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comparison snpSift_filter.xml @ 11:b884686a80dc draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 344140b8df53b8b7024618bb04594607a045c03a
author iuc
date Mon, 04 May 2015 22:37:06 -0400
parents f0faaa4d6ee5
children 6bf58286d795
comparison
equal deleted inserted replaced
10:93577c5e76ec 11:b884686a80dc
1 <tool id="snpSift_filter" name="SnpSift Filter" version="4.0.0"> 1 <tool id="snpSift_filter" name="SnpSift Filter" version="4.0.0">
2 <options sanitize="False" /> 2 <options sanitize="False" />
3 <description>Filter variants using arbitrary expressions</description> 3 <description>Filter variants using arbitrary expressions</description>
4 <expand macro="requirements" />
5 <macros> 4 <macros>
6 <import>snpSift_macros.xml</import> 5 <import>snpSift_macros.xml</import>
7 </macros> 6 </macros>
7 <expand macro="requirements" />
8 <expand macro="stdio" />
8 <command> 9 <command>
9 java -Xmx6G -jar \$SNPEFF_JAR_PATH/SnpSift.jar filter -f $input -e $exprFile $inverse 10 java -Xmx6G -jar \$SNPEFF_JAR_PATH/SnpSift.jar filter -f $input -e $exprFile $inverse
10 #if $filtering.mode == 'field': 11 #if $filtering.mode == 'field':
11 #if $filtering.replace.pass: 12 #if $filtering.replace.pass:
12 --pass 13 --pass
13 #if $filtering.replace.filterId and len($filtering.replace.filterId.__str__.strip()) > 0: 14 #if $filtering.replace.filterId and len($filtering.replace.filterId.__str__.strip()) > 0:
14 --filterId "$filtering.replace.filterId" 15 --filterId "$filtering.replace.filterId"
21 --rmFilter "$filtering.rmFilter" 22 --rmFilter "$filtering.rmFilter"
22 #end if 23 #end if
23 #end if 24 #end if
24 > $output 25 > $output
25 </command> 26 </command>
27 <configfiles>
28 <configfile name="exprFile">
29 $expr#slurp
30 </configfile>
31 </configfiles>
26 <inputs> 32 <inputs>
27 <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/> 33 <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/>
28 <param name="expr" type="text" label="Filter criteria" size="160" help="Need help? See below a few examples." /> 34 <param name="expr" type="text" label="Filter criteria" size="160" help="Need help? See below a few examples." />
29 <param name="inverse" type="boolean" truevalue="--inverse" falsevalue="" checked="false" label="Inverse filter" help="Show lines that do not match filter expression" /> 35 <param name="inverse" type="boolean" truevalue="--inverse" falsevalue="" checked="false" label="Inverse filter" help="Show lines that do not match filter expression" />
30 <conditional name="filtering"> 36 <conditional name="filtering">
31 <param name="mode" type="select" label="Filter mode"> 37 <param name="mode" type="select" label="Filter mode">
32 <option value="entries" selected="true">Retain entries that pass filter, remove other entries</option> 38 <option value="entries" selected="true">Retain entries that pass filter, remove other entries</option>
33 <option value="field">Change the FILTER field, but retain all entries</option> 39 <option value="field">Change the FILTER field, but retain all entries</option>
34 </param> 40 </param>
35 <when value="entries"/> 41 <when value="entries"/>
36 <when value="field"> 42 <when value="field">
37 <conditional name="replace"> 43 <conditional name="replace">
38 <param name="pass" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Set matching entry FILTER to 'PASS'" 44 <param name="pass" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Set matching entry FILTER to 'PASS'"
39 help="appends an ID tag to non-matching entry FILTER "/> 45 help="appends an ID tag to non-matching entry FILTER "/>
40 <when value="no"/> 46 <when value="no"/>
41 <when value="yes"> 47 <when value="yes">
42 <param name="filterId" type="text" value="" optional="true" label="ID appended to non-matching (##FILTER tag in header and FILTER VCF field)." size="10" 48 <param name="filterId" type="text" value="" optional="true" label="ID appended to non-matching (##FILTER tag in header and FILTER VCF field)." size="10"
