </test>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
626 <!-- 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
627 <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
628 <conditional name="functionMode">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
629 <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
630 <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
631 <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
632 <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
633 <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
634 <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
635 <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
636 <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
637 <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
638 </section>
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
639 <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
640 <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
641 <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
642 </section>
0
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
643 </conditional>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
644 </conditional>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
645 <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
646 <assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
647 <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
648 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
649 </output>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
650 <output name="matrix_counts" file="test02_counts.tabular" ftype="tabular" lines_diff="6"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
651 <output name="sample_annotation" file="test02_samples_annotation.tabular" ftype="tabular"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
652 </test>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
653 <!-- 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
654 <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
655 <conditional name="functionMode">
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="data_import"/>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
657 <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
658 <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
659 <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
660 <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
661 <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
662 <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
663 <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
664 <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
665 </section>
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
666 <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
667 <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
668 <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
669 </section>
0
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
670 </conditional>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
671 </conditional>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
672 <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
673 <assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
674 <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
675 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
676 </output>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
677 <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
678 <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
679
0
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
680 </output_collection>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
681 <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
682 <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
683 </output_collection>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
684 </test>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
685 <!-- 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
686 <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
687 <conditional name="functionMode">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
688 <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
689 <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
690 <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
691 <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
692 <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
693 <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
694 <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
695 <section name="prefilter">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
696 <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
697 <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
698 <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
699 <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
700 <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
701 </section>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
702 <section name="dexseq">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
703 <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
704 <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
705 <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
706 <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
707 <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
708 </section>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
709 <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
710 <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
711 <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
712 <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
713 </section>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
714 <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
715 <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
716 <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
717 <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
718 <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
719 </section>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
720 </conditional>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
721 <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
722 <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
723 <assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
724 <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
725 <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
726 <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
727 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
728 </output>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
729 <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
730 <assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
731 <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
732 <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
733 <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
734 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
735 </output>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
736 <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
737 </test>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
738 <!-- 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
739 <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
740 <conditional name="functionMode">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
741 <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
742 <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
743 <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
744 <section name="dexseq">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
745 <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
746 <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
747 <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
748 <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
749 <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
750 </section>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
751 <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
752 <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
753 </section>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
754 </conditional>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
755 <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
756 <assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
757 <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
758 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
759 </output>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
760 </test>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
761 <!--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
762 <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
763 <conditional name="functionMode">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
764 <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
765 <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
766 <section name="analyzeSwitchConsequences">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
767 <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
768 <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
769 <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
770 <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
771 <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
772 <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
773 </section>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
774 <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
775 <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
776 <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
777 <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
778 <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
779 <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
780 <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
781 <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
782 <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
783 <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
784 <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
785 <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
786 <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
787 <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
788 <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
789 <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
790 </section>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
791 </conditional>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
792 </conditional>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
793 <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
794 <assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
795 <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
796 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
797 </output>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
798 <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
799 <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
800 <assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
801 <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
802 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
803 </element>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
804 <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
805 <assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
806 <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
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 </element>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
809 <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
810 <assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
811 <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
812 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
813 </element>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
814 <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
815 <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
816 <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
817 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
818 </element>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
819 <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
820 <assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
821 <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
822 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
823 </element>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
824 <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
825 <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
826 <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
827 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
828 </element>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
829 <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
830 <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
831 <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
832 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
833 </element>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
834 </output_collection>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
835 <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
836 <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
837 <assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
838 <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
839 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
840 </element>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
841 <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
842 <assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
843 <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
844 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
845 </element>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
846 </output_collection>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
847 <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
848 <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
849 <assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
850 <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
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 </element>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
853 <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
854 <assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
855 <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
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 </element>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
858 </output_collection>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
859 <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
860 <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
861 <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
862 <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
863 <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
864 <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
865 <assert_contents>
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
866 <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
867 <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
868 </assert_contents>
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
869 </output>
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
870 <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
871 <assert_contents>
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
872 <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
873 <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
874 </assert_contents>
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
875 </output>
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
876 <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
877 <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
878 <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
879 <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
880 </assert_contents>
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
881 </output>
0
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
882 </test>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
883 <!--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
884 <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
885 <conditional name="functionMode">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
886 <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
887 <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
888 <section name="analyzeSwitchConsequences">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
889 <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
890 <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
891 <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
892 <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
893 <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
894 <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
895 </section>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
896 <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
897 <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
898 <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
899 <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
900 <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
901 <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
902 <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
903 <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
904 <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
905 <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
906 <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
907 <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
908 <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
909 <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
910 <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
911 <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
912 </section>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
