Mercurial > repos > iuc > mothur_reverse_seqs

comparison reverse.seqs.xml @ 0:34812b0dc74f 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/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
author iuc
date Fri, 24 Jun 2016 16:48:48 -0400
parents
children 24279ccecac5
comparison
equal deleted inserted replaced
-1:000000000000 0:34812b0dc74f
1 <tool profile="16.07" id="mothur_reverse_seqs" name="Reverse.seqs" version="@WRAPPER_VERSION@.0">
2 <description>Reverse complement the sequences</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[
9 ## create symlinks to input datasets
10 ln -s "$fasta" fasta.dat &&
11
12 echo 'reverse.seqs(
13 fasta=fasta.dat
14 )'
15 | sed 's/ //g' ## mothur trips over whitespace
16 | mothur
17 ]]></command>
18 <inputs>
19 <param name="fasta" type="data" format="fasta,mothur.align" label="fasta - Sequences to reverse complement"/>
20 </inputs>
21 <outputs>
22 <expand macro="logfile-output"/>
23 <data name="out_fasta" format_source="fasta" from_work_dir="fasta*.rc.*" label="${tool.name} on ${on_string}: rc.fasta"/>
24 </outputs>
25 <tests>
26 <test>
27 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/>
28 <output name="out_fasta" file="Mock_S280_L001_R1_001_small.trim.contigs.good.rc.align_head"/>
29 <expand macro="logfile-test"/>
30 </test>
31 </tests>
32 <help>
33 <![CDATA[
34
35 @MOTHUR_OVERVIEW@
36
37 **Command Documenation**
38
39 The reverse.seqs_ command will generate a fasta containing the reverse complement of each sequence in the input fasta.
40
41 .. _reverse.seqs: http://www.mothur.org/wiki/Reverse.seqs
42 ]]>
43 </help>
44 <expand macro="citations"/>
45 </tool>