Mercurial > repos > iuc > mothur_shhh_seqs

comparison shhh.seqs.xml @ 2:c54bf33450d7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author iuc
date Tue, 20 Mar 2018 22:17:05 -0400
parents fddd81ee5cd4
children 6ee54b761c3c
comparison
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1:c7e60f5aadcb 2:c54bf33450d7
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
8 <expand macro="version_command"/> 8 <expand macro="version_command"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10 @SHELL_OPTIONS@ 10 @SHELL_OPTIONS@
11 11
12 ## create symlinks to input datasets 12 ## create symlinks to input datasets
13 ln -s "$fasta" fasta.dat && 13 ln -s '$fasta' fasta.dat &&
14 ln -s "$name" name.dat && 14 ln -s '$name' name.dat &&
15 ln -s "$group" group.dat && 15 ln -s '$group' group.dat &&
16 16
17 echo 'shhh.seqs( 17 echo 'shhh.seqs(
18 fasta=fasta.dat, 18 fasta=fasta.dat,
19 name=name.dat, 19 name=name.dat,
20 #if $group: 20 #if $group:
21 group=group.dat, 21 group=group.dat,
22 #end if 22 #end if
23 sigma=$sigma, 23 sigma=$sigma,
24 processors='\${GALAXY_SLOTS:-8}' 24 processors='\${GALAXY_SLOTS:-8}'
25 )' 25 )'
26 | sed 's/ //g' ## mothur trips over whitespace 26 | sed 's/ //g' ## mothur trips over whitespace
27 | mothur 27 | mothur
28 | tee mothur.out.log 28 | tee mothur.out.log
29 ]]></command> 29 ]]></command>
30 <inputs> 30 <inputs>
31 <param name="fasta" type="data" format="fasta" label="fasta - Sequences" help=""/> 31 <param name="fasta" type="data" format="fasta" label="fasta - Sequences" help=""/>
32 <param name="name" type="data" format="mothur.names" label="name - Sequences Name reference"/> 32 <param name="name" type="data" format="mothur.names" label="name - Sequences Name reference"/>
33 <param name="group" type="data" format="mothur.groups" optional="true" label="group - Sequences Name reference"/> 33 <param name="group" type="data" format="mothur.groups" optional="true" label="group - Sequences Name reference"/>
34 <param name="sigma" type="float" value=".01" min="0.0" max="1.0" label="sigma" help="default .01"/> 34 <param name="sigma" type="float" value=".01" min="0.0" max="1.0" label="sigma" help="default .01"/>
35 <expand macro="param-savelog"/>
35 </inputs> 36 </inputs>
36 <outputs> 37 <outputs>
37 <expand macro="logfile-output"/> 38 <expand macro="logfile-output"/>
38 <data name="shhh_fasta" format_source="fasta" from_work_dir="fasta*.shhh_seqs.fasta" label="${tool.name} on ${on_string}: shhh.fasta"/> 39 <data name="shhh_fasta" format_source="fasta" from_work_dir="fasta*.shhh_seqs.fasta" label="${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 ${on_string}: shhh.names"/> 40 <data name="shhh_names" format="mothur.names" from_work_dir="fasta*.shhh_seqs.names" label="${tool.name} on ${on_string}: shhh.names"/>
44 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head" ftype="mothur.align"/> 45 <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 <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_fasta" md5="0169152fa33b588cabf3c3b932cc6018" ftype="mothur.align"/>
47 <output name="shhh_names" md5="f3bc939b899d91f7cf3b822c5a822805" ftype="mothur.names"/> 48 <output name="shhh_names" md5="f3bc939b899d91f7cf3b822c5a822805" ftype="mothur.names"/>
48 <output name="shhh_map" md5="0bcfe53ec754878ca5f6a126114671e1" ftype="txt"/> 49 <output name="shhh_map" md5="0bcfe53ec754878ca5f6a126114671e1" ftype="txt"/>
50 <param name="savelog" value="true"/>
49 <expand macro="logfile-test"/> 51 <expand macro="logfile-test"/>
50 </test> 52 </test>
51 </tests> 53 </tests>
52 <help> 54 <help><![CDATA[
53 <![CDATA[
54 55
55 @MOTHUR_OVERVIEW@ 56 @MOTHUR_OVERVIEW@
56 57
57 **Command Documentation** 58 **Command Documentation**
58 59
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 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
61 .. _shhh.seqs: https://www.mothur.org/wiki/Shhh.seqs 62 .. _shhh.seqs: https://www.mothur.org/wiki/Shhh.seqs
62 63
63 ]]> 64 ]]></help>
64 </help>
65 <expand macro="citations"/> 65 <expand macro="citations"/>
66 </tool> 66 </tool>