Mercurial > repos > iuc > mothur_bin_seqs

comparison bin.seqs.xml @ 0:c9045fb0bf49 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 17:31:47 -0400
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1 <tool profile="16.07" id="mothur_bin_seqs" name="Bin.seqs" version="@WRAPPER_VERSION@.0">
2 <description>Order Sequences by OTU</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 "$name" name.dat &&
11 ln -s "$group" group.dat &&
12 ln -s "$fasta" fasta.dat &&
13 ln -s "$otu" otu.dat &&
14 ln -s "$count" count.dat &&
15
16 echo 'bin.seqs(
17 #if $name:
18 name=name.dat,
19 #end if
20 #if $group:
21 group=group.dat,
22 #end if
23 #if $label:
24 label=${ str($label).replace(",","-") },
25 #end if
26 #if $count:
27 count=count.dat,
28 #end if
29 fasta=fasta.dat,
30 list=otu.dat
31 )'
32 | sed 's/ //g' ## mothur trips over whitespace
33 | mothur
34 ]]></command>
35 <inputs>
36 <param name="fasta" type="data" format="fasta" label="fasta - Sequences to Bin"/>
37 <param name="otu" type="data" format="mothur.list" label="list - OTU List"/>
38 <param name="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
39 <param name="label" type="select" label="label - OTU Labels" multiple="true">
40 <expand macro="labeloptions"/>
41 </param>
42 <param name="group" type="data" format="group" optional="true" label="group - Sequences Name reference"/>
43 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - Represents the number of duplicate sequences for a given representitive sequence"/>
44 </inputs>
45 <outputs>
46 <expand macro="logfile-output"/>
47 <collection name="fastafiles" type="list" label="${tool.name} on ${on_string}: fastafiles per label">
48 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.fasta" format="fasta"/>
49 </collection>
50 </outputs>
51 <tests>
52 <test><!-- test with defaults -->
53 <param name="otu" value="amazon.an.list"/>
54 <param name="fasta" value="amazon.fasta"/>
55 <output_collection name="fastafiles" count="36">
56 <element name="0.22" md5="8fd8dd141561dc3e574e0c3f356e7e84" ftype="fasta"/>
57 </output_collection>
58 <expand macro="logfile-test"/>
59 </test>
60 <test><!-- test with group and name file and label select -->
61 <param name="otu" value="amazon.an.list"/>
62 <param name="fasta" value="amazon.fasta"/>
63 <param name="name" value="amazon.names"/>
64 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
65 <param name="label" value="0.03,0.05,0.22"/>
66 <output_collection name="fastafiles" count="3">
67 <element name="0.22" md5="02755d06b535fdcdb5a70b6eb767d1f6" ftype="fasta"/>
68 </output_collection>
69 <expand macro="logfile-test"/>
70 </test>
71 </tests>
72 <help>
73 <![CDATA[
74
75 @MOTHUR_OVERVIEW@
76
77 **Command Documenation**
78
79 The bin.seqs_ command generates fasta-formatted files where sequences are ordered according to the OTU from the list_file_ that they belong to. Such an output may be helpful for generating primers specific to an OTU or for classification of sequences.
80
81 .. _list_file: http://www.mothur.org/wiki/List_file
82 .. _bin.seqs: http://www.mothur.org/wiki/Bin.seqs
83 ]]>
84 </help>
85 <expand macro="citations"/>
86 </tool>