Mercurial > repos > bgruening > salmon
changeset 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 | 7fdb9d1591e2 |
| children | b265be7af3db |
| files | macros.xml salmonquant.xml |
| diffstat | 2 files changed, 9 insertions(+), 14 deletions(-) [+] |
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--- a/macros.xml Tue Oct 15 12:01:08 2019 -0400 +++ b/macros.xml Sat Apr 25 11:49:15 2020 -0400 @@ -4,12 +4,10 @@ <token name="@IDX_VERSION@">q6</token> <xml name="requirements"> <requirements> - <requirement type="package" version="1.0.6">bzip2</requirement> - <requirement type="package" version="1.2">seqtk</requirement> + <requirement type="package" version="1.3">seqtk</requirement> <requirement type="package" version="0.14.1">salmon</requirement> - <requirement type="package" version="1.9">samtools</requirement> + <requirement type="package" version="1.10">samtools</requirement> <requirement type="package" version="0.2.0">vpolo</requirement> - <requirement type="package" version="1.17.2">numpy</requirement> <requirement type="package" version="0.25.1">pandas</requirement> <requirement type="package" version="1.3.1">scipy</requirement> </requirements> @@ -286,6 +284,7 @@ <citation type="doi">10.1038/nmeth.4197</citation> </citations> </xml> + <token name="@bam_sort@"><![CDATA[samtools sort -@ \${GALAXY_SLOTS} --output-fmt=BAM -o ./output/bamout.bam]]></token> <token name="@indexing@"><![CDATA[ mkdir ./index && mkdir ./output &&
--- 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>