Mercurial > repos > iuc > snpsift

comparison snpSift_filter.xml @ 12:6bf58286d795 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit e5a5ad091c621348dc6ce2df861475ebc54a380e
author iuc
date Tue, 13 Oct 2015 17:31:24 -0400
parents b884686a80dc
children ed810da439cc
comparison
equal deleted inserted replaced
11:b884686a80dc 12:6bf58286d795
29 $expr#slurp 29 $expr#slurp
30 </configfile> 30 </configfile>
31 </configfiles> 31 </configfiles>
32 <inputs> 32 <inputs>
33 <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"/>
34 <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" help="Need help? See below a few examples." />
35 <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" />
36 <conditional name="filtering"> 36 <conditional name="filtering">
37 <param name="mode" type="select" label="Filter mode"> 37 <param name="mode" type="select" label="Filter mode">
38 <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>
39 <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>
43 <conditional name="replace"> 43 <conditional name="replace">
44 <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'"
45 help="appends an ID tag to non-matching entry FILTER "/> 45 help="appends an ID tag to non-matching entry FILTER "/>
46 <when value="no"/> 46 <when value="no"/>
47 <when value="yes"> 47 <when value="yes">
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" 48 <param name="filterId" type="text" value="" optional="true" label="ID appended to non-matching (##FILTER tag in header and FILTER VCF field)."
49 help="Default ID is 'SnpSift'"/> 49 help="Default ID is 'SnpSift'"/>
50 </when> 50 </when>
51 </conditional> 51 </conditional>
52 <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."/>
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"/> 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)."/>
54 </when> 54 </when>
55 </conditional> 55 </conditional>
56 </inputs> 56 </inputs>
57 57
58 <outputs> 58 <outputs>