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comparison mmvc.xml @ 0:c5c1faa433e4 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit b'f226ae444ad694bb8d4f8faa80ed541b41cbc993\n'
author rdvelazquez
date Fri, 15 Mar 2019 13:29:34 -0400
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children 12e4a2e84931
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-1:000000000000 0:c5c1faa433e4
1 <?xml version="1.0"?>
2 <tool id="Test_mmvc" version="1.0.2" name="mmvc">
3 <description>Multinomial mixture variant caller</description>
4 <requirements>
5 <requirement type="package" version="1.0.2">mmvc</requirement>
6 </requirements>
7 <stdio>
8 <exit_code range="1:"/>
9 </stdio>
10 <version_command/>
11 <command><![CDATA[
12 mmvc -j '$json_report' -f '$filter_msa'
13 #if str($options.advanced) == 'advanced':
14 -g $options.grid_density -c $options.chain_length -b $options.burnin_fraction -t $options.target_rate -p $options.posterior_threshold
15 #end if
16 '$input_fasta' &&
17 $__tool_directory__/extract_mmvc_consensus '$json_report' '$input_fasta.display_name' '$consensus_fasta'
18 ]]></command>
19 <inputs>
20 <param name="input_fasta" label="Input FASTA" type="data" format="fasta"/>
21 <conditional name="options">
22 <param label="Additional options" name="advanced" type="select">
23 <option value="defaults">Use defaults</option>
24 <option value="advanced">Specify additional
25 parameters</option>
26 </param>
27 <when value="defaults"/>
28 <when value="advanced">
29 <param label="GRID_DENSITY" name="grid_density" type="integer" value="10"/>
30 <param label="CHAIN_LENGTH" name="chain_length" type="integer" value="2000000"/>
31 <param label="BURNIN_FRACTION" name="burnin_fraction" type="float" value="0.5"/>
32 <param label="TARGET_RATE" name="target_rate" type="float" value="0.01"/>
33 <param label="POSTERIOR_THRESHOLD" name="posterior_threshold" type="float" value="0.95"/>
34 </when>
35 </conditional>
36 </inputs>
37 <outputs>
38 <data format="json" name="json_report"/>
39 <data format="fasta" name="filter_msa"/>
40 <data format="fasta" name="consensus_fasta"/>
41 </outputs>
42 <tests>
43 <test>
44 <param name="input_fasta" value="mmvc-in1.fa"/>
45 <param name="advanced" value="advanced"/>
46 <param name="chain_length" value="200"/>
47 <output name="json_report">
48 <assert_contents>
49 <has_text text="variant"/>
50 <has_text text="weight"/>
51 </assert_contents>
52 </output>
53 </test>
54 </tests>
55 <help><![CDATA[
56 MMVC
57 ----
58 Multinomial mixture variant caller
59 ]]></help>
60 <citations>
61 <citation type="bibtex">@UNPUBLISHED{spond, author = "Sergei
62 Kosakovsky Pond", title = "HyPhy: Hypothesis Testing using
63 Phylogenies", year = "2000", note = "http://hyphy.org/", url =
64 "http://hyphy.org/"}</citation>
65 </citations>
66 </tool>