Mercurial > repos > jjohnson > snpeff_cds_report

comparison snpEff_cds_report.xml @ 5:85b933b7d231

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Make the reporting of the SnpEff Amino_Acid_change field an option
author Jim Johnson <jj@umn.edu>
date Fri, 24 May 2013 08:50:03 -0500
parents 57edf4d08816
children
comparison
equal deleted inserted replaced
4:429a6b4df5e5 5:85b933b7d231
1 <tool id="SnpEff-cds-report" name="SnpEff Ensembl CDS" version="1.1"> 1 <tool id="SnpEff-cds-report" name="SnpEff Ensembl CDS" version="1.2">
2 <description>Report Variant coding sequence changes for SnpEffects</description> 2 <description>Report Variant coding sequence changes for SnpEffects</description>
3 <command interpreter="python"> 3 <command interpreter="python">
4 snpEff_cds_report.py --in $snp_effect_vcf 4 snpEff_cds_report.py --in $snp_effect_vcf
5 #if len($ensembl_host.__str__.strip) > 0: 5 #if len($ensembl_host.__str__.strip) > 0:
6 --ensembl_host ${ensembl_host}.archive.ensembl.org 6 --ensembl_host ${ensembl_host}.archive.ensembl.org
14 #if $effects_filter 14 #if $effects_filter
15 --effects_filter=$effects_filter 15 --effects_filter=$effects_filter
16 #end if 16 #end if
17 $all_effects 17 $all_effects
18 $with_ccds 18 $with_ccds
19 $snpeff_aa_change
19 #if $report_format.__str__.find('html') >= 0: 20 #if $report_format.__str__.find('html') >= 0:
20 --html_report $html_report 21 --html_report $html_report
21 --html_dir $html_report.extra_files_path 22 --html_dir $html_report.extra_files_path
22 #end if 23 #end if
23 #if $report_format.__str__.find('tsv') >= 0: 24 #if $report_format.__str__.find('tsv') >= 0:
134 <option value="CUSTOM">CUSTOM</option> 135 <option value="CUSTOM">CUSTOM</option>
135 <option value="CDS">CDS</option> 136 <option value="CDS">CDS</option>
136 </param> 137 </param>
137 <param name="all_effects" type="boolean" truevalue="--all_effects" falsevalue="" checked="false" label="Report the variant coding for each Ensembl Transcript at the variant position" help="Default is to report only the first Transcript that has a cDNA change"/> 138 <param name="all_effects" type="boolean" truevalue="--all_effects" falsevalue="" checked="false" label="Report the variant coding for each Ensembl Transcript at the variant position" help="Default is to report only the first Transcript that has a cDNA change"/>
138 <param name="with_ccds" type="boolean" truevalue="--with_ccds" falsevalue="" checked="false" label="Report the variant coding only for Ensembl Transcripts with a CCDS ID" help=""/> 139 <param name="with_ccds" type="boolean" truevalue="--with_ccds" falsevalue="" checked="false" label="Report the variant coding only for Ensembl Transcripts with a CCDS ID" help=""/>
140 <param name="snpeff_aa_change" type="boolean" truevalue="--snpeff_aa_change" falsevalue="" checked="false" label="Report the Amino_Acid_change from SnpEff" help="Otherwise, report the first changed Animo Acid as: AposA (ref_AA pos_from_Nterminus alt_AA)"/>
139 <param name="polya" type="integer" value="5" optional="true" label="Ignore variants that are part of a Poly-A of at least this length" help="Leave blank to turn off poly A filtering"> 141 <param name="polya" type="integer" value="5" optional="true" label="Ignore variants that are part of a Poly-A of at least this length" help="Leave blank to turn off poly A filtering">
140 <validator type="in_range" message="poly A between 2 and 100 bases" min="2" max="100"/> 142 <validator type="in_range" message="poly A between 2 and 100 bases" min="2" max="100"/>
141 </param> 143 </param>
142 <param name="report_format" type="select" force_select="true" multiple="true" display="checkboxes" label="Report formats" help=""> 144 <param name="report_format" type="select" force_select="true" multiple="true" display="checkboxes" label="Report formats" help="">
143 <option value="html" selected="true">Detailed HTML report</option> 145 <option value="html" selected="true">Detailed HTML report</option>