comparison alevin.xml @ 4:917f8e439160 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 5dfee8ad03865f59c3e1ac9dd5865fd40e4616ef"

3:0a5258e41227

<tool id="alevin" name="Alevin" version="@VERSION@">
    <description>Quantification and analysis of 3’ tagged-end single-cell sequencing data</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>

        #if $optional.lowRegionMinNumBarcodes:
            --lowregionMinNumBarcodes '${optional.lowRegionMinNumBarcodes}'
        #end if
        #if $optional.maxNumBarcodes:
            --maxNumBarcodes '${optional.maxNumBarcodes}'
        #end if

        #if $optional.dumpMtx != "--dumpMtx":
            && python '$__tool_directory__/vpolo_convert.py' -m
        #end if

            <param name="numCellBootstraps" type="integer" optional="true" help="Performs certain number of bootstrap and generate the mean and variance of the count matrix"/>
            <param name="minScoreFraction" type="float" optional="true" help="This value controls the minimum allowed score for a mapping to be considered valid. It matters only when --validateMappings has been passed to Salmon. The maximum possible score for a fragment is ms = read_len * ma (or ms = (left_read_len + right_read_len) * ma for paired-end reads). The argument to --minScoreFraction determines what fraction of the maximum score s a mapping must achieve to be potentially retained. For a minimum score fraction of f, only mappings with a score less than (f * s) will be kept. Mappings with lower scores will be considered as low-quality, and will be discarded."/>
            <param name="keepCBFraction" type="float" optional="true" help="Fraction of cellular barcodes to keep (Between 0 and 1)."/>
            <param name="lowRegionMinNumBarcodes" type="integer" optional="true" help="Minimum number of cell barcodes to use fo learning low confidence region (defaults to 200)"/>
            <param name="maxNumBarcodes" type="integer" optional="true" help="Maximum allowable limit to process the cell barcodes. Defaults to 100000"/>
        </section>
    </inputs>
    <outputs>
        <data name="quants_mat.tsv" label="quants_mat.tsv" format="txt" from_work_dir="quants_mat.tsv">
            <filter>optional["dumpMtx"] is not True</filter>
        </data>
        <data name="quants_mat.mtx.gz" label="quants_mat.mtx.gz" format="mtx" from_work_dir="output/alevin/quants_mat.mtx.gz">
            <filter>optional["dumpMtx"]</filter>
        </data>
        <data name="quants_mat_cols.txt" label="quants_mat_cols.txt" format="txt" from_work_dir="output/alevin/quants_mat_cols.txt"/>
        <data name="quants_mat_rows.txt" label="quants_mat_rows.txt" format="txt" from_work_dir="output/alevin/quants_mat_rows.txt"/>
        <data name="quants_tier_mat.gz" label="quants_tier_mat.gz" format="mtx" from_work_dir="output/alevin/quants_tier_mat.gz"/>
        <data name="alevin.log" label="alevin.log" format="txt" from_work_dir="output/alevin/alevin.log">

            <filter>optional["dumpUmiGraph"]</filter>
            <discover_datasets pattern="__name_and_ext__" ext="pdf" directory="fixed"/>
        </collection>
    </outputs>
    <tests>
        <test expect_num_outputs="10">
            <conditional name="refTranscriptSource">
                <param name="TranscriptSource" value="history"/>
                <section name="s_index">
                    <param name="fasta" value="minitranscript.fa"/>
                </section>

                <param name="strandedness" value="SR"/>
            </conditional>
            <param name="protocol" value="--chromium"/>
            <param name="tgmap" value="minitxp.tsv"/>
            <param name="dumpMtx" value="Yes"/>
            <output name="quants_mat.mtx.gz" file="alevin_mat.mtx.gz" ftype="mtx" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[
        @salmonhelp@

4:917f8e439160

<tool id="alevin" name="Alevin" version="@VERSION@+galaxy1">
    <description>Quantification and analysis of 3’ tagged-end single-cell sequencing data</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>

