Mercurial > repos > iuc > snpeff
changeset 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 | f0ee2b470481 |
| children | 479c4f2f4826 |
| files | snpEff.xml |
| diffstat | 1 files changed, 13 insertions(+), 3 deletions(-) [+] |
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--- a/snpEff.xml Sat Apr 07 15:46:09 2018 -0400 +++ b/snpEff.xml Tue Jun 12 17:31:21 2018 -0400 @@ -47,6 +47,9 @@ #if $statsFile: -stats '$statsFile' #end if + #if $csvStats: + -csvStats '$csvFile' + #end if #if str($offset) != 'default': ${offset} #end if @@ -87,7 +90,11 @@ #if $statsFile: && #import os - #set $genes_file = str($statsFile) + '.genes.txt' + #if $csvStats: + #set $genes_file = str($csvFile) + '.genes.txt' + #else + #set $genes_file = str($statsFile) + '.genes.txt' + #end if #set $genes_file_name = os.path.split($genes_file)[-1] mkdir '$statsFile.files_path' && mv '$genes_file' '#echo os.path.join($statsFile.files_path, $genes_file_name)#' @@ -120,7 +127,7 @@ <when value="bed" /> <when value="bedAnn" /> </conditional> - + <param name="csvStats" type="boolean" truevalue="-csvStats" falsevalue="" checked="false" label="Create CSV report, useful for downstream analysis (-csvStats)" /> <conditional name="snpDb"> <param name="genomeSrc" type="select" label="Genome source"> <!-- These options are referenced in the help section of SnpEff download tool. If you change them, change help of SnpEff download as well --> @@ -352,9 +359,12 @@ <when input="outputConditional.outputFormat" value="bedAnn" format="bed" /> </change_format> </data> - <data name="statsFile" format="html" label="${tool.name} on ${on_string} - stats"> + <data name="statsFile" format="html" label="${tool.name} on ${on_string} - HTML stats"> <filter>generate_stats == True</filter> </data> + <data name="csvFile" format="csv" label="${tool.name} on ${on_string} - CSV stats"> + <filter>csvStats == True</filter> + </data> </outputs> <tests> <test>