comparison scpipe.xml @ 4:3ffca09599ca draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit c2ca988fbdfb512e79e78afb941e1e78de8294d7"

3:7397e6badc11

<tool id="scpipe" name="scPipe" version="1.0.0+galaxy1">
    <description>- preprocessing pipeline for single cell RNA-seq</description>
    <requirements>
        <requirement type="package" version="1.0.0">bioconductor-scpipe</requirement>
        <requirement type="package" version="1.28.1">bioconductor-rsubread</requirement>
        <!-- rhtslib can be removed with a newer scpipe package -->

#end if

TAB=\$(printf '\t') &&

#if $samples.barcodes:
    sed -i.bak -e "s/\${TAB}/,/g" '$samples.barcodes' &&
#end if

## Run scPipe

Rscript '$__tool_directory__/scpipe.R'

#if $samples.format_select == "bam":
    --bam '$bam_name'
    --samplename '$bam_name'
    --barcodes '$samples.barcodes'
#else:
    --fasta '$fasta_name'
    --read1 '$in1_name'
    --read2 '$in2_name'
    --samplename '$in1_name'
    #if $barcodes:
        --barcodes '$samples.barcodes'
    #end if
#end if

--exons '$anno_name'
--organism '$organism'

    <tests>
        <!-- Ensure outputs work -->
        <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="organism" value="mmusculus_gene_ensembl"/>
            <param name="paired_format_selector" value="paired" />
            <param name="in1" ftype="fastqsanger.gz" value="CB51_MT19_R1.gz"/>
            <param name="in2" ftype="fastqsanger.gz" value="CB51_MT19_R2.gz"/>
            <param name="us" value="-1"/>

        </test>
        <!-- Ensure built-in fasta works -->
        <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="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"/>
            <param name="in2" ftype="fastqsanger.gz" dbkey="mm10" value="CB51_MT19_R2.gz"/>
            <param name="us" value="-1"/>

        <!-- Ensure BAM input works -->
        <test>
            <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="organism" value="mmusculus_gene_ensembl"/>
            <param name="us" value="-1"/>
            <output name="out_matrix" >
                <assert_contents>
                    <has_text text="ENSMUSG00000064351" />

        <!-- Ensure BAM input with QC outputs works -->
        <test>
            <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="organism" value="mmusculus_gene_ensembl"/>
            <param name="us" value="-1"/>
            <param name="plots" value="True"/>
            <param name="metrics_matrix" value="True"/>
            <output name="out_matrix" >

4:3ffca09599ca

<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>
        <requirement type="package" version="1.28.1">bioconductor-rsubread</requirement>
        <!-- rhtslib can be removed with a newer scpipe package -->

#end if

TAB=\$(printf '\t') &&

#if $samples.barcodes:
    sed -e "s/\${TAB}/,/g" '$samples.barcodes' > samples.barcodes &&
#end if

## Run scPipe

Rscript '$__tool_directory__/scpipe.R'

#if $samples.format_select == "bam":
    --bam '$bam_name'
    --samplename '$bam_name'
    --barcodes 'samples.barcodes'
#else:
    --fasta '$fasta_name'
    --read1 '$in1_name'
    --read2 '$in2_name'
    --samplename '$in1_name'
    #if $samples.barcodes:
        --barcodes 'samples.barcodes'
    #end if
#end if

--exons '$anno_name'
--organism '$organism'

    <tests>
        <!-- Ensure outputs work -->
        <test>
            <param name="format_select" value="fastq" />
            <param name="fasta_source" value="history"/>
            <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"/>
            <param name="in2" ftype="fastqsanger.gz" value="CB51_MT19_R2.gz"/>
            <param name="us" value="-1"/>

        </test>
        <!-- Ensure built-in fasta works -->
        <test>
            <param name="format_select" value="fastq" />
            <param name="fasta_source" value="cached"/>
            <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"/>
            <param name="in2" ftype="fastqsanger.gz" dbkey="mm10" value="CB51_MT19_R2.gz"/>
            <param name="us" value="-1"/>

        <!-- Ensure BAM input works -->
        <test>
            <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.gz" value="mm10_MT19.gff3.gz"/>
            <param name="organism" value="mmusculus_gene_ensembl"/>
            <param name="us" value="-1"/>
            <output name="out_matrix" >
                <assert_contents>
                    <has_text text="ENSMUSG00000064351" />

        <!-- Ensure BAM input with QC outputs works -->
        <test>
            <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.gz" value="mm10_MT19.gff3.gz"/>
            <param name="organism" value="mmusculus_gene_ensembl"/>
            <param name="us" value="-1"/>
            <param name="plots" value="True"/>
            <param name="metrics_matrix" value="True"/>
            <output name="out_matrix" >