Mercurial > repos > iuc > mothur_parse_list

comparison parse.list.xml @ 0:14062c54b6f6 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 05:46:37 -0400
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children 65ce515b9645
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-1:000000000000 0:14062c54b6f6
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="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" group.dat &&
15 ln -s "$count" count.dat &&
16
17 echo 'parse.list(
18 list=otu.dat,
19 #if $label:
20 label=${ str($label).replace(",","-") },
21 #end if
22 #if $count:
23 count=count.dat,
24 #end if
25 group=group.dat
26 )'
27 | sed 's/ //g' ## mothur trips over whitespace
28 | mothur
29 | tee mothur.out.log
30 ]]></command>
31 <inputs>
32 <param name="otu" type="data" format="mothur.list" label="list - OTU List"/>
33 <param name="group" type="data" format="mothur.groups" label="group - Sequences Name reference"/>
34 <param name="label" type="select" optional="true" multiple="true" label="label - To filter: Select OTU Labels to include">
35 <expand macro="labeloptions"/>
36 </param>
37 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
38 </inputs>
39 <outputs>
40 <expand macro="logfile-output"/>
41 <collection name="listfiles" type="list" label="${tool.name} on ${on_string}: listfiles per group and label">
42 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.list" format="mothur.list"/>
43 </collection>
44 </outputs>
45 <tests>
46 <test>
47 <param name="otu" value="amazon.an.list"/>
48 <param name="group" value="amazon.groups"/>
49 <output_collection name="listfiles" count="72">
50 <element name="pasture.0.21" md5="5c803fd0f0e1de69c51048e02bc02e65" ftype="mothur.list"/>
51 </output_collection>
52 <expand macro="logfile-test"/>
53 </test>
54 <test>
55 <param name="otu" value="amazon.an.list"/>
56 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
57 <param name="label" value="0.03,0.05"/>
58 <output_collection name="listfiles" count="4"/>
59 <expand macro="logfile-test"/>
60 </test>
61 </tests>
62 <help>
63 <![CDATA[
64
65 @MOTHUR_OVERVIEW@
66
67 **Command Documentation**
68
69 The parse.list_ command reads a list_ file and group_ file and generates a list_ file for each group_ in the groupfile.
70
71 .. _list: https://www.mothur.org/wiki/List_file
72 .. _group: https://www.mothur.org/wiki/Group_file
73 .. _parse.list: https://www.mothur.org/wiki/Parse.list
74
75 v.1.19.0: Updated to mothur 1.33, added count parameter
76 ]]>
77 </help>
78 <expand macro="citations"/>
79 </tool>