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comparison varscan_mpileup.xml @ 2:bc1e0cd41241 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/varscan_version_2 commit 9a92cb9da7568fd0482be68dbedd5c30c4c931c7
author devteam
date Fri, 03 Feb 2017 08:26:05 -0500
parents 44d514f3df8f
children
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1:44d514f3df8f 2:bc1e0cd41241
1 <tool id="varscan" name="Varscan" version="0.1"> 1 <tool id="varscan" name="VarScan" version="2.4.2">
2 <description>for variant detection</description> 2 <description>for variant detection</description>
3 3
4 <requirements> 4 <requirements>
5 <requirement type="package" version="2.3.6">varscan</requirement> 5 <requirement type="package" version="2.4.2">varscan</requirement>
6 </requirements> 6 </requirements>
7 7
8 <stdio> 8 <stdio>
9 <regex match="Exception" source="both" level="fatal" description="Tool exception"/> 9 <regex match="Exception" source="both" level="fatal" description="Tool exception"/>
10 <regex match=".*" source="both" level="log" description="tool progress"/> 10 <regex match=".*" source="both" level="log" description="tool progress"/>
11 </stdio> 11 </stdio>
12 12
13 <version_command>java -jar $JAVA_JAR_PATH/VarScan.v2.3.6.jar 2>&amp;1 | head -n 1</version_command> 13 <version_command><![CDATA[
14 varscan 2>&1 | head -n 1
15 ]]></version_command>
14 16
15 <command> 17 <command><![CDATA[
16 ## Set up samples list file. 18 ## Set up samples list file.
17 #if $sample_names.strip() != '': 19 #if $sample_names.strip() != '':
18 echo $sample_names | awk -F ',' '{ for (i = 1; i &lt;= NF; i++) { print \$i; } }' > samples_list.txt; 20 echo $sample_names | awk -F ',' '{ for (i = 1; i <= NF; i++) { print \$i; } }' > samples_list.txt &&
19 #end if 21 #end if
20 22
21 ## Set up command + input. 23 ## Set up command + input.
22 java -jar \$JAVA_JAR_PATH/VarScan.v2.3.6.jar ${cmd} ${input} 24 varscan ${cmd} ${input}
23 --min-coverage ${min_coverage} 25 --min-coverage ${min_coverage}
24 --min-reads2 ${min_supporting_reads} 26 --min-reads2 ${min_supporting_reads}
25 --min-avg-qual ${min_avg_qual} 27 --min-avg-qual ${min_avg_qual}
26 --min-var-freq ${min_var_freq} 28 --min-var-freq ${min_var_freq}
27 --min-freq-for-hom ${min_freq_for_hom} 29 --min-freq-for-hom ${min_freq_for_hom}
39 --output-vcf 1 > $output 41 --output-vcf 1 > $output
40 42
41 #if $sample_names.strip() != '': 43 #if $sample_names.strip() != '':
42 --vcf-sample-list samples_list.txt 44 --vcf-sample-list samples_list.txt
43 #end if 45 #end if
44 </command> 46 ]]></command>
45 47
46 <inputs> 48 <inputs>
47 <param format="pileup" name="input" type="data" label="Pileup dataset" help=""/> 49 <param format="pileup" name="input" type="data" label="Pileup dataset" help=""/>
48 50
49 <param name="cmd" type="select" label="Analysis type"> 51 <param name="cmd" type="select" label="Analysis type">
66 </inputs> 68 </inputs>
67 69
68 <outputs> 70 <outputs>
69 <data name="output" format="vcf"/> 71 <data name="output" format="vcf"/>
70 </outputs> 72 </outputs>
71
72 <trackster_conf>
73 </trackster_conf>
74
75 <tests> 73 <tests>
76 <test> 74 <test>
77 <param name="input" value="test_in1.pileup" /> 75 <param name="input" value="test_in1.pileup" />
78 <param name="cmd" value="mpileup2cns" /> 76 <param name="cmd" value="mpileup2cns" />
79 <param name="min_coverage" value="8" /> 77 <param name="min_coverage" value="8" />