comparison qualimap_bamqc.xml @ 5:30a201c9c310 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit 25200b2c00364b3d371c14cb4624b246446e548b

4:19ece8afbaab

<tool id="qualimap_bamqc" name="QualiMap BamQC" version="@VERSION@+galaxy3">
    <macros>
        <import>qualimap_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <command detect_errors="exit_code"><![CDATA[
        #import os
        #import re

            mv $coverage_file '$output_per_base_coverage' &&
        #end if
        @MASSAGE_OUTPUT@
    ]]></command>
    <inputs>
        <param argument="-bam" name="input1" type="data" format="bam"
        label="Mapped reads input dataset" />
        <conditional name="stats_regions">
            <param name="region_select" type="select" label="Reference genome regions to calculate mapping statistics for">
                <option value="all">All (whole genome)</option>
                <option value="custom_regions">Select regions</option>
            </param>
            <when value="all" />
            <when value="custom_regions">
                <param argument="-gff" name="regions" type="data" format="gff,gtf,bed"
                label="Dataset specifying regions" />
                <param argument="-os" name="outside_stats" type="boolean" truevalue="--outside-stats" falsevalue="" checked="false"
                label="Invert regions"
                help="If selected, report read statistics *outside* the regions in the regions file." />
            </when>
        </conditional>
        <param argument="-oc" name="per_base_coverage" type="boolean" truevalue="--output-genome-coverage" falsevalue="" checked="false"
        label="Generate per-base coverage output"
        help="Produce additional tabular output listing the coverage at every site (omitting only zero-coverage positions) in the selected regions of the genome. Caution: Will generate a huge dataset for anything but small input genomes or restricted regions!" />
        <param argument="--skip-dup-mode" name="duplicate_skipping" type="select" display="checkboxes" multiple="true" optional="true"
        label="Skip duplicate reads">
            <option value="0" selected="true">Reads flagged as duplicates in input</option>
            <option value="1">Duplicates detected by Qualimap</option>
        </param>
        <section name="plot_specific" title="Settings affecting specific plots" expanded="false">
            <param argument="-nw" name="n_bins" type="integer" value="400"
            label="Number of bins to use in across-reference plots"
            help="Affected plots: Coverage, Mapping Quality and Insert Size across reference, Mapped reads GC-content distribution; the value determines the resolution of the affected plots. Note: The lower the value, the higher the memory usage of the tool!" />
            <param argument="-c" name="paint_chromosome_limits" type="boolean" truevalue="--paint-chromosome-limits" falsevalue="" checked="true"
            label="Draw chromosome limits"
            help="Affected plots: Coverage, Mapping Quality and Insert Size across reference; in across-reference plots, indicate chromosome boundaries with dotted lines and labels" />
            <param argument="-gd" name="genome_gc_distr" type="select" optional="true"
            label="Plot expected GC-content distribution of the following reference genome"
            help="Affected plot: Mapped reads GC-content distribution; include a precalculated GC-content distribution for the selected (Qualimap-supported) reference genome in the plot">
                <option value="hg19">Human genome (hg19)</option>
                <option value="mm9">Mouse genome (mm9)</option>
                <option value="mm10">Mouse genome (mm10)</option>
            </param>
            <param argument="-hm" name="homopolymer_size" type="integer" value="3" min="2"
            label="Homopolymer size"
            help="Affected plot: Homopolymer indels; sets the minimal number of consecutive bases that define a homopolymer" />
        </section>
    </inputs>
    <outputs>
        <data name="output_html" format="html"
        label="${tool.name} report on ${on_string}" />
        <data name="output_per_base_coverage" format="tsv"
        label="${tool.name} per-base coverage on ${on_string}">
            <filter>per_base_coverage</filter>
        </data>
        <collection name="raw_data" type="list"
        label="Raw data for ${tool.name} on ${on_string}">
            <data name="genome_results" format="txt" from_work_dir="results/summary_report.txt" />
            <data name="coverage_across_reference" format="tsv" from_work_dir="results/coverage_across_reference.txt" />
            <data name="coverage_histogram" format="tsv" from_work_dir="results/coverage_histogram.txt" />
            <data name="genome_fraction_coverage" format="tsv" from_work_dir="results/genome_fraction_coverage.txt" />
            <data name="duplication_rate_histogram" format="tsv" from_work_dir="results/duplication_rate_histogram.txt" />

