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annotate bedpeToBam.xml @ 21:b3c147390100 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 3113ecabff4cd259d175b638fd5ff14f0fce6da1
author iuc
date Wed, 10 Jan 2018 19:30:53 -0500
parents a8eabd2838f6
children 95a3b2c25bd1
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a8eabd2838f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 542ddc9e98cee5cc2a9e4caae945dee4b2c747b8
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1 <tool id="bedtools_bedpetobam" name="BEDPE to BAM" version="@WRAPPER_VERSION@.0">
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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="requirements" />
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7 <expand macro="stdio" />
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8 <command>
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9 <![CDATA[
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10 bedtools bedpetobam
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11 -mapq $mapq
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12 -i '$input'
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13 -g @GENOME_FILE@
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14 > '$output'
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15 ]]>
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16 </command>
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17 <inputs>
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18 <param name="input" format="bed,gff,vcf" type="data" label="BED/VCF/GFF file"/>
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19 <expand macro="input_conditional_genome_file" />
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20 <param name="mapq" type="integer" value="255"
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21 label="Set a mapping quality (SAM MAPQ field) value for all BED entries"
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22 help="(-mapq)" />
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23 </inputs>
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24 <outputs>
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25 <data format="bam" name="output" metadata_source="input"/>
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26 </outputs>
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27 <tests>
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28 <test>
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29 <param name="input" value="bedpeToBamBed1.bed" ftype="bed" />
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30 <param name="genome_file_opts_selector" value="hist" />
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31 <param name="genome" value="mm9.len"/>
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32 <output name="output" file="bedpeToBam_result1.bam" lines_diff="72" ftype="bam" />
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33 </test>
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34 </tests>
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35 <help>
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36 <![CDATA[
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37 **What it does**
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38
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39 Converts feature records to BAM format.
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40
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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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44
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45 @REFERENCES@
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46 ]]>
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47 </help>
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48 <expand macro="citations" />
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49 </tool>