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comparison gemini_fusions.xml @ 4:b35fd707c586 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
author iuc
date Fri, 14 Dec 2018 12:46:37 -0500
parents 37f9901b674d
children 6e3d2bd01a96
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3:91d53f89ca54 4:b35fd707c586
1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0"> 1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.1">
2 <description>Identify somatic fusion genes from a GEMINI database</description> 2 <description>Identify somatic fusion genes from a GEMINI database</description>
3 <macros> 3 <macros>
4 <import>gemini_macros.xml</import> 4 <import>gemini_macros.xml</import>
5 <token name="@BINARY@">fusions</token> 5 <token name="@BINARY@">fusions</token>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <expand macro="stdio" /> 8 <expand macro="stdio" />
9 <expand macro="version_command" /> 9 <expand macro="version_command" />
10 <command> 10 <command>
11 <![CDATA[ 11 <![CDATA[
12 @PROVIDE_ANNO_DATA@
12 13
13 gemini 14 gemini
14 #if $annotation_databases:
15 --annotation-dir "${ annotation_databases.fields.path }"
16 #end if
17 @BINARY@ 15 @BINARY@
18 $in_cosmic_census 16 $in_cosmic_census
19 17
20 #if float($min_quality) >= 0: 18 #if float($min_quality) >= 0:
21 --min-qual $min_quality 19 --min-qual $min_quality
51 </outputs> 49 </outputs>
52 <tests> 50 <tests>
53 <test> 51 <test>
54 <!-- Like in set_somatic this example is nonsensical because otherwise 52 <!-- Like in set_somatic this example is nonsensical because otherwise
55 the testdata would be too big. The resulting output should be empty.--> 53 the testdata would be too big. The resulting output should be empty.-->
56 <param name="infile" value="gemini_amend_input.db" ftype="gemini.sqlite" /> 54 <param name="infile" value="gemini_load_result1.db" ftype="gemini.sqlite" />
57 <output name="outfile" file="gemini_fusions_result.tabular" /> 55 <output name="outfile" file="gemini_fusions_result.tabular" />
58 </test> 56 </test>
59 </tests> 57 </tests>
60 <help> 58 <help>
61 <![CDATA[ 59 <![CDATA[