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comparison varscan_mpileup.xml @ 4:24670f9f6839 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/varscan_version_2 commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
author devteam
date Mon, 09 Nov 2015 12:01:23 -0500
parents 89702e7ec3c3
children 6e4920c4285f
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3:f82940004c84 4:24670f9f6839
3 3
4 <requirements> 4 <requirements>
5 <requirement type="package" version="2.3.6">varscan</requirement> 5 <requirement type="package" version="2.3.6">varscan</requirement>
6 </requirements> 6 </requirements>
7 7
8 <!-- 8 <stdio>
9 The version command string is not yet a template that can be filled in, so version command is not yet possible. 9 <regex match="Exception" source="both" level="fatal" description="Tool exception"/>
10 <version_command>java -jar ${GALAXY_DATA_INDEX_DIR}/shared/jars/varscan/VarScan.jar 2>&amp;1 | head -n 1</version_command> 10 <regex match=".*" source="both" level="log" description="tool progress"/>
11 --> 11 </stdio>
12
13 <version_command>java -jar $JAVA_JAR_PATH/VarScan.v2.3.6.jar 2>&amp;1 | head -n 1</version_command>
12 14
13 <command> 15 <command>
14 ## Set up samples list file. 16 ## Set up samples list file.
15 #if $sample_names.strip() != '': 17 #if $sample_names.strip() != '':
16 echo $sample_names | awk -F ',' '{ for (i = 1; i &lt;= NF; i++) { print \$i; } }' > samples_list.txt; 18 echo $sample_names | awk -F ',' '{ for (i = 1; i &lt;= NF; i++) { print \$i; } }' > samples_list.txt;
17 #end if 19 #end if
18 20
19 ## Set up command + input. 21 ## Set up command + input.
20 java -jar \$JAVA_JAR_PATH/VarScan.v2.3.6.jar ${cmd} ${input} 22 java -jar \$JAVA_JAR_PATH/VarScan.v2.3.6.jar ${cmd} ${input}
21 --min-coverage ${min_coverage} 23 --min-coverage ${min_coverage}
61 <option value="yes">yes</option> 63 <option value="yes">yes</option>
62 </param> 64 </param>
63 <param name="sample_names" type="text" value="" help="Separate sample names by comma; leave blank to use default sample names."/> 65 <param name="sample_names" type="text" value="" help="Separate sample names by comma; leave blank to use default sample names."/>
64 </inputs> 66 </inputs>
65 67
66 <stdio>
67 <regex match="Exception" source="both" level="fatal" description="Tool exception"/>
68 <regex match=".*" source="both" level="log" description="tool progress"/>
69 </stdio>
70
71 <outputs> 68 <outputs>
72 <data name="output" format="vcf"/> 69 <data name="output" format="vcf"/>
73 </outputs> 70 </outputs>
74 71
75 <trackster_conf> 72 <trackster_conf>
94 <help> 91 <help>
95 **VarScan Overview** 92 **VarScan Overview**
96 93
97 VarScan_ performs variant detection for massively parallel sequencing data, such as exome, WGS, and transcriptome data. It calls variants from a mpileup dataset and produces a VCF 4.1 Full documentation is available online_. 94 VarScan_ performs variant detection for massively parallel sequencing data, such as exome, WGS, and transcriptome data. It calls variants from a mpileup dataset and produces a VCF 4.1 Full documentation is available online_.
98 95
99 Please cite: Koboldt, D., Zhang, Q., Larson, D., Shen, D., McLellan, M., Lin, L., Miller, C., Mardis, E., Ding, L., and Wilson, R. (2012). VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing Genome Research DOI: 10.1101/gr.129684.111 96 .. _VarScan: http://dkoboldt.github.io/varscan/
100 97 .. _online: http://dkoboldt.github.io/varscan/using-varscan.html
101 .. _VarScan: http://varscan.sourceforge.net/
102 .. _online: http://varscan.sourceforge.net/using-varscan.html
103 98
104 **Input** 99 **Input**
105 100
106 :: 101 ::
107 102
148 vcf-sample-list 143 vcf-sample-list
149 For VCF output, a list of sample names in order, one per line 144 For VCF output, a list of sample names in order, one per line
150 145
151 variants 146 variants
152 Report only variant (SNP/indel) positions [0] 147 Report only variant (SNP/indel) positions [0]
148 </help>
153 149
154 </help> 150 <citations>
151 <citation type="doi">10.1101/gr.129684.111</citation>
152 </citations>
155 </tool> 153 </tool>