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comparison parse.list.xml @ 0:0817dd05dbaf 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 16:43:48 -0400
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1 <tool profile="16.07" id="mothur_parse_list" name="Parse.list" version="@WRAPPER_VERSION@.0">
2 <description>Generate a List 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 "$otu" otu.dat &&
11 ln -s "$group" group.dat &&
12 ln -s "$count" count.dat &&
13
14 echo 'parse.list(
15 list=otu.dat,
16 #if $label:
17 label=${ str($label).replace(",","-") },
18 #end if
19 #if $count:
20 count=count.dat,
21 #end if
22 group=group.dat
23 )'
24 | sed 's/ //g' ## mothur trips over whitespace
25 | mothur
26 ]]></command>
27 <inputs>
28 <param name="otu" type="data" format="mothur.list" label="list - OTU List"/>
29 <param name="group" type="data" format="mothur.groups" label="group - Sequences Name reference"/>
30 <param name="label" type="select" optional="true" multiple="true" label="label - To filter: Select OTU Labels to include">
31 <expand macro="labeloptions"/>
32 </param>
33 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
34 </inputs>
35 <outputs>
36 <expand macro="logfile-output"/>
37 <collection name="listfiles" type="list" label="${tool.name} on ${on_string}: listfiles per group and label">
38 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.list" format="mothur.list"/>
39 </collection>
40 </outputs>
41 <tests>
42 <test>
43 <param name="otu" value="amazon.an.list"/>
44 <param name="group" value="amazon.groups"/>
45 <output_collection name="listfiles" count="72">
46 <element name="pasture.0.21" md5="5c803fd0f0e1de69c51048e02bc02e65" ftype="mothur.list"/>
47 </output_collection>
48 <expand macro="logfile-test"/>
49 </test>
50 <test>
51 <param name="otu" value="amazon.an.list"/>
52 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
53 <param name="label" value="0.03,0.05"/>
54 <output_collection name="listfiles" count="4"/>
55 <expand macro="logfile-test"/>
56 </test>
57 </tests>
58 <help>
59 <![CDATA[
60
61 @MOTHUR_OVERVIEW@
62
63 **Command Documenation**
64
65 The parse.list_ command reads a list_ file and group_ file and generates a list_ file for each group_ in the groupfile.
66
67 .. _list: http://www.mothur.org/wiki/List_file
68 .. _group: http://www.mothur.org/wiki/Group_file
69 .. _parse.list: http://www.mothur.org/wiki/Parse.list
70
71 v.1.19.0: Updated to mothur 1.33, added count parameter
72 ]]>
73 </help>
74 <expand macro="citations"/>
75 </tool>