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comparison snpEff.xml @ 17:13d81e5226cd

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Put gene info in Summary Report extra_files_path
author Jim Johnson <jj@umn.edu>
date Mon, 10 Nov 2014 09:33:36 -0600
parents 3790e16a0be0
children 36f3c82323e6
comparison
equal deleted inserted replaced
16:3790e16a0be0 17:13d81e5226cd
30 #end if 30 #end if
31 #if str( $intervals ) != 'None': ### fix this for multiple dataset input 31 #if str( $intervals ) != 'None': ### fix this for multiple dataset input
32 -interval $intervals 32 -interval $intervals
33 #end if 33 #end if
34 #if $statsFile: 34 #if $statsFile:
35 -stats $statsFile 35 -stats snpeff_report
36 #end if 36 #end if
37 #if $offset.__str__ != 'default': 37 #if $offset.__str__ != 'default':
38 ${offset} 38 ${offset}
39 #end if 39 #end if
40 #if $chr.__str__.strip() != '': 40 #if $chr.__str__.strip() != '':
65 #else 65 #else
66 -download 66 -download
67 $snpDb.genome_version 67 $snpDb.genome_version
68 #end if 68 #end if
69 $input > $snpeff_output 69 $input > $snpeff_output
70 #if $statsFile:
71 &amp;&amp; mkdir $statsFile.extra_files_path &amp;&amp; cp snpeff_report.genes.txt $statsFile.extra_files_path
72 #end if
70 </command> 73 </command>
71 <inputs> 74 <inputs>
72 <param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/> 75 <param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/>
73 76
74 <param name="inputFormat" type="select" label="Input format"> 77 <param name="inputFormat" type="select" label="Input format">
218 <when input="outputFormat" value="txt" format="tabular" /> 221 <when input="outputFormat" value="txt" format="tabular" />
219 <when input="outputFormat" value="bed" format="bed" /> 222 <when input="outputFormat" value="bed" format="bed" />
220 <when input="outputFormat" value="bedAnn" format="bed" /> 223 <when input="outputFormat" value="bedAnn" format="bed" />
221 </change_format> 224 </change_format>
222 </data> 225 </data>
223 <data format="html" name="statsFile"> 226 <data format="html" name="statsFile" label="{tool.name} on ${on_string} Summary Report" from_work_dir="snpeff_report">
224 <filter>generate_stats == True</filter> 227 <filter>generate_stats == True</filter>
225 </data> 228 </data>
226 </outputs> 229 </outputs>
227 <expand macro="stdio" /> 230 <expand macro="stdio" />
228 <tests> 231 <tests>