| Previous changeset 4:19ece8afbaab (2020-05-20) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit 25200b2c00364b3d371c14cb4624b246446e548b |
|
modified:
qualimap_bamqc.xml qualimap_macros.xml |
| b |
| diff -r 19ece8afbaab -r 30a201c9c310 qualimap_bamqc.xml --- a/qualimap_bamqc.xml Wed May 20 15:56:11 2020 -0400 +++ b/qualimap_bamqc.xml Thu Jul 11 14:42:43 2024 +0000 |
| [ |
| @@ -1,7 +1,8 @@ -<tool id="qualimap_bamqc" name="QualiMap BamQC" version="@VERSION@+galaxy3"> +<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[ @@ -75,8 +76,7 @@ @MASSAGE_OUTPUT@ ]]></command> <inputs> - <param argument="-bam" name="input1" type="data" format="bam" - label="Mapped reads input dataset" /> + <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> @@ -84,49 +84,32 @@ </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." /> + <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 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"> + <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 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"> + <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 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" /> + <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 ${on_string}"> + <data name="output_html" format="html" label="${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}"> + <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" /> |
| b |
| diff -r 19ece8afbaab -r 30a201c9c310 qualimap_macros.xml --- a/qualimap_macros.xml Wed May 20 15:56:11 2020 -0400 +++ b/qualimap_macros.xml Thu Jul 11 14:42:43 2024 +0000 |
| b |
| @@ -1,5 +1,6 @@ <macros> - <token name="@VERSION@">2.2.2d</token> + <token name="@VERSION@">2.3</token> + <token name="@VERSION_SUFFIX@">0</token> <xml name="requirements"> <requirements> @@ -7,7 +8,11 @@ <yield /> </requirements> </xml> - + <xml name="bio_tools"> + <xrefs> + <xref type="bio.tools">qualimap</xref> + </xrefs> + </xml> <xml name="version_command"> <version_command>qualimap --help | grep 'QualiMap v.' | cut -d '.' -f 2-</version_command> </xml> |