Mercurial > repos > iuc > colibread_lordec

annotate lordec.xml @ 5:87c61a0e1177 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7ea9a5c6d9e7212c38be96baa6615af1ea9d5a8e"
author iuc
date Tue, 13 Oct 2020 21:30:13 +0000
parents a92669266a08
children 434af4cbf682
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
1 <?xml version='1.0' encoding='utf-8'?>
5
87c61a0e1177 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7ea9a5c6d9e7212c38be96baa6615af1ea9d5a8e"
iuc
parents: 4
diff changeset
2 <tool profile="16.04" id="lordec" name="Lordec" version="0.9+galaxy1">
0
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
3 <description>is a set a programs for correcting sequencing errors in PacBio reads</description>
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
4 <macros>
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
5 <import>macros.xml</import>
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
6 </macros>
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
7 <requirements>
2
c44f93b8ed51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit b24ba669c32dd33efcc60eee595a18abd639ca7a
iuc
parents: 0
diff changeset
8 <requirement type="package" version="0.9">lordec</requirement>
0
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
9 </requirements>
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
10 <command><![CDATA[
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
11
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
12 #if str( $program_type_choice.program_type ) == "correct"
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
13 lordec-correct
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
14 @lordec_inputs@
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
15 #if str( $program_type_choice.advanced_options.advanced_options_selector ) == "advanced"
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
16 -t ${program_type_choice.advanced_options.t}
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
17 -b ${program_type_choice.advanced_options.b}
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
18 -e ${program_type_choice.advanced_options.e}
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
19 #end if
5
87c61a0e1177 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7ea9a5c6d9e7212c38be96baa6615af1ea9d5a8e"
iuc
parents: 4
diff changeset
20 -T \${GALAXY_SLOTS:-1}
0
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
21 -o '${corrected_read_file}'
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
22
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
23
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
24 #else if str( $program_type_choice.program_type ) == "trim"
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
25 #if $program_type_choice.split
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
26 lordec-trim-split
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
27 #else
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
28 lordec-trim
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
29 #end if
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
30 -i '${program_type_choice.i}'
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
31 -o '${trimmed_reads_file}'
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
32
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
33 #else
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
34 lordec-stat
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
35 @lordec_inputs@
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
36 -S '${stat_file}'
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
37 #end if
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
38
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
39
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
40 ]]></command>
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
41
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
42 <inputs>
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
43
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
44 <conditional name="program_type_choice">
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
45 <param name="program_type" type="select" label="Choose Lordec program">
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
46 <option value="correct">Lordec Correct</option>
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
47 <option value="trim">Lordec Trim</option>
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
48 <option value="stats">Lordec Statistics</option>
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
49 </param>
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
50
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
51 <when value="correct">
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
52 <expand macro="lordec_inputs" />
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
53 <conditional name="advanced_options">
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
54 <param name="advanced_options_selector" type="select" label="Lordec correct advanced options">
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
55 <option value="default" selected="true">Default</option>
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
56 <option value="advanced">Advanced</option>
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
57 </param>
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
58 <when value="default"></when>
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
59 <when value="advanced">
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
60 <param argument="-t" type="integer" label="Number of target k-mers" value="5" />
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
61 <param argument="-b" type="integer" label="Maximum number of branches to explore" value="200" />
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
62 <param argument="-e" type="float" label="Maximum error rate" value="0.4" />
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
63 </when>
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
64 </conditional>
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
65 </when>
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
66
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
67 <when value="trim">
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
68 <param argument="-i" type="data" format="fasta,fastq.gz,fastq" label="Long read FASTA/Q file" help="PacBio reads files" />
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
69 <param name="split" type="boolean" label="Use the split option" help="Trim all weak regions and split the reads on inner weak regions" />
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
70 </when>
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
71
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
72 <when value="stats">
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
73 <expand macro="lordec_inputs" />
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
74 </when>
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
75
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
76 </conditional>
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
77
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
78 </inputs>
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
79
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
80 <outputs>
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
81 <data format="fasta" name="corrected_read_file" label="Corrected long reads with ${tool.name} on ${on_string}" >
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
82 <filter>program_type_choice['program_type'] == 'correct'</filter>
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
83 </data>
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
84 <data format="fasta" name="trimmed_reads_file" label="Trimmed reads file with ${tool.name} on ${on_string}" >
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
85 <filter>program_type_choice['program_type'] == 'trim'</filter>
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
86 </data>
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
87 <data format="tabular" name="stat_file" label="Stats with ${tool.name} on ${on_string}" >
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
88 <filter>program_type_choice['program_type'] == 'stats'</filter>
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
89 </data>
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
90 </outputs>
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
91
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
92 <tests>
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
93 <test>
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
94 <conditional name="program_type_choice">
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
95 <param name="program_type" value="correct" />
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
96 <param name="inputs" value="lordec/ill-test-5K-1.fa,lordec/ill-test-5K-2.fa" />
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
97 <param name="i" value="lordec/coli-pacbio-test-mini.fa" />
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
98 <param name="k" value="31" />
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
99 </conditional>
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
100 <output name="corrected_read_file" file="lordec/corrected_reads.fa"/>
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
101 </test>
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
102 <test>
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
103 <conditional name="program_type_choice">
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
104 <param name="program_type" value="trim" />
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
105 <param name="i" value="lordec/corrected_reads.fa" />
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
106 </conditional>
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
107 <output name="trimmed_reads_file" file="lordec/trimmed_reads.fa"/>
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
108 </test>
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
109 <test>
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
110 <conditional name="program_type_choice">
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
111 <param name="program_type" value="stats" />
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
112 <param name="inputs" value="lordec/ill-test-5K-1.fa,lordec/ill-test-5K-2.fa" />
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
113 <param name="i" value="lordec/coli-pacbio-test-mini.fa" />
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
114 </conditional>
4
a92669266a08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 0ed02865f048ad7471ea79509c0e23162bc29166"
iuc
parents: 2
diff changeset
115 <output name="stat_file" file="lordec/stat_file.txt" compare="sim_size" delta="10"/>
0
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
116 </test>
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
117 </tests>
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
118 <help><![CDATA[
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
119
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
120 **Lordec Correct**
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
121
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
122 Program for correcting sequencing errors in PacBio reads using highly accurate short reads (e.g. Illumina).
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
123
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
124 LoRDEC outputs the corrected reads to the given file in FASTA format. The regions that remain weak after the correction are outputted in lower case characters and the solid regions are outputted in upper case characters.
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
125
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
126 -------
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
127
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
128 **Lordec Trim**
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
129
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
130 Program for trimming the weak regions from the beginning and end of the corrected reads.
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
131
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
132 -------
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
133
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
134 **Lordec Statistics**
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
135
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
136 Program to generate statistics on solid and weak k-mers.
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
137
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
138 -------
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
139
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
140 **Web site**
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
141
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
142 http://www.atgc-montpellier.fr/lordec/
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
143
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
144
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
145 ]]></help>
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
146 <expand macro="citations">
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
147 <citation type="doi">10.1093/bioinformatics/btu538</citation>
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
148 </expand>
a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff changeset
149 </tool>