Mercurial > repos > iuc > mothur_remove_otus

comparison remove.otus.xml @ 0:8cef8feb87a7 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 16:47:47 -0400
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-1:000000000000 0:8cef8feb87a7
1 <tool profile="16.07" id="mothur_remove_otus" name="Remove.otus" version="@WRAPPER_VERSION@.0">
2 <description>Remove otus containing sequences from specified groups</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 "$otu" otu.dat &&
11 ln -s "$group_in" group_in.dat &&
12
13 echo 'remove.otus(
14 list=otu.dat,
15 label=$label,
16 group=group_in.dat
17 #if $groups:
18 ,groups=${ str($groups).replace(",","-") }
19 #end if
20 )'
21 | sed 's/ //g' ## mothur trips over whitespace
22 | mothur
23 ]]></command>
24 <inputs>
25 <param name="otu" type="data" format="mothur.list" label="list - OTU List"/>
26 <param name="label" type="select" label="label - OTU Labels" help="Select exactly one label">
27 <expand macro="labeloptions"/>
28 </param>
29 <param name="group_in" type="data" format="mothur.groups" label="group - Groups"/>
30 <param name="groups" type="select" label="groups - Pick groups to remove" multiple="true" help="At least one group must be selected">
31 <options>
32 <filter type="data_meta" ref="group_in" key="groups"/>
33 </options>
34 </param>
35 </inputs>
36 <outputs>
37 <expand macro="logfile-output"/>
38 <data name="group_out" format="mothur.groups" from_work_dir="group_in*.pick.dat" label="${tool.name} on ${on_string}: pick.groups"/>
39 <data name="list_out" format="mothur.list" from_work_dir="otu*.pick.dat" label="${tool.name} on ${on_string}: pick.list"/>
40 </outputs>
41 <tests>
42 <test>
43 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
44 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
45 <param name="groups" value="forest"/>
46 <param name="label" value="0.05"/>
47 <output name="list_out" md5="fa5b954ad8e8235dbb700af1a9d8a091" ftype="mothur.list"/>
48 <output name="group_out" md5="3c9f6e88de0f60f2a870c8d4a9d61db8" ftype="mothur.groups"/>
49 <expand macro="logfile-test"/>
50 </test>
51 </tests>
52 <help>
53 <![CDATA[
54
55 @MOTHUR_OVERVIEW@
56
57 **Command Documenation**
58
59 The remove.otus_ command removes otus from a list_ containing sequences from a specific group or set of groups.
60
61 .. _list: http://www.mothur.org/wiki/List_file
62 .. _remove.otus: http://www.mothur.org/wiki/Remove.otus
63
64 ]]>
65 </help>
66 <expand macro="citations"/>
67 </tool>