Mercurial > repos > iuc > snpeff

comparison snpEff.xml @ 18:a9b0163b9fab draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 31abf30ef7abe008e23cb9eadd5268649a00035b
author iuc
date Tue, 12 Jun 2018 17:31:03 -0400
parents 7c4ede6d88a2
children 9939612ba3cf
comparison
equal deleted inserted replaced
17:32705945a08e 18:a9b0163b9fab
44 #if $intervals ### fix this for multiple dataset input 44 #if $intervals ### fix this for multiple dataset input
45 -interval '$intervals' 45 -interval '$intervals'
46 #end if 46 #end if
47 #if $statsFile: 47 #if $statsFile:
48 -stats '$statsFile' 48 -stats '$statsFile'
49 #end if
50 #if $csvStats:
51 -csvStats '$csvFile'
49 #end if 52 #end if
50 #if str($offset) != 'default': 53 #if str($offset) != 'default':
51 ${offset} 54 ${offset}
52 #end if 55 #end if
53 #if str($chr).strip() != '': 56 #if str($chr).strip() != '':
85 #end if 88 #end if
86 '$input' > '$snpeff_output' 89 '$input' > '$snpeff_output'
87 #if $statsFile: 90 #if $statsFile:
88 && 91 &&
89 #import os 92 #import os
90 #set $genes_file = str($statsFile) + '.genes.txt' 93 #if $csvStats:
94 #set $genes_file = str($csvFile) + '.genes.txt'
95 #else
96 #set $genes_file = str($statsFile) + '.genes.txt'
97 #end if
91 #set $genes_file_name = os.path.split($genes_file)[-1] 98 #set $genes_file_name = os.path.split($genes_file)[-1]
92 mkdir '$statsFile.files_path' && 99 mkdir '$statsFile.files_path' &&
93 mv '$genes_file' '#echo os.path.join($statsFile.files_path, $genes_file_name)#' 100 mv '$genes_file' '#echo os.path.join($statsFile.files_path, $genes_file_name)#'
94 #end if 101 #end if
95 #if $outputConditional.outputFormat == 'gatk' and $outputConditional.gatk_v1 102 #if $outputConditional.outputFormat == 'gatk' and $outputConditional.gatk_v1
118 <param name="gatk_v1" type="boolean" checked="true" label="Compatible with GATK 1.x" /> 125 <param name="gatk_v1" type="boolean" checked="true" label="Compatible with GATK 1.x" />
119 </when> 126 </when>
120 <when value="bed" /> 127 <when value="bed" />
121 <when value="bedAnn" /> 128 <when value="bedAnn" />
122 </conditional> 129 </conditional>
123 130 <param name="csvStats" type="boolean" truevalue="-csvStats" falsevalue="" checked="false" label="Create CSV report, useful for downstream analysis (-csvStats)" />
124 <conditional name="snpDb"> 131 <conditional name="snpDb">
125 <param name="genomeSrc" type="select" label="Genome source"> 132 <param name="genomeSrc" type="select" label="Genome source">
126 <!-- These options are referenced in the help section of SnpEff download tool. If you change them, change help of SnpEff download as well --> 133 <!-- These options are referenced in the help section of SnpEff download tool. If you change them, change help of SnpEff download as well -->
127 <option value="cached">Locally installed snpEff database</option> 134 <option value="cached">Locally installed snpEff database</option>
128 <option value="history">Downloaded snpEff database in your history</option> 135 <option value="history">Downloaded snpEff database in your history</option>
350 <change_format> 357 <change_format>
351 <when input="outputConditional.outputFormat" value="bed" format="bed" /> 358 <when input="outputConditional.outputFormat" value="bed" format="bed" />
352 <when input="outputConditional.outputFormat" value="bedAnn" format="bed" /> 359 <when input="outputConditional.outputFormat" value="bedAnn" format="bed" />
353 </change_format> 360 </change_format>
354 </data> 361 </data>
355 <data name="statsFile" format="html" label="${tool.name} on ${on_string} - stats"> 362 <data name="statsFile" format="html" label="${tool.name} on ${on_string} - HTML stats">
356 <filter>generate_stats == True</filter> 363 <filter>generate_stats == True</filter>
364 </data>
365 <data name="csvFile" format="csv" label="${tool.name} on ${on_string} - CSV stats">
366 <filter>csvStats == True</filter>
357 </data> 367 </data>
358 </outputs> 368 </outputs>
359 <tests> 369 <tests>
360 <test> 370 <test>
361 <param name="input" ftype="vcf" value="input.vcf"/> 371 <param name="input" ftype="vcf" value="input.vcf"/>