Mercurial > repos > iuc > mothur_consensus_seqs

comparison consensus.seqs.xml @ 0:fb865c8dc76f 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 16:27:31 -0400
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-1:000000000000 0:fb865c8dc76f
1 <tool profile="16.07" id="mothur_consensus_seqs" name="Consensus.seqs" version="@WRAPPER_VERSION@.0">
2 <description>Find a consensus sequence for each OTU or phylotype</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 "$fasta" fasta.dat &&
11 ln -s "$name" name.dat &&
12 ln -s "$count" count.dat &&
13 #if $perotu.use == "yes":
14 ln -s "$perotu.otu" perotu.otu.dat &&
15 #end if
16
17 echo 'consensus.seqs(
18 fasta=fasta.dat
19 #if $name:
20 ,name=name.dat
21 #end if
22 #if $cutoff:
23 ,cutoff=$cutoff
24 #end if
25 #if $perotu.use == "yes":
26 ,list=perotu.otu.dat
27 #if $perotu.label:
28 ,label=${ str($perotu.label).replace(",","-") }
29 #end if
30 #end if
31 #if $count:
32 ,count=count.dat
33 #end if
34 )'
35 | sed 's/ //g' ## mothur trips over whitespace
36 | mothur
37 ]]></command>
38 <inputs>
39 <param name="fasta" type="data" format="mothur.align" label="fasta - Sequences to Bin" help="Sequences must be aligned"/>
40 <param name="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
41 <conditional name="perotu">
42 <param name="use" type="select" label="Consensus sequence">
43 <option value="no" selected="true">Single consensus sequence</option>
44 <option value="yes">Consensus sequence for each OTU in list</option>
45 </param>
46 <when value="yes">
47 <param name="otu" type="data" format="mothur.list" label="list - OTU List"/>
48 <param name="label" type="select" optional="true" multiple="true" label="label - Select OTU Labels" help="By default all labels are used">
49 <expand macro="labeloptions"/>
50 </param>
51 </when>
52 <when value="no"/>
53 </conditional>
54 <param name="cutoff" type="integer" value="" optional="True" min="1" max="100" label="Cutoff - set a percentage of sequences that support the base" help="For example: cutoff=95 would return the base that was supported by at least 95% of sequences. Must be between 1 and 100. Optional"/>
55 <param name="count" type="data" format="mothur.count_table" optional="true" label="Count - a count table" help="this file can be generated by count.seqs"/>
56 </inputs>
57 <outputs>
58 <expand macro="logfile-output"/>
59 <data name="summary" format="tabular" from_work_dir="fasta*.cons.summary" label="${tool.name} on ${on_string}: cons.summary">
60 <filter>perotu['use'] == 'no'</filter>
61 </data>
62 <data name="cons_fasta" format="mothur.align" from_work_dir="fasta*.cons.fasta" label="${tool.name} on ${on_string}: cons.fasta">
63 <filter>perotu['use'] == 'no'</filter>
64 </data>
65 <collection name="consensusfastas" type="list" label="${tool.name} on ${on_string}: consensus fasta files per OTU">
66 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.cons\.fasta" format="mothur.align"/>
67 <filter>perotu['use'] == 'yes'</filter>
68 </collection>
69 <collection name="consensusnames" type="list" label="${tool.name} on ${on_string}: consensus names files per OTU">
70 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.cons\.names" format="mothur.names"/>
71 <filter>perotu['use'] == 'yes'</filter>
72 </collection>
73 <collection name="consensussummaries" type="list" label="${tool.name} on ${on_string}: consensus summary files per OTU">
74 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.cons\.summary" format="tabular"/>
75 <filter>perotu['use'] == 'yes'</filter>
76 </collection>
77 </outputs>
78 <tests>
79 <test><!-- test with default values -->
80 <param name="fasta" value="amazon.align_head" ftype="mothur.align"/>
81 <output name="summary" md5="61a0e170a8b881135421afd0cea8305a" ftype="tabular"/>
82 <output name="cons_fasta" md5="82f3475b61f240eba09597a409364c04" ftype="mothur.align"/>
83 <expand macro="logfile-test"/>
84 </test>
85 <test><!-- test with list file -->
86 <param name="fasta" value="amazon.align_head" ftype="mothur.align"/>
87 <param name="use" value="yes"/>
88 <param name="otu" value="amazon.align_head.list" ftype="mothur.list"/>
89 <param name="count" value="amazon.align_head.count_table" ftype="mothur.count_table"/>
90 <param name="labels" value="unique,0.30,0.33"/>
91 <output_collection name="consensusfastas" count="3">
92 <element name="0.30" md5="a5c8c17814f02124194dba2e37f566c7" ftype="mothur.align"/>
93 </output_collection>
94 <output_collection name="consensusnames" count="3">
95 <element name="0.30" md5="9de4f7e774e0c16eaf7cf6ffbba9d475" ftype="mothur.names"/>
96 </output_collection>
97 <output_collection name="consensussummaries" count="3">
98 <element name="0.30" md5="d595234c6018dfcc1465e59d35d59205" ftype="tabular"/>
99 </output_collection>
100 <expand macro="logfile-test"/>
101 </test>
102 </tests>
103 <help>
104 <![CDATA[
105
106 @MOTHUR_OVERVIEW@
107
108 **Command Documenation**
109
110 The consensus.seqs_ command can be used in 2 ways: create a consensus sequence from a fastafile, or with a listfile create a consensus sequence for each otu. Sequences must be aligned.
111
112 .. _consensus.seqs: http://www.mothur.org/wiki/Consensus.seqs
113 ]]>
114 </help>
115 <expand macro="citations"/>
116 </tool>