Mercurial > repos > iuc > snpeff
comparison snpEff.xml @ 5:2950d5afa3fe draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
author | iuc |
---|---|
date | Mon, 05 Dec 2016 12:11:06 -0500 |
parents | 698ef30638a8 |
children | 7adfd0589f49 |
comparison
equal
deleted
inserted
replaced
4:698ef30638a8 | 5:2950d5afa3fe |
---|---|
88 mkdir $statsFile.files_path; | 88 mkdir $statsFile.files_path; |
89 mv "$genes_file" #echo os.path.join($statsFile.files_path, $genes_file_name)#; | 89 mv "$genes_file" #echo os.path.join($statsFile.files_path, $genes_file_name)#; |
90 #end if | 90 #end if |
91 #if $outputConditional.outputFormat == 'gatk' and $outputConditional.gatk_v1 | 91 #if $outputConditional.outputFormat == 'gatk' and $outputConditional.gatk_v1 |
92 ## Replace real SnpEff version with 2.0.5 to prevent this GATK 1.x error: "The version of SnpEff used to generate the SnpEff input file (x.x) is not currently supported by the GATK. Supported versions are: [2.0.5]" | 92 ## Replace real SnpEff version with 2.0.5 to prevent this GATK 1.x error: "The version of SnpEff used to generate the SnpEff input file (x.x) is not currently supported by the GATK. Supported versions are: [2.0.5]" |
93 sed -i -e 's/^\#\#SnpEffVersion="\(\S*\s\)/\#\#SnpEffVersion="2.0.5 - real is \1/' "$snpeff_output" | 93 sed -i.bak -e 's/^\#\#SnpEffVersion="\(\S*\s\)/\#\#SnpEffVersion="2.0.5 - real is \1/' "$snpeff_output" |
94 #end if | 94 #end if |
95 ]]> | 95 ]]> |
96 </command> | 96 </command> |
97 <inputs> | 97 <inputs> |
98 <param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/> | 98 <param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/> |
295 <param name="offset" type="select" display="radio" optional="true" label="Chromosomal position"> | 295 <param name="offset" type="select" display="radio" optional="true" label="Chromosomal position"> |
296 <option value="default" selected="true">Use default (based on input type)</option> | 296 <option value="default" selected="true">Use default (based on input type)</option> |
297 <option value="-0">Force zero-based positions (both input and output)</option> | 297 <option value="-0">Force zero-based positions (both input and output)</option> |
298 <option value="-1">Force one-based positions (both input and output)</option> | 298 <option value="-1">Force one-based positions (both input and output)</option> |
299 </param> | 299 </param> |
300 <param name="chr" type="text" optionl="true" label="Text to prepend to chromosome name"> | 300 <param name="chr" type="text" label="Text to prepend to chromosome name"> |
301 <help> | 301 <help> |
302 By default SnpEff simplifies all chromosome names. For instance 'chr1' is just '1'. | 302 By default SnpEff simplifies all chromosome names. For instance 'chr1' is just '1'. |
303 You can prepend any string you want to the chromosome name. | 303 You can prepend any string you want to the chromosome name. |
304 </help> | 304 </help> |
305 <validator type="regex" message="No whitespace allowed">^\S*$</validator> | 305 <validator type="regex" message="No whitespace allowed">^\S*$</validator> |