Mercurial > repos > iuc > snpeff
comparison snpEff.xml @ 14:85ca751407c3 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 31abf30ef7abe008e23cb9eadd5268649a00035b
| author | iuc |
|---|---|
| date | Tue, 12 Jun 2018 17:31:21 -0400 |
| parents | 5a29ab10dba6 |
| children | 65ae79bddc69 |
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| 13:f0ee2b470481 | 14:85ca751407c3 |
|---|---|
| 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"/> |