Mercurial > repos > ulfschaefer > filter_vcf
changeset 1:a60184379a0f draft
Deleted selected files
| author | ulfschaefer |
|---|---|
| date | Thu, 03 Dec 2015 06:03:36 -0500 |
| parents | 505a9f1dd8e0 |
| children | 0742a605c468 |
| files | filter_vcf.xml tool_dependencies.xml |
| diffstat | 2 files changed, 0 insertions(+), 111 deletions(-) [+] |
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--- a/filter_vcf.xml Thu Dec 03 05:41:12 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,99 +0,0 @@ -<tool id="filter_vcf" name="Filter VCF" version="1.0"> - <description>filters a VCF file</description> - <requirements> - <requirement type="package" version="2.7.10">python</requirement> - <requirement type="package" version="0.6.7">pyvcf</requirement> - <requirement type="package" version="3.11">pyyaml</requirement> - </requirements> - <stdio> - <!-- Assume anything other than zero is an error --> - <exit_code range="1:" /> - <exit_code range=":-1" /> - </stdio> - <command interpreter="bash"> - filter_vcf.sh - $output - $input - #for $sf in $snp_filter: - #for $name, $param in $sf.snp_filter_type.iteritems(): - #if $name not in [ "__current_case__", "snp_filter_type_selector" ]: - ${name}:"${param}" - #end if - #end for - #end for - </command> - - <inputs> - <param name="input" type="data" format="vcf" label="VCF File to filter" /> - - <repeat name="snp_filter" title="SNP Filter" help=""> - <conditional name="snp_filter_type"> - <param name="snp_filter_type_selector" type="select" label="SNP Filter Type"> - <option value="gq_score_option">GQ score</option> - <option value="dp4_ratio_option">DP4 ratio</option> - <option value="ad_ratio_option">AD ratio</option> - <option value="mq_score_option">MQ score</option> - <option value="min_depth_option">Minimum depth</option> - <option value="uncall_gt_option">Uncall GT</option> - <option value="mq0_ratio_option">MQ0 ratio</option> - <option value="qual_score_option">Quality score</option> - <option value="mq0f_ratio_option">MQ0F ratio</option> - </param> - <when value="gq_score_option"> - <param name="gq_score" type="integer" value="0" label="Minimum GC score" help="Type integer"/> - </when> - <when value="dp4_ratio_option"> - <param name="dp4_ratio" type="float" value="0.9" label="Minimum DP4 ratio" help="Type float"/> - </when> - <when value="ad_ratio_option"> - <param name="ad_ratio" type="float" value="0.9" label="Minimum AD ratio" help="Type float"/> - </when> - <when value="mq_score_option"> - <param name="mq_score" type="integer" value="30" label="Minimum MQ score" help="Type integer"/> - </when> - <when value="min_depth_option"> - <param name="min_depth" type="integer" value="5" label="Minimum depth" help="Type integer"/> - </when> - <when value="uncall_gt_option"> - <param name="uncall_gt" type="text" value="" hidden="True"/> - </when> - <when value="mq0_ratio_option"> - <param name="mq0_ratio" type="float" value="0.05" label="Minimim MQ0 ratio" help="Type float"/> - </when> - <when value="qual_score_option"> - <param name="qual_score" type="integer" value="30" label="Minimim quality score" help="Type integer"/> - </when> - <when value="mq0f_ratio_option"> - <param name="mq0f_ratio" type="float" value="0.05" label="Minimum MQ0F ratio" help="Type float"/> - </when> - </conditional> - </repeat> - - </inputs> - - <outputs> - <data format="vcf" name="output" label="${tool.name} on ${on_string}: filtered VCF" /> - </outputs> - <tests> - <test> - <param name="input" value="test_input.vcf" ftype="vcf" /> - <param name="min_depth" value="100" /> - <output name="output" file="test_output.vcf" ftype="vcf" /> - </test> - </tests> - <help> - -usage: filter_vcf.py [-h] \-\-vcf VCF \-\-filters FILTERS \-\-output OUTPUT - -optional arguments: - --h, \-\-help show this help message and exit - -\-\-vcf VCF, -v VCF VCF file to (re)filter. - -\-\-filters FILTERS, -f FILTERS Filter(s) to apply as key:threshold pairs, separated by comma. - -\-\-output OUTPUT, -o OUTPUT Location for filtered VCF to be written. - - </help> -</tool>
--- a/tool_dependencies.xml Thu Dec 03 05:41:12 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,12 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="python" version="2.7.10"> - <repository changeset_revision="73631e818d3d" name="package_python_2_7_10" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="pyyaml" version="3.11"> - <repository changeset_revision="b7a084c9e994" name="package_python_2_7_pyyaml_3_11" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"/> - </package> - <package name="pyvcf" version="0.6.7"> - <repository changeset_revision="c05e29a21f10" name="package_pyvcf_0_6_7" owner="saket-choudhary" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"/> - </package> -</tool_dependency>