5:30a201c9c310

<tool id="qualimap_bamqc" name="QualiMap BamQC" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
    <macros>
        <import>qualimap_macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <command detect_errors="exit_code"><![CDATA[
        #import os
        #import re

            mv $coverage_file '$output_per_base_coverage' &&
        #end if
        @MASSAGE_OUTPUT@
    ]]></command>
    <inputs>
        <param name="input1" argument="-bam" type="data" format="bam" label="Mapped reads input dataset" />
        <conditional name="stats_regions">
            <param name="region_select" type="select" label="Reference genome regions to calculate mapping statistics for">
                <option value="all">All (whole genome)</option>
                <option value="custom_regions">Select regions</option>
            </param>
            <when value="all" />
            <when value="custom_regions">
                <param name="regions" argument="-gff" type="data" format="gff,gtf,bed" label="Dataset specifying regions" />
                <param name="outside_stats" argument="-os" type="boolean" truevalue="--outside-stats" falsevalue="" checked="false" label="Invert regions" help="If selected, report read statistics *outside* the regions in the regions file." />
            </when>
        </conditional>
        <param name="per_base_coverage" argument="-oc" type="boolean" truevalue="--output-genome-coverage" falsevalue="" checked="false" label="Generate per-base coverage output" help="Produce additional tabular output listing the coverage at every site (omitting only zero-coverage positions) in the selected regions of the genome. Caution: Will generate a huge dataset for anything but small input genomes or restricted regions!" />
        <param name="duplicate_skipping" argument="--skip-dup-mode" type="select" optional="true" label="Skip duplicate reads" display="checkboxes" multiple="true">
            <option value="0" selected="true">Reads flagged as duplicates in input</option>
            <option value="1">Duplicates detected by Qualimap</option>
        </param>
        <section name="plot_specific" title="Settings affecting specific plots" expanded="false">
            <param name="n_bins" argument="-nw" type="integer" value="400" label="Number of bins to use in across-reference plots" help="Affected plots: Coverage, Mapping Quality and Insert Size across reference, Mapped reads GC-content distribution; the value determines the resolution of the affected plots. Note: The lower the value, the higher the memory usage of the tool!" />
            <param name="paint_chromosome_limits" argument="-c" type="boolean" truevalue="--paint-chromosome-limits" falsevalue="" checked="true" label="Draw chromosome limits" help="Affected plots: Coverage, Mapping Quality and Insert Size across reference; in across-reference plots, indicate chromosome boundaries with dotted lines and labels" />
            <param name="genome_gc_distr" argument="-gd" type="select" optional="true" label="Plot expected GC-content distribution of the following reference genome" help="Affected plot: Mapped reads GC-content distribution; include a precalculated GC-content distribution for the selected (Qualimap-supported) reference genome in the plot">
                <option value="hg19">Human genome (hg19)</option>
                <option value="mm9">Mouse genome (mm9)</option>
                <option value="mm10">Mouse genome (mm10)</option>
            </param>
            <param name="homopolymer_size" argument="-hm" type="integer" min="2" value="3" label="Homopolymer size" help="Affected plot: Homopolymer indels; sets the minimal number of consecutive bases that define a homopolymer" />
        </section>
    </inputs>
    <outputs>
        <data name="output_html" format="html" label="${tool.name} report on ${on_string}" />
        <data name="output_per_base_coverage" format="tsv" label="${tool.name} per-base coverage on ${on_string}">
            <filter>per_base_coverage</filter>
        </data>
        <collection name="raw_data" type="list" label="Raw data for ${tool.name} on ${on_string}">
            <data name="genome_results" format="txt" from_work_dir="results/summary_report.txt" />
            <data name="coverage_across_reference" format="tsv" from_work_dir="results/coverage_across_reference.txt" />
            <data name="coverage_histogram" format="tsv" from_work_dir="results/coverage_histogram.txt" />
            <data name="genome_fraction_coverage" format="tsv" from_work_dir="results/genome_fraction_coverage.txt" />
            <data name="duplication_rate_histogram" format="tsv" from_work_dir="results/duplication_rate_histogram.txt" />