Mercurial > repos > iuc > gemini_set_somatic

comparison gemini_set_somatic.xml @ 5:991049484627 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
author iuc
date Fri, 11 Jan 2019 17:47:44 -0500
parents 7b031989ea12
children 7814e39409d1
comparison
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4:7b031989ea12 5:991049484627
1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.1"> 1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@">
2 <description>Tag somatic mutations in a GEMINI database</description> 2 <description>Tag somatic mutations in a GEMINI database</description>
3 <macros> 3 <macros>
4 <import>gemini_macros.xml</import> 4 <import>gemini_macros.xml</import>
5 <token name="@BINARY@">set_somatic</token> 5 <token name="@BINARY@">set_somatic</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 cp "${ infile }" "${ outfile }" && 12 cp '$infile' '$outfile' &&
13 13
14 gemini @BINARY@ 14 gemini @BINARY@
15 15
16 #if float($min_depth) >= 0: 16 #if float($min_depth) >= 0:
17 --min-depth $min_depth 17 --min-depth $min_depth
48 #if int($min_tumor_depth) >= 0: 48 #if int($min_tumor_depth) >= 0:
49 --min-tumor-depth $min_tumor_depth 49 --min-tumor-depth $min_tumor_depth
50 #end if 50 #end if
51 51
52 #if str($chrom).strip(): 52 #if str($chrom).strip():
53 --chrom "$chrom" 53 --chrom '$chrom'
54 #end if 54 #end if
55 "${ outfile }" 55 '$outfile'
56 ]]> 56 ]]>
57 </command> 57 </command>
58 <inputs> 58 <inputs>
59 59
60 <expand macro="infile" /> 60 <expand macro="infile" />