Mercurial > repos > rnateam > bctools
comparison rm_spurious_events.xml @ 0:119fccb59597 draft
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| author | rnateam |
|---|---|
| date | Thu, 22 Oct 2015 09:52:51 -0400 |
| parents | |
| children | bf5b606f1aa7 |
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| -1:000000000000 | 0:119fccb59597 |
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| 1 <tool id="rm_spurious_events.py" name="rm_spurious_events.py" version="1.0"> | |
| 2 <description>Remove spurious events.</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <expand macro="stdio" /> | |
| 8 <version_command>python rm_spurious_events.py --version</version_command> | |
| 9 <command interpreter="python"><![CDATA[rm_spurious_events.py | |
| 10 #if $positional_1 and $positional_1 is not None: | |
| 11 $positional_1 | |
| 12 #end if | |
| 13 | |
| 14 #if $threshold and $threshold is not None: | |
| 15 --threshold $threshold | |
| 16 #end if | |
| 17 > $default]]></command> | |
| 18 <inputs> | |
| 19 <param area="false" label="bed6 file containing alignments." name="positional_1" type="data" format="bed"/> | |
| 20 <param help="(--threshold)" label="Threshold for spurious event removal." name="threshold" optional="true" type="float" value="0.1"/> | |
| 21 </inputs> | |
| 22 <outputs> | |
| 23 <data format="bed" hidden="false" name="default"/> | |
| 24 </outputs> | |
| 25 <tests> | |
| 26 <test> | |
| 27 <param name="positional_1" value="merged_pcr_dupes_spurious.bed"/> | |
| 28 <param name="threshold" value="0.5"/> | |
| 29 <output name="default" file="merged_pcr_dupes_spurious_filtered_thresh05.bed"/> | |
| 30 </test> | |
| 31 </tests> | |
| 32 <help><![CDATA[ | |
| 33 Remove spurious events originating from errors in random sequence tags. | |
| 34 | |
| 35 This script compares all events sharing the same coordinates. Among each group | |
| 36 of events the maximum number of PCR duplicates is determined. All events that | |
| 37 are supported by less than 10 percent of this maximum count are removed. | |
| 38 | |
| 39 Input: | |
| 40 * bed6 file containing crosslinking events with score field set to number of PCR | |
| 41 duplicates | |
| 42 | |
| 43 Output: | |
| 44 * bed6 file with spurious crosslinking events removed, sorted by fields chrom, | |
| 45 start, stop, strand | |
| 46 | |
| 47 Author: Daniel Maticzka | |
| 48 Copyright: 2015 | |
| 49 License: Apache | |
| 50 Email: maticzkd@informatik.uni-freiburg.de | |
| 51 Status: Testing | |
| 52 ]]></help> | |
| 53 <expand macro="citations" /> | |
| 54 </tool> |