Mercurial > repos > iuc > mothur_remove_otus

comparison remove.otus.xml @ 0:4b07bc776ccb 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 05:53:16 -0400
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-1:000000000000 0:4b07bc776ccb
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="stdio"/>
8 <expand macro="version_command"/>
9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
12 ## create symlinks to input datasets
13 ln -s "$otu" otu.dat &&
14 ln -s "$group_in" group_in.dat &&
15
16 echo 'remove.otus(
17 list=otu.dat,
18 label=$label,
19 group=group_in.dat
20 #if $groups:
21 ,groups=${ str($groups).replace(",","-") }
22 #end if
23 )'
24 | sed 's/ //g' ## mothur trips over whitespace
25 | mothur
26 | tee mothur.out.log
27 ]]></command>
28 <inputs>
29 <param name="otu" type="data" format="mothur.list" label="list - OTU List"/>
30 <param name="label" type="select" label="label - OTU Labels" help="Select exactly one label">
31 <expand macro="labeloptions"/>
32 </param>
33 <param name="group_in" type="data" format="mothur.groups" label="group - Groups"/>
34 <param name="groups" type="select" label="groups - Pick groups to remove" multiple="true" help="At least one group must be selected">
35 <options>
36 <filter type="data_meta" ref="group_in" key="groups"/>
37 </options>
38 </param>
39 </inputs>
40 <outputs>
41 <expand macro="logfile-output"/>
42 <data name="group_out" format="mothur.groups" from_work_dir="group_in*.pick.dat" label="${tool.name} on ${on_string}: pick.groups"/>
43 <data name="list_out" format="mothur.list" from_work_dir="otu*.pick.dat" label="${tool.name} on ${on_string}: pick.list"/>
44 </outputs>
45 <tests>
46 <test>
47 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
48 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
49 <param name="groups" value="forest"/>
50 <param name="label" value="0.05"/>
51 <output name="list_out" md5="fa5b954ad8e8235dbb700af1a9d8a091" ftype="mothur.list"/>
52 <output name="group_out" md5="3c9f6e88de0f60f2a870c8d4a9d61db8" ftype="mothur.groups"/>
53 <expand macro="logfile-test"/>
54 </test>
55 </tests>
56 <help>
57 <![CDATA[
58
59 @MOTHUR_OVERVIEW@
60
61 **Command Documentation**
62
63 The remove.otus_ command removes otus from a list_ containing sequences from a specific group or set of groups.
64
65 .. _list: https://www.mothur.org/wiki/List_file
66 .. _remove.otus: https://www.mothur.org/wiki/Remove.otus
67
68 ]]>
69 </help>
70 <expand macro="citations"/>
71 </tool>