Mercurial > repos > jjohnson > arriba
diff arriba.xml @ 12:73fd7703a743 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit fe2e3c7429c5bea23690a27b5889b502984ad58a"
| author | jjohnson |
|---|---|
| date | Tue, 26 Apr 2022 20:35:35 +0000 |
| parents | 8ed8af5836d1 |
| children | 1d459aaa5765 |
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--- a/arriba.xml Tue Apr 26 20:21:29 2022 +0000 +++ b/arriba.xml Tue Apr 26 20:35:35 2022 +0000 @@ -13,6 +13,30 @@ <expand macro="version_command" /> <command detect_errors="exit_code"><![CDATA[ @GENOME_SOURCE@ +#if $blacklist + #if $blacklist.is_of_type('tabular.gz') + #set $blacklist_file = 'blacklist.tsv.gz' + ln -sf '$blacklist' $blacklist_file && + #else + #set $blacklist_file = $blacklist + #end if +#end if +#if $known_fusions + #if $known_fusions.is_of_type('tabular.gz') + #set $known_fusions_file = 'known_fusions.tsv.gz' + ln -sf '$known_fusions' $known_fusions_file && + #else + #set $known_fusions_file = $known_fusions + #end if +#end if +#if $tags + #if $tags.is_of_type('tabular.gz') + #set $tags_file = 'tags.tsv.gz' + ln -sf '$tags' $tags_file && + #else + #set $tags_file = $tags + #end if +#end if #if str($input_params.input_source) == "use_fastq" #set $readFilesCommand = '' #set $read2 = '' @@ -45,30 +69,6 @@ #else #set $star_index_dir = $input_params.index.arriba_ref.fields.star_index #end if - #if $blacklist - #if $blacklist.is_of_type('tabular.gz') - #set $blacklist_file = 'blacklist.tsv.gz' - ln -sf '$blacklist' $blacklist_file && - #else - #set $blacklist_file = $blacklist - #end if - #end if - #if $known_fusions - #if $known_fusions.is_of_type('tabular.gz') - #set $known_fusions_file = 'known_fusions.tsv.gz' - ln -sf '$known_fusions' $known_fusions_file && - #else - #set $known_fusions_file = $known_fusions - #end if - #end if - #if $tags - #if $tags.is_of_type('tabular.gz') - #set $tags_file = 'tags.tsv.gz' - ln -sf '$tags' $tags_file && - #else - #set $tags_file = $tags - #end if - #end if STAR --runThreadN \${GALAXY_SLOTS:-1}