Mercurial > repos > bgruening > salmon
diff salmonquant.xml @ 13:e3d32471da11 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 30fe16f7d786e4b0c43b8333853fc56c59f6c664"
| author | bgruening |
|---|---|
| date | Sat, 25 Apr 2020 11:49:15 -0400 |
| parents | 4de6e2e40c7a |
| children | 49121db48873 |
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--- a/salmonquant.xml Tue Oct 15 12:01:08 2019 -0400 +++ b/salmonquant.xml Sat Apr 25 11:49:15 2020 -0400 @@ -1,4 +1,4 @@ -<tool id="salmon" name="Salmon quant" version="@VERSION@"> +<tool id="salmon" name="Salmon quant" version="@VERSION@+galaxy1"> <description>Perform dual-phase, reads or mapping-based estimation of transcript abundance from RNA-seq reads</description> <macros> <import>macros.xml</import> @@ -12,15 +12,11 @@ @salalign@ #end if @salquant@ - #if $quant_type.qtype == "reads": - #if $quant_type.writeMappings: - && samtools view -S -b ./output/samout.sam > ./output/bamout.bam - #end if + #if $quant_type.qtype == "reads" and $quant_type.writeMappings: + && @bam_sort@ ./output/samout.sam #end if - #if $quant_type.qtype == "alignment": - #if $quant_type.sampleOut: - && samtools sort -@ 4 -o ./output/postSample_sorted.bam ./output/postSample.bam - #end if + #if $quant_type.qtype == "alignment" and $quant_type.sampleOut: + && @bam_sort@ ./output/postSample.bam #end if ]]> </command> @@ -48,7 +44,7 @@ <data name="output_bam" format="bam" from_work_dir="output/bamout.bam" label="${tool.name} on ${on_string} (BAM format)"> <filter>quant_type['qtype'] == "reads" and quant_type['writeMappings']</filter> </data> - <data name="postSample" format="bam" from_work_dir="./output/postSample_sorted.bam" label="Sampled input alignments on ${on_string}(BAM format)"> + <data name="postSample" format="bam" from_work_dir="output/bamout.bam" label="Sampled input alignments on ${on_string}(BAM format)"> <filter>quant_type['qtype'] == "alignment" and quant_type['sampleOut']</filter> </data> </outputs>