Mercurial > repos > iuc > mothur_consensus_seqs

comparison consensus.seqs.xml @ 0:82a5c9700e76 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 05:41:07 -0400
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children 4f4de4518aca
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-1:000000000000 0:82a5c9700e76
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="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 "$count" count.dat &&
16 #if $perotu.use == "yes":
17 ln -s "$perotu.otu" perotu.otu.dat &&
18 #end if
19
20 echo 'consensus.seqs(
21 fasta=fasta.dat
22 #if $name:
23 ,name=name.dat
24 #end if
25 #if $cutoff:
26 ,cutoff=$cutoff
27 #end if
28 #if $perotu.use == "yes":
29 ,list=perotu.otu.dat
30 #if $perotu.label:
31 ,label=${ str($perotu.label).replace(",","-") }
32 #end if
33 #end if
34 #if $count:
35 ,count=count.dat
36 #end if
37 )'
38 | sed 's/ //g' ## mothur trips over whitespace
39 | mothur
40 | tee mothur.out.log
41 ]]></command>
42 <inputs>
43 <param name="fasta" type="data" format="mothur.align" label="fasta - Sequences to Bin" help="Sequences must be aligned"/>
44 <param name="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
45 <conditional name="perotu">
46 <param name="use" type="select" label="Consensus sequence">
47 <option value="no" selected="true">Single consensus sequence</option>
48 <option value="yes">Consensus sequence for each OTU in list</option>
49 </param>
50 <when value="yes">
51 <param name="otu" type="data" format="mothur.list" label="list - OTU List"/>
52 <param name="label" type="select" optional="true" multiple="true" label="label - Select OTU Labels" help="By default all labels are used">
53 <expand macro="labeloptions"/>
54 </param>
55 </when>
56 <when value="no"/>
57 </conditional>
58 <param name="cutoff" type="integer" value="" optional="True" min="1" max="100" label="Cutoff - set a percentage of sequences that support the base" help="For example: cutoff=95 would return the base that was supported by at least 95% of sequences. Must be between 1 and 100. Optional"/>
59 <param name="count" type="data" format="mothur.count_table" optional="true" label="Count - a count table" help="this file can be generated by count.seqs"/>
60 </inputs>
61 <outputs>
62 <expand macro="logfile-output"/>
63 <data name="summary" format="tabular" from_work_dir="fasta*.cons.summary" label="${tool.name} on ${on_string}: cons.summary">
64 <filter>perotu['use'] == 'no'</filter>
65 </data>
66 <data name="cons_fasta" format="mothur.align" from_work_dir="fasta*.cons.fasta" label="${tool.name} on ${on_string}: cons.fasta">
67 <filter>perotu['use'] == 'no'</filter>
68 </data>
69 <collection name="consensusfastas" type="list" label="${tool.name} on ${on_string}: consensus fasta files per OTU">
70 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.cons\.fasta" format="mothur.align"/>
71 <filter>perotu['use'] == 'yes'</filter>
72 </collection>
73 <collection name="consensusnames" type="list" label="${tool.name} on ${on_string}: consensus names files per OTU">
74 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.cons\.names" format="mothur.names"/>
75 <filter>perotu['use'] == 'yes'</filter>
76 </collection>
77 <collection name="consensussummaries" type="list" label="${tool.name} on ${on_string}: consensus summary files per OTU">
78 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.cons\.summary" format="tabular"/>
79 <filter>perotu['use'] == 'yes'</filter>
80 </collection>
81 </outputs>
82 <tests>
83 <test><!-- test with default values -->
84 <param name="fasta" value="amazon.align_head" ftype="mothur.align"/>
85 <output name="summary" md5="61a0e170a8b881135421afd0cea8305a" ftype="tabular"/>
86 <output name="cons_fasta" md5="82f3475b61f240eba09597a409364c04" ftype="mothur.align"/>
87 <expand macro="logfile-test"/>
88 </test>
89 <test><!-- test with list file -->
90 <param name="fasta" value="amazon.align_head" ftype="mothur.align"/>
91 <param name="use" value="yes"/>
92 <param name="otu" value="amazon.align_head.list" ftype="mothur.list"/>
93 <param name="count" value="amazon.align_head.count_table" ftype="mothur.count_table"/>
94 <param name="labels" value="unique,0.30,0.33"/>
95 <output_collection name="consensusfastas" count="3">
96 <element name="0.30" md5="a5c8c17814f02124194dba2e37f566c7" ftype="mothur.align"/>
97 </output_collection>
98 <output_collection name="consensusnames" count="3">
99 <element name="0.30" md5="9de4f7e774e0c16eaf7cf6ffbba9d475" ftype="mothur.names"/>
100 </output_collection>
101 <output_collection name="consensussummaries" count="3">
102 <element name="0.30" md5="d595234c6018dfcc1465e59d35d59205" ftype="tabular"/>
103 </output_collection>
104 <expand macro="logfile-test"/>
105 </test>
106 </tests>
107 <help>
108 <![CDATA[
109
110 @MOTHUR_OVERVIEW@
111
112 **Command Documentation**
113
114 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.
115
116 .. _consensus.seqs: https://www.mothur.org/wiki/Consensus.seqs
117 ]]>
118 </help>
119 <expand macro="citations"/>
120 </tool>