Mercurial > repos > rnateam > bctools
comparison coords2clnt.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="coords2clnt.py" name="coords2clnt.py" version="1.0"> | |
| 2 <description>Extract crosslinked nucleotide.</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <expand macro="stdio" /> | |
| 8 <stdio> | |
| 9 <exit_code level="fatal" range="1:"/> | |
| 10 </stdio> | |
| 11 <version_command>python coords2clnt.py --version</version_command> | |
| 12 <command interpreter="python"><![CDATA[coords2clnt.py | |
| 13 #if $positional_1 and $positional_1 is not None: | |
| 14 $positional_1 | |
| 15 #end if | |
| 16 | |
| 17 > $default]]></command> | |
| 18 <inputs> | |
| 19 <param area="false" label="Alignments in bed format." name="positional_1" type="data" format="bed"/> | |
| 20 </inputs> | |
| 21 <outputs> | |
| 22 <data hidden="false" name="default" format="bed"/> | |
| 23 </outputs> | |
| 24 <tests> | |
| 25 <test> | |
| 26 <param name="positional_1" value="merged_pcr_dupes.bed"/> | |
| 27 <output name="default" file="merged_pcr_dupes_clnts.bed"/> | |
| 28 </test> | |
| 29 </tests> | |
| 30 <help><![CDATA[ | |
| 31 Given coordinates of the aligned reads, calculate positions of the crosslinked nucleotides. | |
| 32 Crosslinked nts are assumed to be one nt upstream of the 5'-end of the read. | |
| 33 | |
| 34 Input: | |
| 35 * bed6 file containing coordinates of aligned reads | |
| 36 * bed6 file containing coordinates of crosslinking events | |
| 37 | |
| 38 Author: Daniel Maticzka | |
| 39 Copyright: 2015 | |
| 40 License: Apache | |
| 41 Email: maticzkd@informatik.uni-freiburg.de | |
| 42 Status: Testing | |
| 43 ]]></help> | |
| 44 <expand macro="citations" /> | |
| 45 </tool> |