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comparison snpSift_filter.xml @ 8:2f40467536cf draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 93465571cf180554c3548338a68fa0f1604985dc-dirty
author jjohnson
date Sat, 09 Apr 2016 11:53:30 -0400
parents c29f29a6f26c
children 88f4997ccb02
comparison
equal deleted inserted replaced
7:c29f29a6f26c 8:2f40467536cf
1 <tool id="snpSift_filter" name="SnpSift Filter" version="@WRAPPER_VERSION@.0"> 1 <tool id="snpSift_filter" name="SnpSift Filter" version="@WRAPPER_VERSION@.0">
2 <options sanitize="False" />
3 <description>Filter variants using arbitrary expressions</description> 2 <description>Filter variants using arbitrary expressions</description>
4 <macros> 3 <macros>
5 <import>snpSift_macros.xml</import> 4 <import>snpSift_macros.xml</import>
6 </macros> 5 </macros>
7 <expand macro="requirements" /> 6 <expand macro="requirements" />
8 <expand macro="stdio" /> 7 <expand macro="stdio" />
9 <expand macro="version_command" /> 8 <expand macro="version_command" />
9
10 <command><![CDATA[ 10 <command><![CDATA[
11 java -Xmx6G -jar \$SNPEFF_JAR_PATH/SnpSift.jar filter -f $input -e $exprFile $inverse 11 java -Xmx6G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" filter -f "$input" -e "$exprFile" $inverse
12 #if $filtering.mode == 'field': 12 #if $filtering.mode == 'field':
13 #if $filtering.replace.pass: 13 #if $filtering.replace.pass:
14 --pass 14 --pass
15 #if $filtering.replace.filterId and len($filtering.replace.filterId.__str__.strip()) > 0: 15 #if $filtering.replace.filterId and len(str($filtering.replace.filterId).strip()) > 0:
16 --filterId "$filtering.replace.filterId" 16 --filterId "$filtering.replace.filterId"
17 #end if 17 #end if
18 #end if 18 #end if
19 #if $filtering.addFilter and len($filtering.addFilter.__str__.strip()) > 0: 19 #if $filtering.addFilter and len(str($filtering.addFilter).strip()) > 0:
20 --addFilter "$filtering.addFilter" 20 --addFilter "$filtering.addFilter"
21 #end if 21 #end if
22 #if $filtering.rmFilter and len($filtering.rmFilter.__str__.strip()) > 0: 22 #if $filtering.rmFilter and len(str($filtering.rmFilter).strip()) > 0:
23 --rmFilter "$filtering.rmFilter" 23 --rmFilter "$filtering.rmFilter"
24 #end if 24 #end if
25 #end if 25 #end if
26 > $output 26 > "$output"
27 ]]> 27 ]]>
28 </command> 28 </command>
29 <configfiles>
30 <configfile name="exprFile">
31 $expr#slurp
32 </configfile>
33 </configfiles>
29 <inputs> 34 <inputs>
30 <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/> 35 <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/>
31 <param name="expr" type="text" label="Filter criteria" help="Need help? See below a few examples." /> 36 <param name="expr" type="text" label="Filter criteria" help="Need help? See below a few examples." />
32 <param name="inverse" type="boolean" truevalue="--inverse" falsevalue="" checked="false" label="Inverse filter" help="Show lines that do not match filter expression" /> 37 <param name="inverse" type="boolean" truevalue="--inverse" falsevalue="" checked="false" label="Inverse filter" help="Show lines that do not match filter expression" />
33 <conditional name="filtering"> 38 <conditional name="filtering">
49 <param name="addFilter" type="text" value="" optional="true" label="Add a string to FILTER VCF field if 'expression' is true." /> 54 <param name="addFilter" type="text" value="" optional="true" label="Add a string to FILTER VCF field if 'expression' is true." />
50 <param name="rmFilter" type="text" value="" optional="true" label="Remove a string from FILTER VCF field if 'expression' is true (and 'str' is in the field)." /> 55 <param name="rmFilter" type="text" value="" optional="true" label="Remove a string from FILTER VCF field if 'expression' is true (and 'str' is in the field)." />
51 </when> 56 </when>
52 </conditional> 57 </conditional>
53 </inputs> 58 </inputs>
54 <configfiles>
55 <configfile name="exprFile">
56 $expr#slurp
57 </configfile>
58 </configfiles>
59 59
60 <outputs> 60 <outputs>
61 <data format="vcf" name="output" /> 61 <data format="vcf" name="output" />
62 </outputs> 62 </outputs>
63 <tests> 63 <tests>
85 </output> 85 </output>
86 </test> 86 </test>
87 87
88 <test> 88 <test>
89 <param name="input" ftype="vcf" value="test01.vcf"/> 89 <param name="input" ftype="vcf" value="test01.vcf"/>
90 <param name="expr" value="(POS >= 20175) &amp; (POS &lt; 35549)"/> 90 <param name="expr" value="(POS &gt;= 20175) &amp; (POS &lt;= 35549)"/>
91 <param name="mode" value="entries"/> 91 <param name="mode" value="entries"/>
92 <output name="output"> 92 <output name="output">
93 <assert_contents> 93 <assert_contents>
94 <has_text text="20175" /> 94 <has_text text="20175" />
95 <has_text text="35549" /> 95 <has_text text="35549" />
100 </output> 100 </output>
101 </test> 101 </test>
102 102
103 <test> 103 <test>
104 <param name="input" ftype="vcf" value="test01.vcf"/> 104 <param name="input" ftype="vcf" value="test01.vcf"/>
105 <param name="expr" value="( DP >= 5 )"/> 105 <param name="expr" value="( DP &gt;= 5 )"/>
106 <param name="mode" value="entries"/> 106 <param name="mode" value="entries"/>
107 <output name="output"> 107 <output name="output">
108 <assert_contents> 108 <assert_contents>
109 <has_text text="DP=5;" /> 109 <has_text text="DP=5;" />
110 <has_text text="DP=6;" /> 110 <has_text text="DP=6;" />
185 185
186 186
187 @EXTERNAL_DOCUMENTATION@ 187 @EXTERNAL_DOCUMENTATION@
188 http://snpeff.sourceforge.net/SnpSift.html#filter 188 http://snpeff.sourceforge.net/SnpSift.html#filter
189 189
190 @CITATION_SECTION@
191
192 ]]> 190 ]]>
193 </help> 191 </help>
192 <expand macro="citations" />
194 </tool> 193 </tool>