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comparison snpSift_extractFields.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
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2:bf8c1526871b 3:20c7d583fec1
1 <tool id="snpSift_extractFields" name="SnpSift Extract Fields" version="@WRAPPER_VERSION@.1"> 1 <tool id="snpSift_extractFields" name="SnpSift Extract Fields" version="@WRAPPER_VERSION@.0">
2 <options sanitize="False" /> 2 <options sanitize="False" />
3 <description>from a VCF file into a tabular file</description> 3 <description>from a VCF file into a tabular file</description>
4 <macros> 4 <macros>
5 <import>snpSift_macros.xml</import> 5 <import>snpSift_macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <expand macro="stdio" /> 8 <expand macro="stdio" />
9 <expand macro="version_command" /> 9 <expand macro="version_command" />
10 <command><![CDATA[ 10 <command><![CDATA[
11 @CONDA_SNPSIFT_JAR_PATH@ && 11 @CONDA_SNPSIFT_JAR_PATH@ &&
12 cat "$input" 12 cat '$input'
13 #if $one_effect_per_line: 13 #if $one_effect_per_line:
14 | "\$SNPSIFT_JAR_PATH/scripts/vcfEffOnePerLine.pl" 14 | "\$SNPSIFT_JAR_PATH/scripts/vcfEffOnePerLine.pl"
15 #end if 15 #end if
16 | java -Xmx6G -jar "\$SNPSIFT_JAR_PATH/SnpSift.jar" extractFields 16 | SnpSift -Xmx6G extractFields
17 #if $separator: 17 #if $separator:
18 -s '$separator' 18 -s '$separator'
19 #end if 19 #end if
20 #if $empty_text: 20 #if $empty_text:
21 -e '$empty_text' 21 -e '$empty_text'
22 #end if 22 #end if
23 - 23 -
24 #echo ' '.join(['"%s"' % x for x in $extract.split()]) 24 #echo ' '.join(['"%s"' % x for x in $extract.split()])
25 > "$output" 25 > '$output'
26 ]]> 26 ]]></command>
27 </command>
28 <inputs> 27 <inputs>
29 <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/> 28 <param name="input" type="data" format="vcf" label="Variant input file in VCF format"/>
30 <param name="extract" type="text" label="Extract" help="Need help? See below a few examples." /> 29 <param name="extract" type="text" label="Extract" help="Need help? See below a few examples." />
31 <param name="one_effect_per_line" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="One effect per line" help="When variants have more than one effect, lists one effect per line, while all other parameters in the line are repeated across mutiple lines" /> 30 <param name="one_effect_per_line" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="One effect per line" help="When variants have more than one effect, lists one effect per line, while all other parameters in the line are repeated across mutiple lines" />
32 <param name="separator" type="text" value="" label="multiple field separator" help="Separate multiple fields in one column with this character, e.g. a comma, rather than a column for each of the multiple values" /> 31 <param name="separator" type="text" value="" label="multiple field separator" help="Separate multiple fields in one column with this character, e.g. a comma, rather than a column for each of the multiple values" />
33 <param name="empty_text" type="text" value="" label="empty field text" help="Represent empty fields with this value, rather than leaving them blank" /> 32 <param name="empty_text" type="text" value="" label="empty field text" help="Represent empty fields with this value, rather than leaving them blank" />
34 </inputs> 33 </inputs>
35 <outputs> 34 <outputs>
36 <data format="tabular" name="output" /> 35 <data name="output" format="tabular" />
37 </outputs> 36 </outputs>
38 <tests> 37 <tests>
39 <test> 38 <test>
40 <param name="input" ftype="vcf" value="test_rmInfo.vcf"/> 39 <param name="input" ftype="vcf" value="test_rmInfo.vcf"/>
41 <param name="extract" value="CHROM POS REF ALT EFF[*].EFFECT"/> 40 <param name="extract" value="CHROM POS REF ALT EFF[*].EFFECT"/>
55 <assert_contents> 54 <assert_contents>
56 <has_text text="DOWNSTREAM,INTRAGENIC,INTRON,UTR_3_PRIME" /> 55 <has_text text="DOWNSTREAM,INTRAGENIC,INTRON,UTR_3_PRIME" />
57 </assert_contents> 56 </assert_contents>
58 </output> 57 </output>
59 </test> 58 </test>
60
61 </tests> 59 </tests>
62 <help><![CDATA[ 60 <help><![CDATA[
63
64 **SnpSift Extract Fields** 61 **SnpSift Extract Fields**
65 62
66 Extract fields from a VCF file to a TXT, tab separated format, that you can easily load in R, XLS, etc. 63 Extract fields from a VCF file to a TXT, tab separated format, that you can easily load in R, XLS, etc.
