Mercurial > repos > iuc > kallisto_quant
changeset 8:c971db6f0fe5 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit c657f8cc0308cd70b26e3b111e5d8008901cda24"
| author | iuc |
|---|---|
| date | Sun, 18 Jul 2021 17:54:19 +0000 |
| parents | 40985510cd98 |
| children | 2568a3b975cb |
| files | kallisto_quant.xml macros.xml test-data/kallisto_quant_out4.bam test-data/kallisto_quant_out5.bam |
| diffstat | 4 files changed, 8 insertions(+), 7 deletions(-) [+] |
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--- a/kallisto_quant.xml Tue Apr 06 21:07:57 2021 +0000 +++ b/kallisto_quant.xml Sun Jul 18 17:54:19 2021 +0000 @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="kallisto_quant" name="Kallisto quant" version="@VERSION@.4"> +<tool id="kallisto_quant" name="Kallisto quant" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05"> <description>- quantify abundances of RNA-Seq transcripts</description> <macros> <import>macros.xml</import> @@ -40,7 +40,7 @@ $reads #end if #if $pseudobam: - | samtools sort -O bam -@ \${GALAXY_SLOTS:-1} -T "\${TMPDIR:-.}" -o '$pseudobam_output' - + && samtools sort --no-PG -O bam -@ \${GALAXY_SLOTS:-1} -T "\${TMPDIR:-.}" -o '$pseudobam_output' pseudoalignments.bam #end if && cat run_info.json ]]> @@ -148,7 +148,7 @@ <param name="forward" ftype="fastq" value="felCat8_chrM_F.fq" /> <param name="reverse" ftype="fastq" value="felCat8_chrM_R.fq" /> <output name="abundance_tab" file="kallisto_quant_out4.tab" ftype="tabular" /> - <output name="pseudobam_output" file="kallisto_quant_out4.bam" ftype="bam" /> + <output name="pseudobam_output" file="kallisto_quant_out4.bam" ftype="bam" lines_diff="2"/> </test> <test> <param name="reference_transcriptome_source" value="cached" /> @@ -158,7 +158,7 @@ <param name="forward" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_F.fq.gz" /> <param name="reverse" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_R.fq" /> <output name="abundance_tab" file="kallisto_quant_out5.tab" ftype="tabular" /> - <output name="pseudobam_output" file="kallisto_quant_out5.bam" ftype="bam" /> + <output name="pseudobam_output" file="kallisto_quant_out5.bam" ftype="bam" lines_diff="2"/> </test> <test> <param name="reference_transcriptome_source" value="history" />
--- a/macros.xml Tue Apr 06 21:07:57 2021 +0000 +++ b/macros.xml Sun Jul 18 17:54:19 2021 +0000 @@ -1,10 +1,11 @@ <?xml version="1.0"?> <macros> - <token name="@VERSION@">0.46.0</token> + <token name="@TOOL_VERSION@">0.46.2</token> + <token name="@VERSION_SUFFIX@">0</token> <xml name="requirements"> <requirements> - <requirement type="package" version="@VERSION@">kallisto</requirement> - <requirement type="package" version="1.9">samtools</requirement> + <requirement type="package" version="@TOOL_VERSION@">kallisto</requirement> + <requirement type="package" version="1.12">samtools</requirement> </requirements> </xml> <xml name="citations">