Mercurial > repos > iuc > mothur_degap_seqs

comparison degap.seqs.xml @ 0:ae5e88c4d82b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
author iuc
date Fri, 24 Jun 2016 16:29:07 -0400
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1 <tool profile="16.07" id="mothur_degap_seqs" name="Degap.seqs" version="@WRAPPER_VERSION@.0">
2 <description>Remove gap characters from 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 "$fasta" fasta.dat &&
11
12 echo 'degap.seqs(
13 fasta=fasta.dat
14 )'
15 | sed 's/ //g' ## mothur trips over whitespace
16 | mothur
17 ]]></command>
18 <inputs>
19 <param name="fasta" type="data" format="fasta" label="fasta - Dataset"/>
20 </inputs>
21 <outputs>
22 <expand macro="logfile-output"/>
23 <data name="out_fasta" format_source="fasta" from_work_dir="fasta*.ng.fasta" label="${tool.name} on ${on_string}: 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.ng.fasta"/>
29 <expand macro="logfile-test"/>
30 </test>
31 </tests>
32 <help>
33 <![CDATA[
34
35 @MOTHUR_OVERVIEW@
36
37 **Command Documenation**
38
39 The degap.seqs_ command reads a fasta file and outputs a fasta containing the sequences after all gap characters are removed.
40
41 .. _degap.seqs: http://www.mothur.org/wiki/Degap.seqs
42
43 v1.21.0: Updated to Mothur 1.33
44
45 ]]>
46 </help>
47 <expand macro="citations"/>
48 </tool>