Mercurial > repos > iuc > bctools_extract_crosslinked_nucleotides
view coords2clnt.xml @ 3:ca86af119c27 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 758b42538f722759e7b5414f64c9a7973cc221b4"
author | iuc |
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date | Wed, 25 Dec 2019 11:41:01 -0500 |
parents | 91f27e8a2535 |
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<tool id="bctools_extract_crosslinked_nucleotides" name="Get crosslinked nucleotides" version="@VERSION+galaxy1"> <description>from full alignments</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ coords2clnt.py $threeprime '$alignment_coordinates' > '$crosslinking_coordinates' ]]></command> <inputs> <param name="alignment_coordinates" type="data" format="bed" label="Alignments in BED format"/> <param argument="--threeprime" type="boolean" truevalue="--threeprime" falsevalue="" checked="false" label="Set position one nt downstream of 3'-end as crosslinked nucleotide" help="Set position one nt downstream of 3'-end as crosslinked nucleotide. By default the crosslink site will be assumed to be one nt upstream of the 5'-end of the read."/> </inputs> <outputs> <data name="crosslinking_coordinates" format="bed"/> </outputs> <tests> <test> <param name="alignment_coordinates" value="merged_pcr_dupes.bed"/> <output name="crosslinking_coordinates" file="merged_pcr_dupes_clnts.bed"/> </test> </tests> <help><![CDATA[ bctools - Get crosslinked nucleotides from full alignments ========================================================== Given coordinates of aligned reads in BED format, calculate positions of the crosslinked nucleotides. Crosslinked nts are assumed to be one nt upstream of the 5'-end of the read. Input ----- * six column BED file containing coordinates of aligned reads Output ------ * six column BED file containing coordinates of crosslinking events ]]></help> <expand macro="citations"/> </tool>