Mercurial > repos > iuc > bctools_remove_spurious_events

annotate rm_spurious_events.xml @ 2:84aff696aa97 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 758b42538f722759e7b5414f64c9a7973cc221b4"
author iuc
date Wed, 25 Dec 2019 11:39:45 -0500
parents 9ad7bf370022
children 5c72eb992651
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84aff696aa97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 758b42538f722759e7b5414f64c9a7973cc221b4"
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1 <tool id="bctools_remove_spurious_events" name="Remove spurious" version="@VERSION@+galaxy1">
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2 <description>crosslinking events</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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84aff696aa97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 758b42538f722759e7b5414f64c9a7973cc221b4"
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6 <expand macro="requirements">
84aff696aa97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 758b42538f722759e7b5414f64c9a7973cc221b4"
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7 <requirement type="package" version="8.31">coreutils</requirement>
84aff696aa97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 758b42538f722759e7b5414f64c9a7973cc221b4"
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8 </expand>
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9 <command detect_errors="exit_code"><![CDATA[
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10 rm_spurious_events.py
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11 '$events'
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12 --threshold '$threshold'
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13 --outfile '$events_filtered'
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14 ]]></command>
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15 <inputs>
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16 <param name="events" type="data" format="bed" label="BED6 file containing alignments"/>
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17 <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."/>
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18 </inputs>
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19 <outputs>
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20 <data name="events_filtered" format="bed"/>
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21 </outputs>
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22 <tests>
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23 <test>
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24 <param name="events" value="merged_pcr_dupes_spurious.bed"/>
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25 <param name="threshold" value="0.5"/>
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26 <output name="events_filtered" file="merged_pcr_dupes_spurious_filtered_thresh05.bed"/>
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27 </test>
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28 </tests>
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29 <help><![CDATA[
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31 bctools - Remove spurious events originating from errors in unique molecular identifiers (UMIs)
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32 ===============================================================================================
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34 This tool compares all events sharing the same coordinates. Among each group
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35 of events the maximum number of PCR duplicates is determined. By default, all events that
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36 are supported by less than 10 percent of this maximum count are removed.
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38 Input
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39 -----
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41 * BED6 containing crosslinking events with score field set to number of PCR duplicates
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43 Output
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44 ------
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46 * BED6 with spurious crosslinking events removed, sorted by fields chrom, start, stop, strand
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48 ]]></help>
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49 <expand macro="citations"/>
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50 </tool>