Mercurial > repos > iuc > mothur_split_groups

comparison split.groups.xml @ 0:089c0f0c6c18 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 16:51:01 -0400
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-1:000000000000 0:089c0f0c6c18
1 <tool profile="16.07" id="mothur_split_groups" name="Split.groups" version="@WRAPPER_VERSION@.0">
2 <description>Generates a fasta file for each group</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 "$name" name.dat &&
11 ln -s "$count" count.dat &&
12 ln -s "$fasta" fasta.dat &&
13 ln -s "$group" group.dat &&
14
15 echo 'split.groups(
16 #if $name:
17 name=name.dat,
18 #end if
19 #if $groups:
20 groups=${ str($groups).replace(",","-") },
21 #end if
22 #if $count:
23 count=count.dat,
24 #end if
25 fasta=fasta.dat,
26 group=group.dat
27 )'
28 | sed 's/ //g' ## mothur trips over whitespace
29 | mothur
30 ]]></command>
31 <inputs>
32 <param name="fasta" type="data" format="fasta" label="fasta - Fasta to split by group"/>
33 <param name="name" type="data" format="mothur.names" label="name - Names to split by group" optional="true"/>
34 <param name="group" type="data" format="mothur.groups" label="group - Groups"/>
35 <param name="groups" type="select" optional="true" label="groups - Pick groups to analyze" multiple="true">
36 <options>
37 <filter type="data_meta" ref="group" key="groups"/>
38 </options>
39 </param>
40 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
41 </inputs>
42 <outputs>
43 <expand macro="logfile-output"/>
44 <collection name="groupfastas" type="list" label="${tool.name} on ${on_string}: fasta per group">
45 <!-- TODO: format_source on discovered collection elements doesn't seem to work yet, change to format_source="fasta" once it does -->
46 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.fasta" format="fasta"/>
47 </collection>
48 </outputs>
49 <tests>
50 <test>
51 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
52 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
53 <output_collection name="groupfastas" count="2">
54 <element name="pasture" md5="3844bc02ec09acbbf31845ea6ac6632d" ftype="fasta"/>
55 <element name="forest" md5="f0e662d1d82e96b4977864925493dbf5" ftype="fasta"/>
56 </output_collection>
57 <expand macro="logfile-test"/>
58 </test>
59 </tests>
60 <help>
61 <![CDATA[
62
63 @MOTHUR_OVERVIEW@
64
65 **Command Documenation**
66
67 The split.groups_ command reads a fasta file and group_ file and generates a fasta file for each group in the groupfile. A name_ file can also be split into groups.
68
69 .. _group: http://www.mothur.org/wiki/Group_file
70 .. _name: http://www.mothur.org/wiki/Name_file
71 .. _split.groups: http://www.mothur.org/wiki/Split.groups
72 ]]>
73 </help>
74 <expand macro="citations"/>
75 </tool>