        #if $optional.lowRegionMinNumBarcodes:
            --lowregionMinNumBarcodes '${optional.lowRegionMinNumBarcodes}'
        #end if
        #if $optional.maxNumBarcodes:
            --maxNumBarcodes '${optional.maxNumBarcodes}'
        #end if
        #if $optional.freqThreshold:
            --freqThreshold '${optional.freqThreshold}'
        #end if

        #if $optional.dumpMtx != "--dumpMtx":
            && python '$__tool_directory__/vpolo_convert.py' -m
        #end if

            <param name="numCellBootstraps" type="integer" optional="true" help="Performs certain number of bootstrap and generate the mean and variance of the count matrix"/>
            <param name="minScoreFraction" type="float" optional="true" help="This value controls the minimum allowed score for a mapping to be considered valid. It matters only when --validateMappings has been passed to Salmon. The maximum possible score for a fragment is ms = read_len * ma (or ms = (left_read_len + right_read_len) * ma for paired-end reads). The argument to --minScoreFraction determines what fraction of the maximum score s a mapping must achieve to be potentially retained. For a minimum score fraction of f, only mappings with a score less than (f * s) will be kept. Mappings with lower scores will be considered as low-quality, and will be discarded."/>
            <param name="keepCBFraction" type="float" optional="true" help="Fraction of cellular barcodes to keep (Between 0 and 1)."/>
            <param name="lowRegionMinNumBarcodes" type="integer" optional="true" help="Minimum number of cell barcodes to use fo learning low confidence region (defaults to 200)"/>
            <param name="maxNumBarcodes" type="integer" optional="true" help="Maximum allowable limit to process the cell barcodes. Defaults to 100000"/>
            <param name="freqThreshold" type="integer" optional="true" help="Minimum frequency for a barcode to be considered. Defaults to 10"/>
        </section>
    </inputs>
    <outputs>
        <data name="quants_mat.tsv" label="quants_mat.tsv" format="txt" from_work_dir="quants_mat.tsv">
            <filter>optional["dumpMtx"] is not True</filter>
        </data>
        <data name="quants_mat.mtx.gz" label="quants_mat.mtx.gz" format="mtx" from_work_dir="output/alevin/quants_mat.mtx.gz">
            <filter>optional["dumpMtx"]</filter>
        </data>
        <data name="raw_cb_frequency.txt" label="raw_cb_frequency.txt" format="txt" from_work_dir="output/alevin/raw_cb_frequency.txt">
            <filter>optional["dumpFeatures"]</filter>
        </data>
        <data name="quants_mat_cols.txt" label="quants_mat_cols.txt" format="txt" from_work_dir="output/alevin/quants_mat_cols.txt"/>
        <data name="quants_mat_rows.txt" label="quants_mat_rows.txt" format="txt" from_work_dir="output/alevin/quants_mat_rows.txt"/>
        <data name="quants_tier_mat.gz" label="quants_tier_mat.gz" format="mtx" from_work_dir="output/alevin/quants_tier_mat.gz"/>
        <data name="alevin.log" label="alevin.log" format="txt" from_work_dir="output/alevin/alevin.log">

            <filter>optional["dumpUmiGraph"]</filter>
            <discover_datasets pattern="__name_and_ext__" ext="pdf" directory="fixed"/>
        </collection>
    </outputs>
    <tests>
        <test expect_num_outputs="11">
            <conditional name="refTranscriptSource">
                <param name="TranscriptSource" value="history"/>
                <section name="s_index">
                    <param name="fasta" value="minitranscript.fa"/>
                </section>

                <param name="strandedness" value="SR"/>
            </conditional>
            <param name="protocol" value="--chromium"/>
            <param name="tgmap" value="minitxp.tsv"/>
            <param name="dumpMtx" value="Yes"/>
            <param name="freqThreshold" value="5"/>
            <param name="dumpFeatures" value="Yes"/>
            <param name="keepCBFraction" value="1"/>
            <output name="quants_mat.mtx.gz" file="alevin_mat.mtx.gz" ftype="mtx" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[
        @salmonhelp@