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comparison split.groups.xml @ 0:dba66f208b1a 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 05:18:43 -0400
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children 5f34cf40f36d
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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="stdio"/>
8 <expand macro="version_command"/>
9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
12 ## create symlinks to input datasets
13 ln -s "$name" name.dat &&
14 ln -s "$count" count.dat &&
15 ln -s "$fasta" fasta.dat &&
16 ln -s "$group" group.dat &&
17
18 echo 'split.groups(
19 #if $name:
20 name=name.dat,
21 #end if
22 #if $groups:
23 groups=${ str($groups).replace(",","-") },
24 #end if
25 #if $count:
26 count=count.dat,
27 #end if
28 fasta=fasta.dat,
29 group=group.dat
30 )'
31 | sed 's/ //g' ## mothur trips over whitespace
32 | mothur
33 | tee mothur.out.log
34 ]]></command>
35 <inputs>
36 <param name="fasta" type="data" format="fasta" label="fasta - Fasta to split by group"/>
37 <param name="name" type="data" format="mothur.names" label="name - Names to split by group" optional="true"/>
38 <param name="group" type="data" format="mothur.groups" label="group - Groups"/>
39 <param name="groups" type="select" optional="true" label="groups - Pick groups to analyze" multiple="true">
40 <options>
41 <filter type="data_meta" ref="group" key="groups"/>
42 </options>
43 </param>
44 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
45 </inputs>
46 <outputs>
47 <expand macro="logfile-output"/>
48 <collection name="groupfastas" type="list" label="${tool.name} on ${on_string}: fasta per group">
49 <!-- TODO: format_source on discovered collection elements doesn't seem to work yet, change to format_source="fasta" once it does -->
50 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.fasta" format="fasta"/>
51 </collection>
52 </outputs>
53 <tests>
54 <test>
55 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
56 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
57 <output_collection name="groupfastas" count="2">
58 <element name="pasture" md5="3844bc02ec09acbbf31845ea6ac6632d" ftype="fasta"/>
59 <element name="forest" md5="f0e662d1d82e96b4977864925493dbf5" ftype="fasta"/>
60 </output_collection>
61 <expand macro="logfile-test"/>
62 </test>
63 </tests>
64 <help>
65 <![CDATA[
66
67 @MOTHUR_OVERVIEW@
68
69 **Command Documentation**
70
71 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.
72
73 .. _group: https://www.mothur.org/wiki/Group_file
74 .. _name: https://www.mothur.org/wiki/Name_file
75 .. _split.groups: https://www.mothur.org/wiki/Split.groups
76 ]]>
77 </help>
78 <expand macro="citations"/>
79 </tool>