Mercurial > repos > iuc > bedtools

annotate bedpeToBam.xml @ 64:f6c88d2e9ae5 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 73ebd55430874a3c1483b6dd6cce0482175482f9
author iuc
date Fri, 21 Feb 2025 21:38:34 +0000
parents 9f6bd4c9479f
children
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1 <tool id="bedtools_bedpetobam" name="bedtools BEDPE to BAM" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
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2 <description>converter</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="bio_tools" />
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7 <!-- bedtobam broken in 2.29.0 <expand macro="requirements" /> -->
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8 <requirements>
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9 <requirement type="package" version="2.31.1">bedtools</requirement>
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10 </requirements>
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11 <expand macro="stdio" />
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12 <command><![CDATA[
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13 bedtools bedpetobam
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14 -mapq $mapq
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15 -i '$input'
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16 @GENOME_FILE@
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17 > '$output'
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18 ]]></command>
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19 <inputs>
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20 <param name="input" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
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21 <expand macro="input_conditional_genome_file" />
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22 <param argument="-mapq" type="integer" value="255"
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23 label="Set a mapping quality (SAM MAPQ field) value for all BED entries" />
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24 </inputs>
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25 <outputs>
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26 <data name="output" format="unsorted.bam" metadata_source="input"/>
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27 </outputs>
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28 <tests>
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29 <test>
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30 <param name="input" value="bedpeToBamBed1.bed" ftype="bed" />
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31 <param name="genome_file_opts|genome_file_opts_selector" value="hist" />
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32 <param name="genome_file_opts|genome" value="mm9.len"/>
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33 <output name="output" file="bedpeToBam_result1.bam" lines_diff="72" ftype="unsorted.bam" />
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34 </test>
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35 </tests>
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36 <help><![CDATA[
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37 **What it does**
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39 Converts feature records to BAM format.
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41 .. class:: warningmark
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43 BED files must be at least BED4 to create BAM (needs name field).
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45 @REFERENCES@
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46 ]]></help>
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47 <expand macro="citations" />
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48 </tool>