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annotate tagBed.xml @ 50:df28283b3778 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
author iuc
date Mon, 29 Apr 2019 05:54:22 -0400
parents 2f457890d8c8
children 9a9f1a7abf54
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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_tagbed" name="bedtools TagBed" version="@TOOL_VERSION@+galaxy1">
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2 <description>tag BAM alignments based on overlaps with interval files</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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df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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8 <command><![CDATA[
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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9 bedtools tag
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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10 -i '${inputA}'
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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11 -files
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12 #for $file in $inputB
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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13 '$file'
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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14 #end for
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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15 @OVERLAP@
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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16 $strand
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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17 -tag '${tag}'
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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18 $field
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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19 > '${output}'
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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20 ]]></command>
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21 <inputs>
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22 <param name="inputA" argument="-i" type="data" format="bam" label="BAM file"/>
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23 <param name="inputB" argument="-files" type="data" format="@STD_BEDTOOLS_INPUTS@" multiple="true" label="@STD_BEDTOOLS_INPUT_LABEL@ file" />
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24 <expand macro="strand2" />
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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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25 <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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26 <param argument="-tag" type="text" value="YB" label="Specify the tag to use" />
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27 <param name="field" type="select" label="Field from the annotation files to populate tags?">
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28 <option value="-labels" selected="true">Labels</option>
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29 <option value="-scores">Scores</option>
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30 <option value="-names">Names</option>
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31 <option value="-labels -intervals">Intervals</option>
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32 </param>
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33 </inputs>
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34 <outputs>
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35 <data name="output" format="bam" />
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36 </outputs>
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37 <tests>
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38 <test>
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39 <param name="inputA" value="srma_in3.bam" ftype="bam" />
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40 <param name="inputB" value="tagBed1.bed" ftype="bed" />
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41 <param name="field" value="-names" />
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42 <output name="output" file="tagBed_result1.bam" ftype="bam" />
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43 </test>
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44 </tests>
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45 <help><![CDATA[
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46 **What it does**
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47
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48 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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50 @REFERENCES@
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51 ]]></help>
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52 <expand macro="citations" />
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53 </tool>