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comparison stacks_stats.xml @ 0:072a0329a18e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
author iuc
date Thu, 27 Apr 2017 04:15:02 -0400
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children 7c23b1406c41
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1 <tool id="stacks_stats" name="Stacks: statistics" version="@WRAPPER_VERSION@.0">
2 <description>on stacks found for multiple samples</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
8 <command><![CDATA[
9 mkdir stacks_inputs
10
11 &&
12
13 #for $input_file in $input_col
14 #set $ext = ""
15 #if not str($input_file.element_identifier).endswith('.tsv')
16 #set $ext = ".tsv"
17 #end if
18 ln -s '${input_file}' 'stacks_inputs/${input_file.element_identifier}${ext}' &&
19 #end for
20
21 stacks_summary.py --stacks-prog '$program' --res-dir stacks_inputs --logfile '$logfile' --summary summary.html
22 ]]></command>
23
24 <inputs>
25
26 <param name="program" type="select" argument="--stacks-prog" label="Program which generated the stacks">
27 <option value="ustacks">ustacks (denovo)</option>
28 <option value="pstacks">pstacks (refmap)</option>
29 </param>
30
31 <param name="logfile" argument="--logfile" format="txt" type="data" label="Log generated by the program" />
32
33 <param name="input_col" format="tabular,txt" type="data_collection" collection_type="list" label="Output from ustacks or pstacks" />
34 </inputs>
35
36 <outputs>
37 <data format="html" name="output_summary" label="Summary from ${tool.name} on ${on_string}" from_work_dir="summary.html" />
38 </outputs>
39
40 <tests>
41 <test>
42 <param name="program" value="ustacks"/>
43 <param name="logfile" ftype="txt" value="ustacks/ustacks.out"/>
44 <param name="input_col">
45 <collection type="list">
46 <element name="batch_1.catalog.alleles.tsv" ftype="tabular" value="genotypes/batch_1.catalog.alleles.tsv" />
47 <element name="batch_1.catalog.snps.tsv" ftype="tabular" value="genotypes/batch_1.catalog.snps.tsv" />
48 <element name="batch_1.catalog.tags.tsv" ftype="tabular" value="genotypes/batch_1.catalog.tags.tsv" />
49 <element name="PopA_01.alleles.tsv" ftype="tabular" value="genotypes/PopA_01.alleles.tsv" />
50 <element name="PopA_01.matches.tsv" ftype="tabular" value="genotypes/PopA_01.matches.tsv" />
51 <element name="PopA_01.snps.tsv" ftype="tabular" value="genotypes/PopA_01.snps.tsv" />
52 <element name="PopA_01.tags.tsv" ftype="tabular" value="genotypes/PopA_01.tags.tsv" />
53 <element name="PopA_02.alleles.tsv" ftype="tabular" value="genotypes/PopA_02.alleles.tsv" />
54 <element name="PopA_02.matches.tsv" ftype="tabular" value="genotypes/PopA_02.matches.tsv" />
55 <element name="PopA_02.snps.tsv" ftype="tabular" value="genotypes/PopA_02.snps.tsv" />
56 <element name="PopA_02.tags.tsv" ftype="tabular" value="genotypes/PopA_02.tags.tsv" />
57 </collection>
58 </param>
59
60 <output name="output_summary">
61 <assert_contents>
62 <has_text text="Stacks Statistics" />
63 </assert_contents>
64 </output>
65 </test>
66 </tests>
67
68 <help>
69 <![CDATA[
70 .. class:: infomark
71
72 **What it does**
73
74 When given the output of ustacks or pstacks, this will generate a report containing various statistics about the detected stacks in a set of samples.
75
76 --------
77
78 @STACKS_INFOS@
79 ]]>
80 </help>
81 <expand macro="citation" />
82 </tool>