67 64
68 http://snpeff.sourceforge.net/SnpSift.html#Extract 65 http://snpeff.sourceforge.net/SnpSift.html#Extract
69 66
70 You can also use sub-fields and genotype fields / sub-fields such as: 67 You can also use sub-fields and genotype fields / sub-fields such as::
71
72 ::
73 68
74 Standard VCF fields: 69 Standard VCF fields:
75 CHROM 70 CHROM
76 POS 71 POS
77 ID 72 ID
125 "NMD[*].GENE" 120 "NMD[*].GENE"
126 "NMD[*].GENEID" 121 "NMD[*].GENEID"
127 "NMD[*].NUMTR" 122 "NMD[*].NUMTR"
128 "NMD[*].PERC" 123 "NMD[*].PERC"
129 124
130
131 Some examples: 125 Some examples:
132 126
133 - *Extracting chromosome, position, ID and allele frequency from a VCF file:* 127 - *Extracting chromosome, position, ID and allele frequency from a VCF file*:
134 128
135 **CHROM POS ID AF** 129 **CHROM POS ID AF**
136 130
137 The result will look something like: 131 The result will look something like::
138 132
139 :: 133 #CHROM POS ID AF
134 1 69134 0.086
135 1 69496 rs150690004 0.001
140 136
141 #CHROM POS ID AF 137 - *Extracting genotype fields*:
142 1 69134 0.086
143 1 69496 rs150690004 0.001
144 138
139 **CHROM POS ID THETA GEN[0].GL[1] GEN[1].GL GEN[3].GL[*] GEN[*].GT**
145 140
146 - *Extracting genotype fields:* 141 This means to extract:
147 142
148 **CHROM POS ID THETA GEN[0].GL[1] GEN[1].GL GEN[3].GL[*] GEN[*].GT** 143 - CHROM POS ID: regular fields (as in the previous example)
144 - THETA : This one is from INFO
145 - GEN[0].GL[1] : Second likelihood from first genotype
146 - GEN[1].GL : The whole GL fiels (all entries without separating them)
147 - GEN[3].GL[*] : All likelihoods form genotype 3 (this time they will be tab separated, as opposed to the previous one).
148 - GEN[*].GT : Genotype subfields (GT) from ALL samples (tab separated).
149 149
150 This means to extract: 150 The result will look something like::
151 151
152 - CHROM POS ID: regular fields (as in the previous example) 152 #CHROM POS ID THETA GEN[0].GL[1] GEN[1].GL GEN[3].GL[*] GEN[*].GT
153 - THETA : This one is from INFO 153 1 10583 rs58108140 0.0046 -0.47 -0.24,-0.44,-1.16 -0.48 -0.48 -0.48 0|0 0|0 0|0 0|1 0|0 0|1 0|0 0|0 0|1
154 - GEN[0].GL[1] : Second likelihood from first genotype 154 1 10611 rs189107123 0.0077 -0.48 -0.24,-0.44,-1.16 -0.48 -0.48 -0.48 0|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0
155 - GEN[1].GL : The whole GL fiels (all entries without separating them) 155 1 13302 rs180734498 0.0048 -0.58 -2.45,-0.00,-5.00 -0.48 -0.48 -0.48 0|0 0|1 0|0 0|0 0|0 1|0 0|0 0|1 0|0
156 - GEN[3].GL[*] : All likelihoods form genotype 3 (this time they will be tab separated, as opposed to the previous one).
157 - GEN[*].GT : Genotype subfields (GT) from ALL samples (tab separated).
