Mercurial > repos > iuc > bedtools

annotate bedpeToBam.xml @ 52:9a9f1a7abf54 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
author iuc
date Fri, 06 Sep 2019 14:28:37 -0400
parents df28283b3778
children 7a06bb42dbb1
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df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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1 <tool id="bedtools_bedpetobam" name="bedtools BEDPE to BAM" version="@TOOL_VERSION@">
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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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9a9f1a7abf54 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
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6 <!-- bedtobam broken in 2.29.0 <expand macro="requirements" /> -->
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7 <requirements>
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8 <requirement type="package" version="2.27.1">bedtools</requirement>
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9 </requirements>
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10 <expand macro="stdio" />
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11 <command><![CDATA[
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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12 bedtools bedpetobam
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13 -mapq $mapq
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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14 -i '$input'
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15 -g @GENOME_FILE@
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16 > '$output'
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17 ]]></command>
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18 <inputs>
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19 <param name="input" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
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20 <expand macro="input_conditional_genome_file" />
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21 <param argument="-mapq" type="integer" value="255"
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22 label="Set a mapping quality (SAM MAPQ field) value for all BED entries" />
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23 </inputs>
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24 <outputs>
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25 <data name="output" format="unsorted.bam" 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="unsorted.bam" />
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33 </test>
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34 </tests>
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35 <help><![CDATA[
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36 **What it does**
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38 Converts feature records to BAM format.
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40 .. class:: warningmark
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42 BED files must be at least BED4 to create BAM (needs name field).
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44 @REFERENCES@
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45 ]]></help>
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46 <expand macro="citations" />
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47 </tool>