| Previous changeset 3:7397e6badc11 (2020-06-11) Next changeset 5:a3b3ec00bf8f (2021-02-26) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit c2ca988fbdfb512e79e78afb941e1e78de8294d7" |
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modified:
scpipe.xml |
| b |
| diff -r 7397e6badc11 -r 3ffca09599ca scpipe.xml --- a/scpipe.xml Thu Jun 11 07:18:37 2020 -0400 +++ b/scpipe.xml Fri Oct 16 14:38:33 2020 +0000 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="scpipe" name="scPipe" version="1.0.0+galaxy1"> +<tool id="scpipe" name="scPipe" version="1.0.0+galaxy2" profile="19.01"> <description>- preprocessing pipeline for single cell RNA-seq</description> <requirements> <requirement type="package" version="1.0.0">bioconductor-scpipe</requirement> @@ -74,7 +74,7 @@ TAB=\$(printf '\t') && #if $samples.barcodes: - sed -i.bak -e "s/\${TAB}/,/g" '$samples.barcodes' && + sed -e "s/\${TAB}/,/g" '$samples.barcodes' > samples.barcodes && #end if ## Run scPipe @@ -84,14 +84,14 @@ #if $samples.format_select == "bam": --bam '$bam_name' --samplename '$bam_name' - --barcodes '$samples.barcodes' + --barcodes 'samples.barcodes' #else: --fasta '$fasta_name' --read1 '$in1_name' --read2 '$in2_name' --samplename '$in1_name' - #if $barcodes: - --barcodes '$samples.barcodes' + #if $samples.barcodes: + --barcodes 'samples.barcodes' #end if #end if @@ -244,8 +244,8 @@ <test> <param name="format_select" value="fastq" /> <param name="fasta_source" value="history"/> - <param name="ref_fa_hist" ftype="fasta" value="mm10_MT19.fa.gz"/> - <param name="exons" ftype="gff3" value="mm10_MT19.gff3.gz"/> + <param name="ref_fa_hist" ftype="fasta.gz" value="mm10_MT19.fa.gz"/> + <param name="exons" ftype="gff3.gz" value="mm10_MT19.gff3.gz"/> <param name="organism" value="mmusculus_gene_ensembl"/> <param name="paired_format_selector" value="paired" /> <param name="in1" ftype="fastqsanger.gz" value="CB51_MT19_R1.gz"/> @@ -269,7 +269,7 @@ <test> <param name="format_select" value="fastq" /> <param name="fasta_source" value="cached"/> - <param name="exons" ftype="gff3" value="mm10_MT19.gff3.gz"/> + <param name="exons" ftype="gff3.gz" value="mm10_MT19.gff3.gz"/> <param name="organism" value="mmusculus_gene_ensembl"/> <param name="paired_format_selector" value="paired" /> <param name="in1" ftype="fastqsanger.gz" dbkey="mm10" value="CB51_MT19_R1.gz"/> @@ -288,7 +288,7 @@ <param name="format_select" value="bam" /> <param name="bam" ftype="bam" value="aligned.mapped.bam"/> <param name="barcodes" ftype="tabular" value="barcode_anno.tsv"/> - <param name="exons" ftype="gff3" value="mm10_MT19.gff3.gz"/> + <param name="exons" ftype="gff3.gz" value="mm10_MT19.gff3.gz"/> <param name="organism" value="mmusculus_gene_ensembl"/> <param name="us" value="-1"/> <output name="out_matrix" > @@ -302,7 +302,7 @@ <param name="format_select" value="bam" /> <param name="bam" ftype="bam" value="aligned.mapped.bam"/> <param name="barcodes" ftype="tabular" value="barcode_anno.tsv"/> - <param name="exons" ftype="gff3" value="mm10_MT19.gff3.gz"/> + <param name="exons" ftype="gff3.gz" value="mm10_MT19.gff3.gz"/> <param name="organism" value="mmusculus_gene_ensembl"/> <param name="us" value="-1"/> <param name="plots" value="True"/> |