Mercurial > repos > iuc > bctools_remove_spurious_events
comparison rm_spurious_events.xml @ 0:9ad7bf370022 draft
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 |
| parents | |
| children | 84aff696aa97 |
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| -1:000000000000 | 0:9ad7bf370022 |
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| 1 <tool id="bctools_remove_spurious_events" name="Remove spurious" version="@VERSION@"> | |
| 2 <description>crosslinking events</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements"/> | |
| 7 <command detect_errors="exit_code"><![CDATA[ | |
| 8 rm_spurious_events.py | |
| 9 '$events' | |
| 10 --threshold '$threshold' | |
| 11 --outfile '$events_filtered' | |
| 12 ]]></command> | |
| 13 <inputs> | |
| 14 <param name="events" type="data" format="bed" label="BED6 file containing alignments"/> | |
| 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."/> | |
| 16 </inputs> | |
| 17 <outputs> | |
| 18 <data name="events_filtered" format="bed"/> | |
| 19 </outputs> | |
| 20 <tests> | |
| 21 <test> | |
| 22 <param name="events" value="merged_pcr_dupes_spurious.bed"/> | |
| 23 <param name="threshold" value="0.5"/> | |
| 24 <output name="events_filtered" file="merged_pcr_dupes_spurious_filtered_thresh05.bed"/> | |
| 25 </test> | |
| 26 </tests> | |
| 27 <help><![CDATA[ | |
| 28 | |
| 29 bctools - Remove spurious events originating from errors in unique molecular identifiers (UMIs) | |
| 30 =============================================================================================== | |
| 31 | |
| 32 This tool compares all events sharing the same coordinates. Among each group | |
| 33 of events the maximum number of PCR duplicates is determined. By default, all events that | |
| 34 are supported by less than 10 percent of this maximum count are removed. | |
| 35 | |
| 36 Input | |
| 37 ----- | |
| 38 | |
| 39 * BED6 containing crosslinking events with score field set to number of PCR duplicates | |
| 40 | |
| 41 Output | |
| 42 ------ | |
| 43 | |
| 44 * BED6 with spurious crosslinking events removed, sorted by fields chrom, start, stop, strand | |
| 45 | |
| 46 ]]></help> | |
| 47 <expand macro="citations"/> | |
| 48 </tool> |