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comparison chop.seqs.xml @ 0:b7635a7037a7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 05:00:19 -0400
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children 35a4e758bbed
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-1:000000000000 0:b7635a7037a7
1 <tool profile="16.07" id="mothur_chop_seqs" name="Chop.seqs" version="@WRAPPER_VERSION@.0">
2 <description>Trim sequences to a specified length</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
8 <expand macro="version_command"/>
9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
12 ## create symlinks to input datasets
13 ln -s "$fasta" fasta.dat &&
14 ln -s "$name" name.dat &&
15 ln -s "$group" group.dat &&
16 ln -s "$count" count.dat &&
17
18 echo 'chop.seqs(
19 fasta=fasta.dat,
20 numbases=$numbases,
21 keep=$keep,
22 countgaps=$countgaps,
23 short=$short,
24 #if $name:
25 name=name.dat,
26 #end if
27 #if $group:
28 group=group.dat,
29 #end if
30 #if $count:
31 count=count.dat,
32 #end if
33 processors='\${GALAXY_SLOTS:-8}'
34 )'
35 | sed 's/ //g' ## mothur trips over whitespace
36 | mothur
37 | tee mothur.out.log
38 ]]></command>
39 <inputs>
40 <param name="fasta" type="data" format="fasta,mothur.align" label="fasta - Sequences to be chopped"/>
41 <param name="numbases" type="integer" value="10" label="numbases - Number of bases to keep"/>
42 <param name="keep" type="select" label="keep - Part of the sequence to keep">
43 <option value="front">front</option>
44 <option value="back">back</option>
45 </param>
46 <param name="countgaps" type="boolean" truevalue="true" falsevalue="false" checked="false" label="countgaps - Count gaps as bases"/>
47 <param name="short" type="boolean" truevalue="true" falsevalue="false" checked="false" label="short - keep sequences that are too short to chop"/>
48 <param name="name" type="data" format="name" optional="true" label="name file"/>
49 <param name="group" type="data" format="group" optional="true" label="group file"/>
50 <param name="count" type="data" format="mothur.count_table" optional="true" label="count file"/>
51 </inputs>
52 <outputs>
53 <expand macro="logfile-output"/>
54 <data name="out_fasta" format_source="fasta" from_work_dir="fasta*.chop.fasta" label="${tool.name} on ${on_string}: chop.fasta"/>
55 </outputs>
56 <tests>
57 <test>
58 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/>
59 <param name="name" value="Mock_S280_L001_R1_001_small.trim.contigs.good.names"/>
60 <output name="out_fasta" file="Mock_S280_L001_R1_001_small.trim.contigs.good.chop.fasta" compare="contains"/>
61 <expand macro="logfile-test"/>
62 </test>
63 </tests>
64 <help>
65 <![CDATA[
66
67 @MOTHUR_OVERVIEW@
68
69 **Command Documentation**
70
71 The chop.seqs_ command reads a fasta file of sequences and outputs a .chop.fasta file containing the trimmed sequences. It works on both aligned and unaligned sequences.
72
73 .. _chop.seqs: https://www.mothur.org/wiki/Chop.seqs
74
75 v1.20.0: Updated to 1.33. Added name, group and count options for mothur version 1.31.0
76 ]]>
77 </help>
78 <expand macro="citations"/>
79 </tool>