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

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit 25200b2c00364b3d371c14cb4624b246446e548b
author iuc
date Thu, 11 Jul 2024 14:42:43 +0000
parents 19ece8afbaab
children
comparison
equal deleted inserted replaced
4:19ece8afbaab 5:30a201c9c310
1 <tool id="qualimap_bamqc" name="QualiMap BamQC" version="@VERSION@+galaxy3"> 1 <tool id="qualimap_bamqc" name="QualiMap BamQC" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
2 <macros> 2 <macros>
3 <import>qualimap_macros.xml</import> 3 <import>qualimap_macros.xml</import>
4 </macros> 4 </macros>
5 <expand macro="bio_tools"/>
5 <expand macro="requirements" /> 6 <expand macro="requirements" />
6 <expand macro="version_command" /> 7 <expand macro="version_command" />
7 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
8 #import os 9 #import os
9 #import re 10 #import re
73 mv $coverage_file '$output_per_base_coverage' && 74 mv $coverage_file '$output_per_base_coverage' &&
74 #end if 75 #end if
75 @MASSAGE_OUTPUT@ 76 @MASSAGE_OUTPUT@
76 ]]></command> 77 ]]></command>
77 <inputs> 78 <inputs>
78 <param argument="-bam" name="input1" type="data" format="bam" 79 <param name="input1" argument="-bam" type="data" format="bam" label="Mapped reads input dataset" />
79 label="Mapped reads input dataset" />
80 <conditional name="stats_regions"> 80 <conditional name="stats_regions">
81 <param name="region_select" type="select" label="Reference genome regions to calculate mapping statistics for"> 81 <param name="region_select" type="select" label="Reference genome regions to calculate mapping statistics for">
82 <option value="all">All (whole genome)</option> 82 <option value="all">All (whole genome)</option>
83 <option value="custom_regions">Select regions</option> 83 <option value="custom_regions">Select regions</option>
84 </param> 84 </param>
85 <when value="all" /> 85 <when value="all" />
86 <when value="custom_regions"> 86 <when value="custom_regions">
87 <param argument="-gff" name="regions" type="data" format="gff,gtf,bed" 87 <param name="regions" argument="-gff" type="data" format="gff,gtf,bed" label="Dataset specifying regions" />
88 label="Dataset specifying regions" /> 88 <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." />
89 <param argument="-os" name="outside_stats" type="boolean" truevalue="--outside-stats" falsevalue="" checked="false"
90 label="Invert regions"
91 help="If selected, report read statistics *outside* the regions in the regions file." />
92 </when> 89 </when>
93 </conditional> 90 </conditional>
94 <param argument="-oc" name="per_base_coverage" type="boolean" truevalue="--output-genome-coverage" falsevalue="" checked="false" 91 <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!" />
95 label="Generate per-base coverage output" 92 <param name="duplicate_skipping" argument="--skip-dup-mode" type="select" optional="true" label="Skip duplicate reads" display="checkboxes" multiple="true">
96 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!" />
97 <param argument="--skip-dup-mode" name="duplicate_skipping" type="select" display="checkboxes" multiple="true" optional="true"
98 label="Skip duplicate reads">
99 <option value="0" selected="true">Reads flagged as duplicates in input</option> 93 <option value="0" selected="true">Reads flagged as duplicates in input</option>
100 <option value="1">Duplicates detected by Qualimap</option> 94 <option value="1">Duplicates detected by Qualimap</option>
101 </param> 95 </param>
102 <section name="plot_specific" title="Settings affecting specific plots" expanded="false"> 96 <section name="plot_specific" title="Settings affecting specific plots" expanded="false">
103 <param argument="-nw" name="n_bins" type="integer" value="400" 97 <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!" />
104 label="Number of bins to use in across-reference plots" 98 <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" />
105 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!" /> 99 <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">
106 <param argument="-c" name="paint_chromosome_limits" type="boolean" truevalue="--paint-chromosome-limits" falsevalue="" checked="true"
107 label="Draw chromosome limits"
108 help="Affected plots: Coverage, Mapping Quality and Insert Size across reference; in across-reference plots, indicate chromosome boundaries with dotted lines and labels" />
109 <param argument="-gd" name="genome_gc_distr" type="select" optional="true"
110 label="Plot expected GC-content distribution of the following reference genome"
111 help="Affected plot: Mapped reads GC-content distribution; include a precalculated GC-content distribution for the selected (Qualimap-supported) reference genome in the plot">
112 <option value="hg19">Human genome (hg19)</option> 100 <option value="hg19">Human genome (hg19)</option>
113 <option value="mm9">Mouse genome (mm9)</option> 101 <option value="mm9">Mouse genome (mm9)</option>
114 <option value="mm10">Mouse genome (mm10)</option> 102 <option value="mm10">Mouse genome (mm10)</option>
115 </param> 103 </param>
116 <param argument="-hm" name="homopolymer_size" type="integer" value="3" min="2" 104 <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" />
117 label="Homopolymer size"
118 help="Affected plot: Homopolymer indels; sets the minimal number of consecutive bases that define a homopolymer" />
119 </section> 105 </section>
120 </inputs> 106 </inputs>
121 <outputs> 107 <outputs>
122 <data name="output_html" format="html" 108 <data name="output_html" format="html" label="${tool.name} report on ${on_string}" />
123 label="${tool.name} report on ${on_string}" /> 109 <data name="output_per_base_coverage" format="tsv" label="${tool.name} per-base coverage on ${on_string}">
124 <data name="output_per_base_coverage" format="tsv"
125 label="${tool.name} per-base coverage on ${on_string}">
126 <filter>per_base_coverage</filter> 110 <filter>per_base_coverage</filter>
127 </data> 111 </data>
128 <collection name="raw_data" type="list" 112 <collection name="raw_data" type="list" label="Raw data for ${tool.name} on ${on_string}">
129 label="Raw data for ${tool.name} on ${on_string}">
130 <data name="genome_results" format="txt" from_work_dir="results/summary_report.txt" /> 113 <data name="genome_results" format="txt" from_work_dir="results/summary_report.txt" />
131 <data name="coverage_across_reference" format="tsv" from_work_dir="results/coverage_across_reference.txt" /> 114 <data name="coverage_across_reference" format="tsv" from_work_dir="results/coverage_across_reference.txt" />
132 <data name="coverage_histogram" format="tsv" from_work_dir="results/coverage_histogram.txt" /> 115 <data name="coverage_histogram" format="tsv" from_work_dir="results/coverage_histogram.txt" />
133 <data name="genome_fraction_coverage" format="tsv" from_work_dir="results/genome_fraction_coverage.txt" /> 116 <data name="genome_fraction_coverage" format="tsv" from_work_dir="results/genome_fraction_coverage.txt" />
134 <data name="duplication_rate_histogram" format="tsv" from_work_dir="results/duplication_rate_histogram.txt" /> 117 <data name="duplication_rate_histogram" format="tsv" from_work_dir="results/duplication_rate_histogram.txt" />