Mercurial > repos > iuc > snpsift
annotate snpSift_filter.xml @ 8:5fab4f81391d draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit df8a21df77acffe40c0bc0fe0409ca1b529cd7fc"
author | iuc |
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date | Sat, 11 Sep 2021 07:17:51 +0000 |
parents | 2e497a770bca |
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rev | line source |
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2e497a770bca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
iuc
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1 <tool id="snpSift_filter" name="SnpSift Filter" version="@WRAPPER_VERSION@.galaxy1"> |
0 | 2 <description>Filter variants using arbitrary expressions</description> |
3 <macros> | |
4 <import>snpSift_macros.xml</import> | |
5 </macros> | |
1
98708b88af9f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
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6 <expand macro="requirements" /> |
98708b88af9f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
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7 <expand macro="stdio" /> |
98708b88af9f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
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8 <expand macro="version_command" /> |
98708b88af9f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
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9 <command><![CDATA[ |
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20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
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10 SnpSift -Xmx6G filter -f '$input' -e '$exprFile' $inverse |
7
2e497a770bca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
iuc
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11 #if str($filter_expression.type) == 'complex': |
2e497a770bca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
iuc
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12 #for $set_file in $filter_expression.set: |
2e497a770bca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
iuc
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13 --set $set_file |
2e497a770bca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
iuc
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14 #end for |
2e497a770bca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
iuc
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15 #end if |
2e497a770bca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
iuc
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16 #if $filtering.mode == 'set_filter': |
2e497a770bca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
iuc
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17 --filterID $filtering.filter_id |
2e497a770bca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
iuc
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18 #elif $filtering.mode == 'remove_filter': |
2e497a770bca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
iuc
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19 --rmFilter $filtering.rm_filter |
2e497a770bca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
iuc
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20 #elif $filtering.mode == 'add_filter': |
2e497a770bca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
iuc
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21 --addFilter $filtering.add_filter |
3
20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
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22 #end if |
20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
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23 > '$output' |
20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
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24 ]]></command> |
1
98708b88af9f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
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25 <configfiles> |
98708b88af9f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
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26 <configfile name="exprFile"> |
7
2e497a770bca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
iuc
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27 $filter_expression.expr#slurp |
2
bf8c1526871b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
iuc
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28 </configfile> |
1
98708b88af9f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
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29 </configfiles> |
0 | 30 <inputs> |
7
2e497a770bca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
iuc
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31 <param name="input" type="data" format="vcf" label="Input variant list in VCF format"/> |
2e497a770bca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
iuc
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32 <conditional name="filter_expression"> |
2e497a770bca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
iuc
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33 <param name="type" type="select" |
2e497a770bca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
iuc
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34 label="Type of filter expression"> |
2e497a770bca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
iuc
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35 <option value="simple">Simple expression</option> |
2e497a770bca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
iuc
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36 <option value="complex">Expression using value set(s)</option> |
2e497a770bca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
iuc
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37 </param> |
2e497a770bca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
iuc
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38 <when value="simple"> |
2e497a770bca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
iuc
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39 <param name="expr" type="text" label="Filter criteria" |
2e497a770bca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
iuc
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40 help="Need help? See the tool help below for some examples."> |
2e497a770bca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
iuc
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41 <sanitizer sanitize="False"/> |
2e497a770bca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
iuc
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42 </param> |
2e497a770bca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
iuc
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43 </when> |
2e497a770bca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
iuc
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44 <when value="complex"> |
2e497a770bca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
iuc
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45 <param name="expr" type="text" label="Filter criteria" |
2e497a770bca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
iuc
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46 help="Need help? See the tool help below for some examples."> |
2e497a770bca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
iuc
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47 <sanitizer sanitize="False"/> |
2e497a770bca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
iuc
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48 </param> |
2e497a770bca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
iuc
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49 <param name="set" type="data" format="txt" multiple="true" optional="False" |
2e497a770bca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
iuc
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50 label="Set value source" |
2e497a770bca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
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51 help="Select one or more datasets for construction of value sets. The datasets are supposed to specify one value per line. See also: the help section on Sets below." /> |
