comparison nugen_nudup.xml @ 4:0d24a02c555f draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup commit 26045b518c15c3f18996f6dc2af7064a9c1941dd

3:2bad02c1cb0d

<tool id="nugen_nudup" name="NuDUP" version="2.3.3" profile="17.01">
    <description>
        mark/remove PCR duplicates based on molecular tags
    </description>
    <requirements>
        <requirement type="package" version="2.3.3">nudup</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />

        <param type="data" name="umi_fastq"
            label="Fastq file containing molecular tag sequence"
            format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" help="FASTQ
            file containing the molecular tag sequence for each read name in
            the corresponding SAM/BAM file" />
        <param type="boolean" argument="--paired-end"
            label="Paired-end deduping" name="paired_end"
            truevalue="--paired-end" falsevalue=""
            checked="false"
            help="use paired end deduping with template. SAM/BAM alignment
            must contain paired end reads. Degenerate read pairs
            (alignments for one read of pair) will be discarded." />
        <param type="integer" argument="--start" label="Tag sequence start
            position from 3' end" value="6" help="position in index read where
            molecular tag sequence begins. This should be a 1-based value that
            counts in from the 3' END of the read." />
        <param type="integer" argument="--length" label="Tag sequence length"
            value="6" help="length of molecular tag sequence" />
        <param type="boolean" argument="--rmdup-only" name="rmdup_only"
            label="Only output BAM with duplicates removed"
            truevalue="--rmdup-only" falsevalue="" checked="false"
            help="Do not ouput BAM with duplicates marked. Default is to ouput
            both marked duplicates and removed duplicates BAM files." />
    </inputs>

        <data format="txt" name="log"
              label="${tool.name} on ${on_string}: Log"
              from_work_dir="prefix_dup_log.txt" />
    </outputs>
    <tests>
        <test>
            <param name="input" value="nudup_test_1.bam" ftype="bam" />
            <param name="umi_fastq" value="nudup_umis.fastq"
                ftype="fastqsanger" />
            <param name="start" value="8" />
            <param name="length" value="8" />
            <output name="markdup" file="nudup_markdup_1.bam" ftype="bam" />
            <output name="dedup" file="nudup_dedup_1.bam" ftype="bam" />
            <output name="log" file="nudup_log_1.txt" ftype="txt" />
        </test>
        <test>
            <param name="input" value="nudup_test_1.bam" ftype="bam" />
            <param name="umi_fastq" value="nudup_umis.fastq.gz"
                ftype="fastqsanger.gz" />
            <param name="start" value="8" />
            <param name="length" value="8" />

4:0d24a02c555f

<tool id="nugen_nudup" name="NuDUP" version="2.3.3" profile="17.01">
    <description>
        mark/remove PCR duplicates based on molecular tags
    </description>
    <xrefs>
        <xref type="bio.tools">nudup</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="2.3.3">nudup</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />

        <param type="data" name="umi_fastq"
            label="Fastq file containing molecular tag sequence"
            format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" help="FASTQ
            file containing the molecular tag sequence for each read name in
            the corresponding SAM/BAM file" />
        <param type="boolean" argument="--paired-end" label="Paired-end deduping"
            truevalue="--paired-end" falsevalue="" checked="false"
            help="use paired end deduping with template. SAM/BAM alignment
            must contain paired end reads. Degenerate read pairs
            (alignments for one read of pair) will be discarded." />
        <param type="integer" argument="--start" label="Tag sequence start
            position from 3' end" value="6" help="position in index read where
            molecular tag sequence begins. This should be a 1-based value that
            counts in from the 3' END of the read." />
        <param type="integer" argument="--length" label="Tag sequence length"
            value="6" help="length of molecular tag sequence" />
        <param type="boolean" argument="--rmdup-only"
            label="Only output BAM with duplicates removed"
            truevalue="--rmdup-only" falsevalue="" checked="false"
            help="Do not ouput BAM with duplicates marked. Default is to ouput
            both marked duplicates and removed duplicates BAM files." />
    </inputs>

        <data format="txt" name="log"
              label="${tool.name} on ${on_string}: Log"
              from_work_dir="prefix_dup_log.txt" />
    </outputs>
    <tests>
        <test expect_num_outputs="3">
            <param name="input" value="nudup_test_1.bam" ftype="bam" />
            <param name="umi_fastq" value="nudup_umis.fastq"
                ftype="fastqsanger" />
            <param name="start" value="8" />
            <param name="length" value="8" />
            <output name="markdup" file="nudup_markdup_1.bam" ftype="bam" />
            <output name="dedup" file="nudup_dedup_1.bam" ftype="bam" />
            <output name="log" file="nudup_log_1.txt" ftype="txt" />
        </test>
        <test expect_num_outputs="3">
            <param name="input" value="nudup_test_1.bam" ftype="bam" />
            <param name="umi_fastq" value="nudup_umis.fastq.gz"
                ftype="fastqsanger.gz" />
            <param name="start" value="8" />
            <param name="length" value="8" />