| Previous changeset 7:25d207f7ff83 (2021-10-11) Next changeset 9:8c4c97fd0555 (2021-10-13) |
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Commit message:
"planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit f5af83950615d8c77a3a43cf45f5ddf46000701b" |
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modified:
arriba.xml |
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| diff -r 25d207f7ff83 -r 1a56888ddb7d arriba.xml --- a/arriba.xml Mon Oct 11 16:40:51 2021 +0000 +++ b/arriba.xml Mon Oct 11 19:00:45 2021 +0000 |
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| @@ -7,8 +7,10 @@ <expand macro="version_command" /> <command detect_errors="exit_code"><![CDATA[ #if str($input_params.input_source) == "use_fastq" + #set $readFilesCommand = '' #if $input_params.left_fq.is_of_type("fastq.gz"): #set read1 = 'input_1.fastq.gz' + #set $readFilesCommand = '--readFilesCommand zcat' #else: #set read1 = 'input_1.fastq' #end if @@ -27,7 +29,7 @@ --genomeDir $star_index_dir --genomeLoad NoSharedMemory --readFilesIn $read1 $read2 - --readFilesCommand zcat + $readFilesCommand --outStd BAM_Unsorted --outSAMtype BAM Unsorted --outSAMunmapped Within |