Mercurial > repos > iuc > mothur_degap_seqs

comparison degap.seqs.xml @ 0:7cd72305d496 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 05:09:06 -0400
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children f643cbd3a967
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-1:000000000000 0:7cd72305d496
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="stdio"/>
8 <expand macro="version_command"/>
9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
12 ## create symlinks to input datasets
13 ln -s "$fasta" fasta.dat &&
14
15 echo 'degap.seqs(
16 fasta=fasta.dat
17 )'
18 | sed 's/ //g' ## mothur trips over whitespace
19 | mothur
20 | tee mothur.out.log
21 ]]></command>
22 <inputs>
23 <param name="fasta" type="data" format="fasta" label="fasta - Dataset"/>
24 </inputs>
25 <outputs>
26 <expand macro="logfile-output"/>
27 <data name="out_fasta" format_source="fasta" from_work_dir="fasta*.ng.fasta" label="${tool.name} on ${on_string}: fasta"/>
28 </outputs>
29 <tests>
30 <test>
31 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/>
32 <output name="out_fasta" file="Mock_S280_L001_R1_001_small.trim.contigs.good.ng.fasta"/>
33 <expand macro="logfile-test"/>
34 </test>
35 </tests>
36 <help>
37 <![CDATA[
38
39 @MOTHUR_OVERVIEW@
40
41 **Command Documentation**
42
43 The degap.seqs_ command reads a fasta file and outputs a fasta containing the sequences after all gap characters are removed.
44
45 .. _degap.seqs: https://www.mothur.org/wiki/Degap.seqs
46
47 v1.21.0: Updated to Mothur 1.33
48
49 ]]>
50 </help>
51 <expand macro="citations"/>
52 </tool>