comparison alevin.xml @ 10:e4c01dcece8b draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"

9:ecb9ea6269ee

<tool id="alevin" name="Alevin" version="@VERSION@+galaxy2">
    <description>Quantification and analysis of 3’ tagged-end single-cell sequencing data</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>

        #end if

        && ln -s '${tgmap}' ./alevinmap.tsv
        && salmon alevin -l
        #if $pairstraight.readselect == 'paired':
            ${pairstraight.orientation}${pairstraight.strandedness}
            -i $index_path
            -1 ./mate1.fastq
            -2 ./mate2.fastq
        #else:
            '${pairstraight.strandedness}'
            -i $index_path
            -r zcat ./unmate.fastq
        #end if
        -o ./output
        -p "\${GALAXY_SLOTS:-4}"

                <option value="unmated">Single-end</option>
            </param>
            <when value="paired">
                <param name="file1" type="data" format="fastq,fastq.gz,fastqsanger.gz,fastq.bz2" help="CB+UMI raw sequence file(s)"/>
                <param name="file2" type="data" format="fastq,fastq.gz,fastqsanger.gz,fastq.bz2" help="Read-sequence file(s)"/>
                <expand macro="orient"/>
                <expand macro="stranded"/>
            </when>
            <when value="unmated">
                <param name="unmatedreads" type="data" format="fastq,fastq.gz,fastqsanger.gz,fastq.bz2" label="Unmated reads files"/>
                <expand macro="stranded"/>
            </when>
        </conditional>
        <param name="protocol" type="select">
            <option value="--dropseq">DropSeq Single Cell protocol</option>
            <option value="--chromium">10x chromium v2 Single Cell protocol</option>

            <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" label="quants_mat.mtx" format="mtx" from_work_dir="output/alevin/quants_mat.mtx">
            <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" label="quants_tier_mat" format="mtx" from_work_dir="output/alevin/quants_tier_mat"/>
        <data name="alevin.log" label="alevin.log" format="txt" from_work_dir="output/alevin/alevin.log">
            <filter>allout</filter>
        </data>
        <data name="featureDump.txt" label="featureDump.txt" format="txt" from_work_dir="output/alevin/featureDump.txt"/>
        <data name="whitelist.txt" label="whitelist.txt" format="txt" from_work_dir="output/alevin/whitelist.txt"/>
        <data name="bfh.txt" label="bfh.txt" format="txt" from_work_dir="output/alevin/bfh.txt">
            <filter>optional["dumpBfh"]</filter>
        </data>
        <data name="quants_mean_mat" label="quants_mean_mat" format="mtx" from_work_dir="output/alevin/quants_mean_mat">
            <filter>optional["numCellBootstraps"]</filter>
        </data>
        <data name="quants_var_mat" label="quants_var_mat" format="mtx" from_work_dir="output/alevin/quants_var_mat">
            <filter>optional["numCellBootstraps"]</filter>
        </data>
        <data name="quants_boot_rows.txt" label="quants_boot_rows.txt" format="txt" from_work_dir="output/alevin/quants_boot_rows.txt">
            <filter>optional["numCellBootstraps"]</filter>
        </data>
        <data name="alevinmeta_info.json" format="json" label="meta_info.json" from_work_dir="output/aux_info/alevin_meta_info.json">
            <filter>allout</filter>
        </data>
        <data name="ambig_info.tsv" format="tsv" label="ambig_info.tsv" from_work_dir="output/aux_info/ambig_info.tsv">
            <filter>allout</filter>
        </data>
        <data name="meta_info.json" format="json" label="meta_info.json" from_work_dir="output/aux_info/meta_info.json">
            <filter>allout</filter>
        </data>
        <data name="expected_bias" format="txt" label="expected_bias" from_work_dir="output/aux_info/fld"/>
        <data name="observed_bias" format="txt" label="observed_bias" from_work_dir="output/aux_info/observed_bias"/>
        <data name="observed_bias_3p" format="txt" label="observed_bias_3p" from_work_dir="output/aux_info/observed_bias_3p"/>
        <data name="flenDist.txt" format="txt" label="flenDist.txt" from_work_dir="output/libParams/flenDist.txt"/>
        <data name="salmon_quant.log" format="txt" label="salmon_quant.log" from_work_dir="output/logs/salmon_quant.log">
            <filter>allout</filter>
        </data>
        <collection name="umigraphs" type="list" label="Umi graph PDFs">
            <filter>optional["dumpUmiGraph"]</filter>
            <discover_datasets pattern="__name_and_ext__" ext="pdf" directory="fixed"/>

                <param name="keepCBFraction" value="1"/>
                <param name="dumpFeatures" value="Yes"/>
                <param name="freqThreshold" value="5"/>
                <param name="dumpMtx" value="Yes"/>
            </section>
            <output name="quants_mat.mtx" file="alevin_mat.mtx" ftype="mtx"/>
        </test>
        <test expect_num_outputs="14">
            <conditional name="refTranscriptSource">
                <param name="TranscriptSource" value="history"/>
                <section name="s_index">

                <param name="dumpFeatures" value="Yes"/>
                <param name="numCellBootstraps" value="2"/>
                <param name="freqThreshold" value="5"/>
                <param name="dumpMtx" value="Yes"/>
            </section>
            <output name="quants_mat.mtx" file="alevin_mat.mtx" ftype="mtx"/>
        </test>
    </tests>
    <help><![CDATA[
        @salmonhelp@
        @alevinhelp@

