Mercurial > repos > iuc > mothur_shhh_seqs

comparison shhh.seqs.xml @ 0:fddd81ee5cd4 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 05:07:22 -0400
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-1:000000000000 0:fddd81ee5cd4
1 <tool profile="16.07" id="mothur_shhh_seqs" name="Shhh.seqs" version="@WRAPPER_VERSION@.0">
2 <description>Denoise program (Quince SeqNoise)</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
17 echo 'shhh.seqs(
18 fasta=fasta.dat,
19 name=name.dat,
20 #if $group:
21 group=group.dat,
22 #end if
23 sigma=$sigma,
24 processors='\${GALAXY_SLOTS:-8}'
25 )'
26 | sed 's/ //g' ## mothur trips over whitespace
27 | mothur
28 | tee mothur.out.log
29 ]]></command>
30 <inputs>
31 <param name="fasta" type="data" format="fasta" label="fasta - Sequences" help=""/>
32 <param name="name" type="data" format="mothur.names" label="name - Sequences Name reference"/>
33 <param name="group" type="data" format="mothur.groups" optional="true" label="group - Sequences Name reference"/>
34 <param name="sigma" type="float" value=".01" min="0.0" max="1.0" label="sigma" help="default .01"/>
35 </inputs>
36 <outputs>
37 <expand macro="logfile-output"/>
38 <data name="shhh_fasta" format_source="fasta" from_work_dir="fasta*.shhh_seqs.fasta" label="${tool.name} on ${on_string}: shhh.fasta"/>
39 <data name="shhh_names" format="mothur.names" from_work_dir="fasta*.shhh_seqs.names" label="${tool.name} on ${on_string}: shhh.names"/>
40 <data name="shhh_map" format="txt" from_work_dir="fasta*.shhh_seqs.map" label="${tool.name} on ${on_string}: shhh.map"/>
41 </outputs>
42 <tests>
43 <test>
44 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head" ftype="mothur.align"/>
45 <param name="name" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head.names"/>
46 <output name="shhh_fasta" md5="0169152fa33b588cabf3c3b932cc6018" ftype="mothur.align"/>
47 <output name="shhh_names" md5="f3bc939b899d91f7cf3b822c5a822805" ftype="mothur.names"/>
48 <output name="shhh_map" md5="0bcfe53ec754878ca5f6a126114671e1" ftype="txt"/>
49 <expand macro="logfile-test"/>
50 </test>
51 </tests>
52 <help>
53 <![CDATA[
54
55 @MOTHUR_OVERVIEW@
56
57 **Command Documentation**
58
59 The shhh.seqs_ command is a mothur-based rewrite of Chris Quince's sequence denoting program, SeqNoise. Schloss prefers pre.cluster for this operation.
60
61 .. _shhh.seqs: https://www.mothur.org/wiki/Shhh.seqs
62
63 ]]>
64 </help>
65 <expand macro="citations"/>
66 </tool>