Mercurial > repos > iuc > mothur_parse_list

comparison parse.list.xml @ 2:65ce515b9645 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author iuc
date Tue, 20 Mar 2018 22:25:29 -0400
parents 14062c54b6f6
children b52a0ca5e21c
comparison
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1:b1e417780bee 2:65ce515b9645
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
8 <expand macro="version_command"/> 8 <expand macro="version_command"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10 @SHELL_OPTIONS@ 10 @SHELL_OPTIONS@
11 11
12 ## create symlinks to input datasets 12 ## create symlinks to input datasets
13 ln -s "$otu" otu.dat && 13 ln -s '$otu' otu.dat &&
14 ln -s "$group" group.dat && 14 ln -s '$group' group.dat &&
15 ln -s "$count" count.dat && 15 ln -s '$count' count.dat &&
16 16
17 echo 'parse.list( 17 echo 'parse.list(
18 list=otu.dat, 18 list=otu.dat,
19 #if $label: 19 #if $label:
20 label=${ str($label).replace(",","-") }, 20 label=${ str($label).replace(",","-") },
21 #end if 21 #end if
22 #if $count: 22 #if $count:
23 count=count.dat, 23 count=count.dat,
24 #end if 24 #end if
25 group=group.dat 25 group=group.dat
26 )' 26 )'
27 | sed 's/ //g' ## mothur trips over whitespace 27 | sed 's/ //g' ## mothur trips over whitespace
28 | mothur 28 | mothur
29 | tee mothur.out.log 29 | tee mothur.out.log
30 ]]></command> 30 ]]></command>
31 <inputs> 31 <inputs>
32 <param name="otu" type="data" format="mothur.list" label="list - OTU List"/> 32 <param name="otu" type="data" format="mothur.list" label="list - OTU List"/>
33 <param name="group" type="data" format="mothur.groups" label="group - Sequences Name reference"/> 33 <param name="group" type="data" format="mothur.groups" label="group - Sequences Name reference"/>
34 <param name="label" type="select" optional="true" multiple="true" label="label - To filter: Select OTU Labels to include"> 34 <param name="label" type="select" optional="true" multiple="true" label="label - To filter: Select OTU Labels to include">
35 <expand macro="labeloptions"/> 35 <expand macro="labeloptions"/>
36 </param> 36 </param>
37 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> 37 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
38 <expand macro="param-savelog"/>
38 </inputs> 39 </inputs>
39 <outputs> 40 <outputs>
40 <expand macro="logfile-output"/> 41 <expand macro="logfile-output"/>
41 <collection name="listfiles" type="list" label="${tool.name} on ${on_string}: listfiles per group and label"> 42 <collection name="listfiles" type="list" label="${tool.name} on ${on_string}: listfiles per group and label">
42 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.list" format="mothur.list"/> 43 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.list" format="mothur.list"/>
47 <param name="otu" value="amazon.an.list"/> 48 <param name="otu" value="amazon.an.list"/>
48 <param name="group" value="amazon.groups"/> 49 <param name="group" value="amazon.groups"/>
49 <output_collection name="listfiles" count="72"> 50 <output_collection name="listfiles" count="72">
50 <element name="pasture.0.21" md5="5c803fd0f0e1de69c51048e02bc02e65" ftype="mothur.list"/> 51 <element name="pasture.0.21" md5="5c803fd0f0e1de69c51048e02bc02e65" ftype="mothur.list"/>
51 </output_collection> 52 </output_collection>
53 <param name="savelog" value="true"/>
52 <expand macro="logfile-test"/> 54 <expand macro="logfile-test"/>
53 </test> 55 </test>
54 <test> 56 <test>
55 <param name="otu" value="amazon.an.list"/> 57 <param name="otu" value="amazon.an.list"/>
56 <param name="group" value="amazon.groups" ftype="mothur.groups"/> 58 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
57 <param name="label" value="0.03,0.05"/> 59 <param name="label" value="0.03,0.05"/>
58 <output_collection name="listfiles" count="4"/> 60 <output_collection name="listfiles" count="4"/>
61 <param name="savelog" value="true"/>
59 <expand macro="logfile-test"/> 62 <expand macro="logfile-test"/>
60 </test> 63 </test>
61 </tests> 64 </tests>
62 <help> 65 <help><![CDATA[
63 <![CDATA[
64 66
65 @MOTHUR_OVERVIEW@ 67 @MOTHUR_OVERVIEW@
66 68
67 **Command Documentation** 69 **Command Documentation**
68 70
71 .. _list: https://www.mothur.org/wiki/List_file 73 .. _list: https://www.mothur.org/wiki/List_file
72 .. _group: https://www.mothur.org/wiki/Group_file 74 .. _group: https://www.mothur.org/wiki/Group_file
73 .. _parse.list: https://www.mothur.org/wiki/Parse.list 75 .. _parse.list: https://www.mothur.org/wiki/Parse.list
74 76
75 v.1.19.0: Updated to mothur 1.33, added count parameter 77 v.1.19.0: Updated to mothur 1.33, added count parameter
76 ]]> 78
77 </help> 79 ]]></help>
78 <expand macro="citations"/> 80 <expand macro="citations"/>
79 </tool> 81 </tool>