Mercurial > repos > iuc > bctools_extract_crosslinked_nucleotides

comparison coords2clnt.xml @ 2:91f27e8a2535 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 513a54a013c5762aa6099fe044b2d3acf4a76881
author iuc
date Tue, 10 Jul 2018 13:50:10 -0400
parents 66d1f96c5600
children 12a5e6fa850e
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1:ca1320644fad 2:91f27e8a2535
1 <tool id="bctools_extract_crosslinked_nucleotides" name="Get crosslinked nucleotides" version="@VERSION@"> 1 <tool id="bctools_extract_crosslinked_nucleotides" name="Get crosslinked nucleotides" version="@VERSION+galaxy1">
2 <description>from full alignments</description> 2 <description>from full alignments</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 coords2clnt.py 8 coords2clnt.py
9 $threeprime
9 '$alignment_coordinates' 10 '$alignment_coordinates'
10 > '$crosslinking_coordinates' 11 > '$crosslinking_coordinates'
11 ]]></command> 12 ]]></command>
12 <inputs> 13 <inputs>
13 <param name="alignment_coordinates" type="data" format="bed" label="Alignments in BED format"/> 14 <param name="alignment_coordinates" type="data" format="bed" label="Alignments in BED format"/>
15 <param argument="--threeprime" type="boolean" truevalue="--threeprime" falsevalue="" checked="false"
16 label="Set position one nt downstream of 3'-end as crosslinked nucleotide"
17 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."/>
14 </inputs> 18 </inputs>
15 <outputs> 19 <outputs>
16 <data name="crosslinking_coordinates" format="bed"/> 20 <data name="crosslinking_coordinates" format="bed"/>
17 </outputs> 21 </outputs>
18 <tests> 22 <tests>