158 156
159 The result will look something like: 157 - *Extracting fields with multiple values*:
158 (notice that there are multiple effect columns per line because there are mutiple effects per variant)
160 159
161 :: 160 **CHROM POS REF ALT ANN[*].EFFECT**
162 161
163 #CHROM POS ID THETA GEN[0].GL[1] GEN[1].GL GEN[3].GL[*] GEN[*].GT 162 The result will look something like::
164 1 10583 rs58108140 0.0046 -0.47 -0.24,-0.44,-1.16 -0.48 -0.48 -0.48 0|0 0|0 0|0 0|1 0|0 0|1 0|0 0|0 0|1
165 1 10611 rs189107123 0.0077 -0.48 -0.24,-0.44,-1.16 -0.48 -0.48 -0.48 0|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0
166 1 13302 rs180734498 0.0048 -0.58 -2.45,-0.00,-5.00 -0.48 -0.48 -0.48 0|0 0|1 0|0 0|0 0|0 1|0 0|0 0|1 0|0
167 163
168 - *Extracting fields with multiple values:* 164 #CHROM POS REF ALT ANN[*].EFFECT
169 (notice that there are multiple effect columns per line because there are mutiple effects per variant) 165 22 17071756 T C 3_prime_UTR_variant downstream_gene_variant
166 22 17072035 C T missense_variant downstream_gene_variant
167 22 17072258 C A missense_variant downstream_gene_variant
170 168
171 **CHROM POS REF ALT ANN[*].EFFECT** 169 - *Extracting fields with multiple values using a comma as a multipe field separator:*
172 170
173 The result will look something like: 171 **CHROM POS REF ALT ANN[*].EFFECT ANN[*].HGVS_P**
174 172
175 :: 173 The result will look something like::
176 174
177 #CHROM POS REF ALT ANN[*].EFFECT 175 #CHROM POS REF ALT ANN[*].EFFECT ANN[*].HGVS_P
178 22 17071756 T C 3_prime_UTR_variant downstream_gene_variant 176 22 17071756 T C 3_prime_UTR_variant,downstream_gene_variant .,.
179 22 17072035 C T missense_variant downstream_gene_variant 177 22 17072035 C T missense_variant,downstream_gene_variant p.Gly469Glu,.
180 22 17072258 C A missense_variant downstream_gene_variant 178 22 17072258 C A missense_variant,downstream_gene_variant p.Gly395Cys,.
181 179
182 - *Extracting fields with multiple values using a comma as a multipe field separator:* 180 - *Extracting fields with multiple values, one effect per line:*
183 181
184 **CHROM POS REF ALT ANN[*].EFFECT ANN[*].HGVS_P** 182 **CHROM POS REF ALT ANN[*].EFFECT**
185 183
186 The result will look something like: 184 The result will look something like::
187 185
188 :: 186 #CHROM POS REF ALT ANN[*].EFFECT
189 187 22 17071756 T C 3_prime_UTR_variant
190 #CHROM POS REF ALT ANN[*].EFFECT ANN[*].HGVS_P 188 22 17071756 T C downstream_gene_variant
191 22 17071756 T C 3_prime_UTR_variant,downstream_gene_variant .,. 189 22 17072035 C T missense_variant
192 22 17072035 C T missense_variant,downstream_gene_variant p.Gly469Glu,. 190 22 17072035 C T downstream_gene_variant
193 22 17072258 C A missense_variant,downstream_gene_variant p.Gly395Cys,. 191 22 17072258 C A missense_variant
194 192 22 17072258 C A downstream_gene_variant
195
196 - *Extracting fields with multiple values, one effect per line:*
197
198 **CHROM POS REF ALT ANN[*].EFFECT**
199
200 The result will look something like:
201
202 ::
203
204 #CHROM POS REF ALT ANN[*].EFFECT
205 22 17071756 T C 3_prime_UTR_variant
206 22 17071756 T C downstream_gene_variant
207 22 17072035 C T missense_variant
208 22 17072035 C T downstream_gene_variant
209 22 17072258 C A missense_variant
210 22 17072258 C A downstream_gene_variant
211
212 193
213 @EXTERNAL_DOCUMENTATION@ 194 @EXTERNAL_DOCUMENTATION@
214 http://snpeff.sourceforge.net/SnpSift.html#Extract 195 - http://snpeff.sourceforge.net/SnpSift.html#Extract
215 196 ]]></help>
216 ]]>
217 </help>
218 <expand macro="citations" /> 197 <expand macro="citations" />
219 </tool> 198 </tool>