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comparison gemini_fusions.xml @ 0:c974176a17cc draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
author iuc
date Tue, 16 Feb 2016 05:52:33 -0500
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-1:000000000000 0:c974176a17cc
1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
2 <description>Identify somatic fusion genes from a GEMINI database</description>
3 <macros>
4 <import>gemini_macros.xml</import>
5 <token name="@BINARY@">fusions</token>
6 </macros>
7 <expand macro="requirements" />
8 <expand macro="stdio" />
9 <expand macro="version_command" />
10 <command>
11 <![CDATA[
12
13 gemini @BINARY@
14
15 #if $annotation_databases:
16 --annotation-dir "${ annotation_databases.fields.path }"
17 #end if
18
19 $in_cosmic_census
20
21 #if float($min_quality) >= 0:
22 --min-qual $min_quality
23 #end if
24
25 #if str($evidence_type):
26 --evidence_type $evidence_type
27 #end if
28
29 "${ infile }" | tr -s ' ' '\t'
30 > "${ outfile }"
31 ]]>
32 </command>
33 <inputs>
34
35 <expand macro="infile" />
36 <expand macro="annotation_dir" />
37
38 <param argument="--in_cosmic_census" type="boolean" truevalue="--in_cosmic_census" falsevalue="" checked="False" label="One or both genes in fusion is in COSMIC cancer census" />
39
40 <param name="min_quality" type="float" value="-1" label="The min variant quality (VCF QUAL)" help="default: -1 (not set) (--min_qual)"/>
41
42 <param argument="--evidence_type" type="select" label="The supporting evidence types for the variant" >
43 <option value="" selected="True">select one (optional)</option>
44 <option value="PE">PE</option>
45 <option value="SR">SR</option>
46 <option value="PE,SR">PE,SR</option>
47 </param>
48
49 </inputs>
50 <outputs>
51 <data name="outfile" format="tabular" />
52 </outputs>
53 <tests>
54 <test>
55 <!-- Like in set_somatic this example is nonsensical because otherwise
56 the testdata would be too big. The resulting output should be empty.-->
57 <param name="infile" value="gemini_amend_input.db" ftype="gemini.sqlite" />
58 <output name="outfile" file="gemini_fusions_result.tabular" />
59 </test>
60 </tests>
61 <help>
62 <![CDATA[
63 **What it does**
64
65 Identifies somatic fusion genes from a GEMINI database.
66 ]]>
67 </help>
68 <expand macro="citations"/>
69 </tool>