2e497a770bca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
iuc
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52 </when> |
2e497a770bca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
iuc
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53 </conditional> |
2e497a770bca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
iuc
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54 <param argument="--inverse" type="boolean" truevalue="--inverse" falsevalue="" checked="false" label="Invert filter" help="Select variants that do not match the filter expression." /> |
0 | 55 <conditional name="filtering"> |
56 <param name="mode" type="select" label="Filter mode"> | |
7
2e497a770bca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
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57 <option value="entries" selected="true">Retain selected variants, remove others</option> |
2e497a770bca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
iuc
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58 <option value="set_filter">Add a value to FILTER field of non-selected variants</option> |
2e497a770bca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
iuc
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59 <option value="remove_filter">Remove a value from FILTER field of selected variants</option> |
2e497a770bca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
iuc
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60 <option value="add_filter">Add a value to the FILTER field of selected variants</option> |
2
bf8c1526871b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
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61 </param> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
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62 <when value="entries" /> |
2e497a770bca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
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63 <when value="set_filter"> |
2e497a770bca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
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64 <param argument="--filterID" name="filter_id" type="text" optional="false" |
2e497a770bca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
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65 label="Value to add to FILTER field of non-selected variants" |
2e497a770bca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
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66 help="The value provided here will be added to the FILTER field of variants that are NOT selected by the expression above. Selected variants, in contrast, will have their FILTER field cleared and set to PASS." /> |
2e497a770bca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
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67 </when> |
2e497a770bca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
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68 <when value="remove_filter"> |
2e497a770bca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
iuc
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69 <param argument="--rmFilter" name="rm_filter" type="text" optional="false" |
2e497a770bca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
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70 label="Value to remove from FILTER field of selected variants" |
2e497a770bca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
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71 help="The FILTER field of variants that are selected by the expression above will be checked for existence of the specified value. When the value is found it will be removed, but other values will be preserved. If the removed value was the only value in a FILTER field, that field will be set to the '.' (missing) value." /> |
2e497a770bca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
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72 </when> |
2e497a770bca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
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73 <when value="add_filter"> |
2e497a770bca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
iuc
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74 <param argument="--addFilter" name="add_filter" type="text" optional="false" |
2e497a770bca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
iuc
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75 label="Value to add to FILTER field of selected variants" |
2e497a770bca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
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76 help="The value provided here will be added to the FILTER field of variants that are selected by the expression above. USE WITH CARE: The tool will NOT add a corresponding FILTER entry to the VCF header of the output, i.e. will produce output that violates the VCF format specification. To avoid issues with downstream tools it may be necessary to add such a header line using standard text processing tools before proceeding." /> |
0 | 77 </when> |
78 </conditional> | |
79 </inputs> | |
80 <outputs> | |
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81 <data name="output" format="vcf" /> |
0 | 82 </outputs> |
83 <tests> | |
84 <test> | |
85 <param name="input" ftype="vcf" value="test01.vcf"/> | |
86 <param name="expr" value="QUAL >= 50"/> | |
87 <param name="mode" value="entries"/> | |
88 <output name="output"> | |
89 <assert_contents> | |
90 <has_text text="28837706" /> | |
91 <not_has_text text="NT_166464" /> | |
92 </assert_contents> | |
93 </output> | |
94 </test> | |
95 <test> | |
96 <param name="input" ftype="vcf" value="test01.vcf"/> | |
97 <param name="expr" value="(CHROM = '19')"/> | |
98 <param name="mode" value="entries"/> | |
99 <output name="output"> | |
100 <assert_contents> | |
101 <has_text text="3205820" /> | |
102 <not_has_text text="NT_16" /> | |
103 </assert_contents> | |
104 </output> | |
105 </test> | |
106 <test> | |
107 <param name="input" ftype="vcf" value="test01.vcf"/> | |
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108 <param name="expr" value="(POS >= 20175) & (POS <= 35549)"/> |
0 | 109 <param name="mode" value="entries"/> |
110 <output name="output"> | |
111 <assert_contents> | |
112 <has_text text="20175" /> | |
113 <has_text text="35549" /> | |
114 <has_text text="22256" /> | |
115 <not_has_text text="18933" /> | |
116 <not_has_text text="37567" /> | |
117 </assert_contents> | |
118 </output> | |
119 </test> | |
120 <test> | |
121 <param name="input" ftype="vcf" value="test01.vcf"/> | |
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122 <param name="expr" value="( DP >= 5 )"/> |
0 | 123 <param name="mode" value="entries"/> |
124 <output name="output"> | |
125 <assert_contents> | |
126 <has_text text="DP=5;" /> | |
127 <has_text text="DP=6;" /> | |
128 <not_has_text text="DP=1;" /> | |
129 </assert_contents> | |
130 </output> | |
131 </test> | |
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132 <test> |
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133 <param name="input" ftype="vcf" value="test01.vcf"/> |
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134 <conditional name="filter_expression"> |
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135 <param name="type" value="complex" /> |
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136 <param name="expr" value="( POS in SET[0] ) | ( POS in SET[1] )" /> |
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137 <param name="set" ftype="txt" value="test_set1.txt,test_set2.txt" /> |
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138 </conditional> |
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139 <param name="mode" value="entries"/> |
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140 <output name="output"> |
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141 <assert_contents> |