43 help="Default ID is 'SnpSift'"/> 49 help="Default ID is 'SnpSift'"/>
46 <param name="addFilter" type="text" value="" optional="true" label="Add a string to FILTER VCF field if 'expression' is true." size="10"/> 52 <param name="addFilter" type="text" value="" optional="true" label="Add a string to FILTER VCF field if 'expression' is true." size="10"/>
47 <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)." size="10"/> 53 <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)." size="10"/>
48 </when> 54 </when>
49 </conditional> 55 </conditional>
50 </inputs> 56 </inputs>
51 <configfiles>
52 <configfile name="exprFile">
53 $expr#slurp
54 </configfile>
55 </configfiles>
56 57
57 <outputs> 58 <outputs>
58 <data format="vcf" name="output" /> 59 <data format="vcf" name="output" />
59 </outputs> 60 </outputs>
60 <expand macro="stdio" />
61 <tests> 61 <tests>
62 <test> 62 <test>
63 <param name="input" ftype="vcf" value="test01.vcf"/> 63 <param name="input" ftype="vcf" value="test01.vcf"/>
64 <param name="expr" value="QUAL >= 50"/> 64 <param name="expr" value="QUAL >= 50"/>
65 <param name="mode" value="entries"/> 65 <param name="mode" value="entries"/>
127 127
128 - *Filter value is either 'PASS' or it is missing*: 128 - *Filter value is either 'PASS' or it is missing*:
129 129
130 :: 130 ::
131 131
132 (FILTER = 'PASS') | ( na FILTER ) 132 (FILTER = 'PASS') | ( na FILTER )
133 133
134 - *I want to filter lines with an EFF of 'frameshift_variant' ( for vcf files using Sequence Ontology terms )*: 134 - *I want to filter lines with an EFF of 'frameshift_variant' ( for vcf files using Sequence Ontology terms )*:
135 135
136 :: 136 ::
137 137
138 ( EFF[*].EFFECT = 'frameshift_variant' ) 138 ( EFF[*].EFFECT = 'frameshift_variant' )
139 139
140 - *I want to filter lines with an EFF of 'FRAME_SHIFT' ( for vcf files using Classic Effect names )*: 140 - *I want to filter lines with an EFF of 'FRAME_SHIFT' ( for vcf files using Classic Effect names )*:
141 141
142 :: 142 ::
143 143
144 ( EFF[*].EFFECT = 'FRAME_SHIFT' ) 144 ( EFF[*].EFFECT = 'FRAME_SHIFT' )
145 145
146 - *I want to filter out samples with quality less than 30*: 146 - *I want to filter out samples with quality less than 30*:
147 147
148 :: 148 ::
152 - *...but we also want InDels that have quality 20 or more*: 152 - *...but we also want InDels that have quality 20 or more*:
153 153
154 :: 154 ::
155 155
156 (( exists INDEL ) &amp; (QUAL >= 20)) | (QUAL >= 30 ) 156 (( exists INDEL ) &amp; (QUAL >= 20)) | (QUAL >= 30 )
157 157
158 - *...or any homozygous variant present in more than 3 samples*: 158 - *...or any homozygous variant present in more than 3 samples*:
159 159
160 :: 160 ::
161 161
162 (countHom() > 3) | (( exists INDEL ) &amp; (QUAL >= 20)) | (QUAL >= 30 ) 162 (countHom() > 3) | (( exists INDEL ) &amp; (QUAL >= 20)) | (QUAL >= 30 )
163 163
164 - *...or any heterozygous sample with coverage 25 or more*: 164 - *...or any heterozygous sample with coverage 25 or more*:
165 165
166 :: 166 ::
167 167
168 ((countHet() > 0) &amp; (DP >= 25)) | (countHom() > 3) | (( exists INDEL ) &amp; (QUAL >= 20)) | (QUAL >= 30 ) 168 ((countHet() > 0) &amp; (DP >= 25)) | (countHom() > 3) | (( exists INDEL ) &amp; (QUAL >= 20)) | (QUAL >= 30 )
169 169
170 - *I want to keep samples where the genotype for the first sample is homozygous variant and the genotype for the second sample is reference*: 170 - *I want to keep samples where the genotype for the first sample is homozygous variant and the genotype for the second sample is reference*:
171 171
172 :: 172 ::
173 173
174 (isHom( GEN[0] ) &amp; isVariant( GEN[0] ) &amp; isRef( GEN[1] )) 174 (isHom( GEN[0] ) &amp; isVariant( GEN[0] ) &amp; isRef( GEN[1] ))
175 175
176 176
177 **For information regarding HGVS and Sequence Ontology terms versus classic names**: 177 **For information regarding HGVS and Sequence Ontology terms versus classic names**:
178 178