comparison scpipe.xml @ 1:4ec6717872b1 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit ffcc4ba8dcf01fd19bee6d946f9789bcf4ed680a

0:32e1bfc6b7b2

#if $ref_fasta.fasta_source == "history":
    #set $fasta_name = re.sub('[^\w\-\s]', '_', str($ref_fasta.ref_fa_hist.element_identifier))
    ln -s '$ref_fasta.ref_fa_hist' '$fasta_name' &&
#else:
    #set $fasta_name = re.sub('[^\w\-\s]', '_', str($ref_fasta.ref_fa_builtin.element_identifier))
    ln -s '$ref_fasta.ref_fa_builtin.fields.path' '$fasta_name' &&
#end if

#set $anno_name = re.sub('[^\w\-\s]', '_', str($exons.element_identifier))
#set $anno_name = $anno_name + ".gff3"

        <param name="rscript" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Output Rscript?" help="If this option is set to Yes, the Rscript used to annotate the IDs will be provided as a text file in the output. Default: No" />
        <param name="rdata" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output RData file?"
            help="Output all the data used by R to construct the tables and plots, can be loaded into R. Default: No">
        </param>
        <section name="adv" title="Advanced Options">
            <param argument="--rmlow" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Remove reads with N in barcode or UMI. Default: Yes" />
            <param argument="--rmN" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Remove reads with low quality. Default: Yes" />
            <param argument="--minq" type="integer" min="0" value="20" label="Minimum read quality. Default: 20" />
            <param argument="--numbq" type="integer" min="0" value="2" label="Maximum number of bases below minq. Default: 2" />
            <param argument="--stnd" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Perform strand-specific mapping. Default: Yes" />
            <param argument="--max_mis" type="integer" min="0" value="1" label="Maximum mismatch allowed in barcode. Default: 1" />
            <param argument="--UMI_cor" type="integer" min="0" value="1" label="Correct UMI sequence error" help="0 means no correction, 1 means simple correction and merge UMI with distance 1. Default: 1" />
            <param argument="--gene_fl" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Remove low abundant genes" help="Low abundant is defined as only one copy of one UMI for this gene. Default: No" />
            <param argument="--max_reads" type="integer" min="0" value="1000000" label="Maximum reads processed" help="Maximum reads processed if detecting barcodes. Default: 1,000,000" />
            <param argument="--min_count" type="integer" min="0" value="10" label="Minimum count to keep" help="Minimum count to keep if detecting barcodes. Barcode will be discarded if it has lower count. This should be set according to --max_reads. Default: 10" />
        </section>

                <assert_contents>
                    <has_text text="scPipe report for sample" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
.. class:: infomark

**What it does**

1:4ec6717872b1

#if $ref_fasta.fasta_source == "history":
    #set $fasta_name = re.sub('[^\w\-\s]', '_', str($ref_fasta.ref_fa_hist.element_identifier))
    ln -s '$ref_fasta.ref_fa_hist' '$fasta_name' &&
#else:
    #set $fasta_name = os.path.basename(str($ref_fasta.ref_fa_builtin.fields.path))
    ln -s '$ref_fasta.ref_fa_builtin.fields.path' '$fasta_name' &&
#end if

#set $anno_name = re.sub('[^\w\-\s]', '_', str($exons.element_identifier))
#set $anno_name = $anno_name + ".gff3"

        <param name="rscript" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Output Rscript?" help="If this option is set to Yes, the Rscript used to annotate the IDs will be provided as a text file in the output. Default: No" />
        <param name="rdata" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output RData file?"
            help="Output all the data used by R to construct the tables and plots, can be loaded into R. Default: No">
        </param>
        <section name="adv" title="Advanced Options">
            <param argument="--rmlow" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Remove reads with N in barcode or UMI" help="Default: Yes" />
            <param argument="--rmN" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Remove reads with low quality" help="Default: Yes" />
            <param argument="--minq" type="integer" min="0" value="20" label="Minimum read quality" help="Default: 20" />
            <param argument="--numbq" type="integer" min="0" value="2" label="Maximum number of bases below minq" help="Default: 2" />
            <param argument="--stnd" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Perform strand-specific mapping" help="Default: Yes" />
            <param argument="--max_mis" type="integer" min="0" value="1" label="Maximum mismatch allowed in barcode" help="Default: 1" />
            <param argument="--UMI_cor" type="integer" min="0" value="1" label="Correct UMI sequence error" help="0 means no correction, 1 means simple correction and merge UMI with distance 1. Default: 1" />
            <param argument="--gene_fl" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Remove low abundant genes" help="Low abundant is defined as only one copy of one UMI for this gene. Default: No" />
            <param argument="--max_reads" type="integer" min="0" value="1000000" label="Maximum reads processed" help="Maximum reads processed if detecting barcodes. Default: 1,000,000" />
            <param argument="--min_count" type="integer" min="0" value="10" label="Minimum count to keep" help="Minimum count to keep if detecting barcodes. Barcode will be discarded if it has lower count. This should be set according to --max_reads. Default: 10" />
        </section>

                <assert_contents>
                    <has_text text="scPipe report for sample" />
                </assert_contents>
            </output>
        </test>
        <!-- Ensure built-in fasta works -->
        <test>
            <param name="fasta_source" value="cached"/>
            <param name="exons" ftype="gff3" value="mm10_MT19.gff3.gz"/>
            <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"/>
            <param name="max_reads" value="5000000"/>
            <param name="min_count" value="100"/>
            <param name="report" value="False" />
            <output name="out_matrix" >
                <assert_contents>
                    <has_text text="ENSMUSG00000064351" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
.. class:: infomark

**What it does**