913 </conditional>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
914 <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
915 <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
916 <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
917 <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
918 <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
919 </conditional>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
920 <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
921 <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
922 <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
923 </conditional>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
924 <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
925 <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
926 <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
927 <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
928 </conditional>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
929 <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
930 <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
931 <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
932 <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
933 <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
934 <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
935 <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
936 <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
937 <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
938 </conditional>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
939 </conditional>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
940 <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
941 <assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
942 <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
943 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
944 </output>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
945 <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
946 <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
947 <assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
948 <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
949 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
950 </element>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
951 <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
952 <assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
953 <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
954 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
955 </element>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
956 <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
957 <assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
958 <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
959 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
960 </element>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
961 <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
962 <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
963 <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
964 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
965 </element>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
966 <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
967 <assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
968 <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
969 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
970 </element>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
971 <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
972 <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
973 <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
974 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
975 </element>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
976 <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
977 <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
978 <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
979 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
980 </element>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
981 </output_collection>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
982 <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
983 <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
984 <assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
985 <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
986 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
987 </element>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
988 <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
989 <assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
990 <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
991 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
992 </element>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
993 </output_collection>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
994 <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
995 <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
996 <assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
997 <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
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 </element>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1000 <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
1001 <assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1002 <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
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 </element>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1005 </output_collection>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1006 <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
1007 <assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1008 <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
1009 <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
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 </output>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1012 <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
1013 <assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1014 <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
1015 <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
1016 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1017 </output>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1018 <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
1019 <assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1020 <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
1021 <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
1022 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1023 </output>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1024 <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
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 <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
1027 <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
1028 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1029 </output>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1030 <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
1031 <assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1032 <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
1033 <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
1034 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1035 </output>
4
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
1036 <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
1037 <assert_contents>
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
1038 <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
1039 <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
1040 </assert_contents>
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
1041 </output>
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
1042 <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
1043 <assert_contents>
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
1044 <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
1045 <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
1046 </assert_contents>
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
1047 </output>
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
1048 <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
1049 <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
1050 <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
1051 <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
1052 </assert_contents>
8575def9219d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3
iuc
parents: 2
diff changeset
1053 </output>
0
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1054 </test>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1055 <!-- 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
1056 <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
1057 <conditional name="functionMode">
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1058 <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
1059 <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
1060 <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
1061 <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
1062 <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
1063 </conditional>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1064 </conditional>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1065 <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
1066 <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
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 <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
1069 </assert_contents>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1070 </output>
bb611fa3bc3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380
iuc
parents:
diff changeset
1071 </test>
5
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
1072 <!-- 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
1073 <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
1074 <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
1075 <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
1076 <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
1077 <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
1078 <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
1079 <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
1080 <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
1081 <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
1082 <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
1083 <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
1084 </section>
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
1085 <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
1086 <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
1087 <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
1088 </section>
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
1089 </conditional>
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
1090 </conditional>
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
1091 <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
1092 </test>
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
1093 <!-- 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
1094 <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
1095 <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
1096 <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
1097 <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
1098 <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
1099 <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
1100 <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
1101 <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
1102 <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
1103 <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
1104 <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
1105 <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
1106 </section>
69fa05891f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
iuc
parents: 4
diff changeset
1107 <section name="second_factor">
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1108 <param name="factorLevel" value="cancer"/>
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1109 <param name="trans_counts" value="salmon_cond2_rep1.sf,salmon_cond2_rep2.sf"/>
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1110 </section>
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1111 </conditional>
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1112 </conditional>
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1113 <output name="switchList" ftype="rdata">
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1114 <assert_contents>
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1115 <has_size value="652170" delta="300"/>
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1116 </assert_contents>
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1117 </output>
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1118 <output name="sample_annotation" file="test10_samples_annotation.tabular" ftype="tabular"/>
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1119 </test>
0
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1120 </tests>
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1121 <help><![CDATA[
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1122
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1123 .. class:: infomark
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1124
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1125 **Purpose**
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1126
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1127 IsoformSwitchAnalyzeR is an easy-to use-R package that enables statistical identification of isoform switching from RNA-seq derived quantification
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1128 of novel and/or annotated full-length isoforms. IsoformSwitchAnalyzeR facilitates integration of many sources of (predicted) annotation such as Open
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1129 Reading Frame (ORF/CDS), protein domains (via Pfam), signal peptides (via SignalP), Intrinsically Disordered Regions (IDR, via NetSurfP-2 or IUPred2A),
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1130 coding potential (via CPAT or CPC2) and sensitivity to Non-sense Mediated Decay (NMD) and more. The combination of identified isoform switches and
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1131 their annotation enables IsoformSwitchAnalyzeR to predict potential functional consequences of the identified isoform switches — such as loss of
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1132 protein domains — thereby identifying isoform switches of particular interest. Lastly, IsoformSwitchAnalyzeR provides article-ready visualization
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1133 methods for isoform switches for individual genes as well as both summary statistics and visualization of the genome-wide changes/consequences of
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1134 isoform switches, their consequences and the associated alternative splicing.
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1135
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1136 -----
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1137
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1138 .. class:: infomark
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1139
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1140 **Differential isoform expression (DIE) and differential isoform usage (DIU)**
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1141
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1142 Differential isoform expression (DIE) and differential isoform usage (DIU) are related but distinct concepts. DIE assesses the difference of
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1143 absolute expression in isoform level. In contrast, DIU assesses the difference of relative expression in isoform level. For example, if the
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1144 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
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1145 expression of the first isoform is 1/3 in both case and control.
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1146
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1147 -----
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1148
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1149 .. class:: infomark
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1150
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1151 **ORF identification methods (novel isoform analysis)**
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1152
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1153 - **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.
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1154 - **LongestAnnotated**: Identifies the longest ORF (after filtering via minORFlength) downstream of an annotated translation start site (which are supplied via the cds argument).
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1155 - **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.
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1156 - **MostUpstream**: Identifies the most upstream ORF in the transcript (after filtering via minORFlength).
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1157 - **MostUpstreamAnnoated**: Identifies the ORF (after filtering via minORFlength) downstream of the most upstream overlapping annotated translation start site (supplied via the cds argument).
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1158
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1159 ]]></help>
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1160 <expand macro="citations" />
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1161 </tool>