Mercurial > repos > petr-novak > various_galaxy_tools

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