Mercurial > repos > iuc > stacks_stats
comparison stacks_stats.xml @ 0:fe6be53294c9 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
author | iuc |
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date | Thu, 27 Apr 2017 04:18:05 -0400 |
parents | |
children | 93b16407d6e9 |
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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> |