10:e4c01dcece8b

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

        #end if

        && ln -s '${tgmap}' ./alevinmap.tsv
        && salmon alevin -l
        #if $pairstraight.readselect == 'paired':
            #if $pairstraight.libtype.strandedness == 'A'
                A
            #else
                ${pairstraight.libtype.orientation}${pairstraight.libtype.strandedness}
            #end if
            -i $index_path
            -1 ./mate1.fastq
            -2 ./mate2.fastq
        #else:
            '${pairstraight.libtype.strandedness}'
            -i $index_path
            -r zcat ./unmate.fastq
        #end if
        -o ./output
        -p "\${GALAXY_SLOTS:-4}"

                <option value="unmated">Single-end</option>
            </param>
            <when value="paired">
                <param name="file1" type="data" format="fastq,fastq.gz,fastqsanger.gz,fastq.bz2" help="CB+UMI raw sequence file(s)"/>
                <param name="file2" type="data" format="fastq,fastq.gz,fastqsanger.gz,fastq.bz2" help="Read-sequence file(s)"/>
                <expand macro="stranded_pe"/>
            </when>
            <when value="unmated">
                <param name="unmatedreads" type="data" format="fastq,fastq.gz,fastqsanger.gz,fastq.bz2" label="Unmated reads files"/>
                <expand macro="stranded_se"/>
            </when>
        </conditional>
        <param name="protocol" type="select">
            <option value="--dropseq">DropSeq Single Cell protocol</option>
            <option value="--chromium">10x chromium v2 Single Cell protocol</option>

            <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" label="quants_mat.mtx" format="mtx" from_work_dir="output/alevin/quants_mat.mtx">
            <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" label="quants_tier_mat" format="mtx" from_work_dir="output/alevin/quants_tier_mat"/>
        <data name="alevin_log" label="alevin.log" format="txt" from_work_dir="output/alevin/alevin.log">
            <filter>allout</filter>
        </data>
        <data name="featureDump_txt" label="featureDump.txt" format="txt" from_work_dir="output/alevin/featureDump.txt"/>
        <data name="whitelist_txt" label="whitelist.txt" format="txt" from_work_dir="output/alevin/whitelist.txt"/>
        <data name="bfh_txt" label="bfh.txt" format="txt" from_work_dir="output/alevin/bfh.txt">
            <filter>optional["dumpBfh"]</filter>
        </data>
        <data name="quants_mean_mat" label="quants_mean_mat" format="mtx" from_work_dir="output/alevin/quants_mean_mat">
            <filter>optional["numCellBootstraps"]</filter>
        </data>
        <data name="quants_var_mat" label="quants_var_mat" format="mtx" from_work_dir="output/alevin/quants_var_mat">
            <filter>optional["numCellBootstraps"]</filter>
        </data>
        <data name="quants_boot_rows_txt" label="quants_boot_rows.txt" format="txt" from_work_dir="output/alevin/quants_boot_rows.txt">
            <filter>optional["numCellBootstraps"]</filter>
        </data>
        <data name="alevinmeta_info_json" format="json" label="meta_info.json" from_work_dir="output/aux_info/alevin_meta_info.json">
            <filter>allout</filter>
        </data>
        <data name="ambig_info_tsv" format="tsv" label="ambig_info.tsv" from_work_dir="output/aux_info/ambig_info.tsv">
            <filter>allout</filter>
        </data>
        <data name="meta_info_json" format="json" label="meta_info.json" from_work_dir="output/aux_info/meta_info.json">
            <filter>allout</filter>
        </data>
        <data name="expected_bias" format="txt" label="expected_bias" from_work_dir="output/aux_info/fld"/>
        <data name="observed_bias" format="txt" label="observed_bias" from_work_dir="output/aux_info/observed_bias"/>
        <data name="observed_bias_3p" format="txt" label="observed_bias_3p" from_work_dir="output/aux_info/observed_bias_3p"/>
        <data name="flenDist_txt" format="txt" label="flenDist.txt" from_work_dir="output/libParams/flenDist.txt"/>
        <data name="salmon_quant_log" format="txt" label="salmon_quant.log" from_work_dir="output/logs/salmon_quant.log">
            <filter>allout</filter>
        </data>
        <collection name="umigraphs" type="list" label="Umi graph PDFs">
            <filter>optional["dumpUmiGraph"]</filter>
            <discover_datasets pattern="__name_and_ext__" ext="pdf" directory="fixed"/>

                <param name="keepCBFraction" value="1"/>
                <param name="dumpFeatures" value="Yes"/>
                <param name="freqThreshold" value="5"/>
                <param name="dumpMtx" value="Yes"/>
            </section>
            <output name="quants_mat_mtx" file="alevin_mat.mtx" ftype="mtx" sort="true" lines_diff="62"/>
        </test>
        <test expect_num_outputs="14">
            <conditional name="refTranscriptSource">
                <param name="TranscriptSource" value="history"/>
                <section name="s_index">

                <param name="dumpFeatures" value="Yes"/>
                <param name="numCellBootstraps" value="2"/>
                <param name="freqThreshold" value="5"/>
                <param name="dumpMtx" value="Yes"/>
            </section>
            <output name="quants_mat_mtx" file="alevin_mat.mtx" ftype="mtx" sort="true" lines_diff="62"/>
        </test>
    </tests>
    <help><![CDATA[
        @salmonhelp@
        @alevinhelp@