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comparison bed2bigwig.xml @ 3:1069776f7ae2 draft default tip

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planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 3b9f93ed06cc32dbfa271789739e7a1e8fac528c
author petr-novak
date Tue, 30 Apr 2024 08:27:27 +0000
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2:90c46e40d222 3:1069776f7ae2
1 <tool id="calculate_density" name="Calculate Density" version="1.0.0">
2 <description>Calculate coverage density from BED/GFF files</description>
3 <requirements>
4 <requirement type="package" version="1.7.3">r-optparse</requirement>
5 <requirement type="package" version="1.54.0">bioconductor-rtracklayer</requirement>
6 </requirements>
7 <required_files>
8 <include type="literal" path="calculate_density.R"/>
9 </required_files>
10 <command detect_errors="exit_code"><![CDATA[
11 Rscript '$__tool_directory__/calculate_density.R'
12 --bed '$input_bed'
13 --window '$window_size'
14 --output '$output_bigwig'
15 --format '$input_bed.ext'
16 #if $merge:
17 --merge
18 #end if
19 ]]></command>
20 <inputs>
21 <param type="data" format="bed,gff" name="input_bed" label="Input BED/GFF file" help="BED or GFF file containing genomic regions" />
22 <param type="integer" name="window_size" label="Window size" value="1000000" min="1" help="Size of the window for density calculation" />
23 <param type="boolean" name="merge" label="Merge overlapping regions" truevalue="true" falsevalue="false" checked="true" help="Merge overlapping regions before calculating density" />
24 </inputs>
25 <outputs>
26 <data format="bigwig" name="output_bigwig" label="${tool.name} on ${on_string}: BigWig output"/>
27 </outputs>
28 <help><![CDATA[
29 This tool calculates the coverage density from a provided BED or GFF file over specified window sizes and outputs the results in BigWig format.
30 ]]></help>
31
32 </tool>