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142 <has_text text="NT_166464	7268	" /> |
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143 <has_text text="NT_166464	7283	" /> |
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144 <has_text text="NT_166464	7335	" /> |
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145 <has_text text="NT_166480	12474	" /> |
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146 <has_text text="NT_166480	12483	" /> |
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147 <not_has_text text="NT_166464	7258	" /> |
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148 <not_has_text text="NT_166452	16693	" /> |
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149 </assert_contents> |
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150 </output> |
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151 </test> |
0 | 152 </tests> |
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153 <help><![CDATA[ |
0 | 154 **SnpSift filter** |
155 | |
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156 This tool provides a flexible solution for filtering the variants in a VCF input dataset through the use of arbitrary, possibly rather complex expressions. |
0 | 157 |
158 Some examples: | |
159 | |
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160 - *I want just the variants from the second million bases of chr1*:: |
0 | 161 |
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162 ( CHROM = 'chr1' ) & ( POS > 1000000 ) & ( POS < 2000000 ) |
0 | 163 |
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164 - *Filter value is either 'PASS' or it is missing*:: |
0 | 165 |
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166 (FILTER = 'PASS') | ( na FILTER ) |
0 | 167 |
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168 - *Variants that have either a QUAL score above 30, or are indel variants, or for which at least two samples have a heterozygous genotype called*:: |
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169 |
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170 (QUAL > 30) | (exists INDEL) | ( countHet() > 2 ) |
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171 |
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172 - *Variants that are supported by at least 10 reads (as calculated from the DP4 attribute in the INFO field through zero-based index-access to the multiple values)*:: |
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173 |
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174 (DP4[2] + DP4[3] >= 10) |
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175 |
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176 ---- |
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177 |
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178 Sets: |
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179 |
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180 The tool can construct sets of values for use in expressions from text files listing one value per line. Variants can then be filtered based on whether a given field in the variant record has a value that's contained in a set. For example, the expression:: |
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181 |
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182 ( ID in SET[2] ) |
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183 |
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184 would filter variants based on whether their ID field value appears in the set parsed from the third dataset used for set construction (the first set can be addressed with index ``[0]``, the second with index ``[1]``, and so on). |
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185 |
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186 ---- |
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187 |
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188 Genotype-based filtering: |
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189 |
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190 Genotypes of specific samples can be accessed via zero-based indexing or via sample names. |
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191 |
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192 - *I want to keep samples where the genotype for the first sample is homozygous variant and the genotype for the second sample is reference*:: |
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193 |
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194 (isHom( GEN[0] ) & isVariant( GEN[0] ) & isRef( GEN[1] )) |
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195 |
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196 ---- |
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197 |
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198 Filtering based on SnpEff annotations (``ANN`` or ``EFF`` fields): |
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199 |
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200 - *I want to filter lines with an ANN annotation EFFECT of 'frameshift_variant' ( for vcf files using Sequence Ontology terms )*:: |
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201 |
3
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202 ( ANN[*].EFFECT has 'frameshift_variant' ) |
0 | 203 |
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204 .. class:: infomark |
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205 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
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206 According to the specification, there can be more than one EFFECT separated by ``&`` (e.g. ``'missense_variant&splice_region_variant'``), thus using the ``has`` operator is better than using the equality operator (``=``). For instance, ``'missense_variant&splice_region_variant' = 'missense_variant'`` is false, whereas ``'missense_variant&splice_region_variant' has 'missense_variant'`` is true. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
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207 |
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208 - *I want to filter lines with an EFF of 'FRAME_SHIFT' ( for vcf files using Classic Effect names )*:: |
0 | 209 |
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210 ( EFF[*].EFFECT = 'FRAME_SHIFT' ) |
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212 | |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
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213 .. class:: infomark |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
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214 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
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215 For information regarding HGVS and Sequence Ontology terms versus classic names: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
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216 |
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217 - https://pcingola.github.io/SnpEff/se_commandline/ for the options: ``-classic``, ``-hgvs``, and ``-sequenceOntology`` |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
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218 - https://pcingola.github.io/SnpEff/se_inputoutput/#effect-prediction-details for the table containing the classic name and sequence onology term for each effect |
0 | 219 |
220 @EXTERNAL_DOCUMENTATION@ | |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
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221 - https://pcingola.github.io/SnpEff/ss_filter/ |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
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222 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
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223 The second link in particular has further details and more examples about the tool's expression syntax. |
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224 ]]></help> |
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225 <expand macro="citations" /> |
0 | 226 </tool> |