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comparison snpSift_int.xml @ 3:20c7d583fec1 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
author iuc
date Mon, 12 Jun 2017 10:25:32 -0400
parents bf8c1526871b
children 09d6806c609e
comparison
equal deleted inserted replaced
2:bf8c1526871b 3:20c7d583fec1
1 <tool id="snpSift_int" name="SnpSift Intervals" version="@WRAPPER_VERSION@.1"> 1 <tool id="snpSift_int" name="SnpSift Intervals" version="@WRAPPER_VERSION@.0">
2 <description>Filter variants using intervals</description> 2 <description>Filter variants using intervals</description>
3 <!-- 3 <!--
4 You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) 4 You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
5 --> 5 -->
6 <macros> 6 <macros>
7 <import>snpSift_macros.xml</import> 7 <import>snpSift_macros.xml</import>
8 </macros> 8 </macros>
9 <expand macro="requirements" /> 9 <expand macro="requirements" />
10 <expand macro="stdio" /> 10 <expand macro="stdio" />
11 <expand macro="version_command" /> 11 <expand macro="version_command" />
12 <command><![CDATA[ 12 <command><![CDATA[
13 @CONDA_SNPSIFT_JAR_PATH@ && 13 SnpSift -Xmx2G intervals
14 java -Xmx2G -jar "\$SNPSIFT_JAR_PATH/SnpSift.jar" intervals -i "$input" $exclude "$bedFile" > "$output" 14 -i '$input'
15 ]]> 15 $exclude
16 </command> 16 '$bedFile'
17 > '$output'
18 ]]></command>
17 <inputs> 19 <inputs>
18 <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/> 20 <param name="input" type="data" format="vcf" label="Variant input file in VCF format"/>
19 <param format="bed" name="bedFile" type="data" label="Intervals (BED file)"/> 21 <param name="bedFile" type="data" format="bed" label="Intervals (BED file)"/>
20 <param name="exclude" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Exclude Intervals" 22 <param name="exclude" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Exclude Intervals"
21 help="Filter out (exclude) VCF entries that match any interval in the BED files"/> 23 help="Filter out (exclude) VCF entries that match any interval in the BED files"/>
22 </inputs> 24 </inputs>
23 <outputs> 25 <outputs>
24 <data format="vcf" name="output" /> 26 <data name="output" format="vcf" />
25 </outputs> 27 </outputs>
26 <tests> 28 <tests>
27 <test> 29 <test>
28 <param name="input" ftype="vcf" value="annotate_5.vcf"/> 30 <param name="input" ftype="vcf" value="annotate_5.vcf"/>
29 <param name="bedFile" ftype="bed" value="interval.bed"/> 31 <param name="bedFile" ftype="bed" value="interval.bed"/>
46 </assert_contents> 48 </assert_contents>
47 </output> 49 </output>
48 </test> 50 </test>
49 </tests> 51 </tests>
50 <help><![CDATA[ 52 <help><![CDATA[
51
52 You can filter using intervals (BED file). 53 You can filter using intervals (BED file).
53 54
54 @EXTERNAL_DOCUMENTATION@ 55 @EXTERNAL_DOCUMENTATION@
55 http://snpeff.sourceforge.net/SnpSift.html#intervals 56 - http://snpeff.sourceforge.net/SnpSift.html#intervals
56 57 ]]></help>
57 ]]>
58 </help>
59 <expand macro="citations" /> 58 <expand macro="citations" />
60 </tool> 59 </tool>