Mercurial > repos > iuc > bedtools

annotate tagBed.xml @ 56:7a06bb42dbb1 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Tue, 31 Aug 2021 07:45:56 +0000
parents 9a9f1a7abf54
children 1d0a0d6a78b1
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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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1 <tool id="bedtools_tagbed" name="bedtools TagBed" version="@TOOL_VERSION@">
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2 <description>tag BAM alignments based on overlaps with interval files</description>
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7a06bb42dbb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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3 <expand macro="bio_tools" />
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <expand macro="stdio" />
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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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9 <command><![CDATA[
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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10 bedtools tag
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11 -i '${inputA}'
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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12 -files
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13 #for $file in $inputB
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14 '$file'
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15 #end for
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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16 @OVERLAP@
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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17 $strand
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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18 -tag '${tag}'
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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19 $field
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20 > '${output}'
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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21 ]]></command>
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22 <inputs>
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23 <param name="inputA" argument="-i" type="data" format="bam" label="BAM file"/>
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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24 <param name="inputB" argument="-files" type="data" format="@STD_BEDTOOLS_INPUTS@" multiple="true" label="@STD_BEDTOOLS_INPUT_LABEL@ file" />
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25 <expand macro="strand2" />
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26 <expand macro="overlap" fracof="the alignment"/>
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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27 <param argument="-tag" type="text" value="YB" label="Specify the tag to use" />
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28 <param name="field" type="select" label="Field from the annotation files to populate tags?">
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29 <option value="-labels" selected="true">Labels</option>
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30 <option value="-scores">Scores</option>
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31 <option value="-names">Names</option>
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32 <option value="-labels -intervals">Intervals</option>
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33 </param>
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34 </inputs>
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35 <outputs>
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36 <data name="output" format="bam" />
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37 </outputs>
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38 <tests>
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39 <test>
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40 <param name="inputA" value="srma_in3.bam" ftype="bam" />
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41 <param name="inputB" value="tagBed1.bed" ftype="bed" />
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42 <param name="field" value="-names" />
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43 <output name="output" file="tagBed_result1.bam" ftype="bam" />
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44 </test>
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45 </tests>
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46 <help><![CDATA[
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47 **What it does**
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49 Annotates a BAM file based on overlaps with multiple @STD_BEDTOOLS_INPUT_LABEL@ files on the intervals in an input bam file
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51 @REFERENCES@
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52 ]]></help>
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53 <expand macro="citations" />
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54 </tool>