Mercurial > repos > iuc > bctools_remove_spurious_events

annotate rm_spurious_events.xml @ 0:9ad7bf370022 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
author iuc
date Tue, 14 Nov 2017 05:54:14 -0500
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9ad7bf370022 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
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1 <tool id="bctools_remove_spurious_events" name="Remove spurious" version="@VERSION@">
9ad7bf370022 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
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2 <description>crosslinking events</description>
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3 <macros>
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4 <import>macros.xml</import>
9ad7bf370022 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
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5 </macros>
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6 <expand macro="requirements"/>
9ad7bf370022 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
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7 <command detect_errors="exit_code"><![CDATA[
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8 rm_spurious_events.py
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9 '$events'
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10 --threshold '$threshold'
9ad7bf370022 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
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11 --outfile '$events_filtered'
9ad7bf370022 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
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12 ]]></command>
9ad7bf370022 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
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13 <inputs>
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14 <param name="events" type="data" format="bed" label="BED6 file containing alignments"/>
9ad7bf370022 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
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15 <param name="threshold" argument="--threshold" type="float" value="0.1" optional="true" label="Threshold for spurious event removal" help="Remove all crosslinking events that combine less reads than this fraction of the maximum number of reads at this position."/>
9ad7bf370022 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
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16 </inputs>
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17 <outputs>
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18 <data name="events_filtered" format="bed"/>
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19 </outputs>
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20 <tests>
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21 <test>
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22 <param name="events" value="merged_pcr_dupes_spurious.bed"/>
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23 <param name="threshold" value="0.5"/>
9ad7bf370022 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
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24 <output name="events_filtered" file="merged_pcr_dupes_spurious_filtered_thresh05.bed"/>
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25 </test>
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26 </tests>
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27 <help><![CDATA[
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28
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29 bctools - Remove spurious events originating from errors in unique molecular identifiers (UMIs)
9ad7bf370022 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
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30 ===============================================================================================
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31
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32 This tool compares all events sharing the same coordinates. Among each group
9ad7bf370022 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
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33 of events the maximum number of PCR duplicates is determined. By default, all events that
9ad7bf370022 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
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34 are supported by less than 10 percent of this maximum count are removed.
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36 Input
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37 -----
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39 * BED6 containing crosslinking events with score field set to number of PCR duplicates
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40
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41 Output
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42 ------
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44 * BED6 with spurious crosslinking events removed, sorted by fields chrom, start, stop, strand
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46 ]]></help>
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47 <expand macro="citations"/>
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48 </tool>