Mercurial > repos > iuc > crossmap_bw

annotate macros.xml @ 1:3b82b6febfd3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
author iuc
date Fri, 20 Oct 2017 02:50:41 -0400
parents 143ec4d1c8f3
children 566f43df9ef4
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143ec4d1c8f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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1 <?xml version="1.0"?>
143ec4d1c8f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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2 <macros>
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3 <xml name="requirements">
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4 <requirements>
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5 <requirement type="package" version="0.2.5">crossmap</requirement>
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6 <yield/>
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7 </requirements>
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8 </xml>
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9 <token name="@WRAPPER_VERSION@">0.2.5</token>
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10 <xml name="stdio">
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11 <stdio>
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12 <regex match="Aborted (core dumped)" source="stdout" level="fatal"/>
143ec4d1c8f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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13 <regex match=".*" source="both" level="log"/>
143ec4d1c8f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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14 <exit_code range="1:"/>
143ec4d1c8f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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15 </stdio>
143ec4d1c8f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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16 </xml>
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17 <xml name="version_command">
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18 <version_command><![CDATA[
3b82b6febfd3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
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19 CrossMap.py 2>&1 | head -n 1 | grep -E --only-matching 'CrossMap.*'
3b82b6febfd3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
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20 ]]></version_command>
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21 </xml>
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22 <xml name="chain">
143ec4d1c8f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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23 <conditional name="chain_source">
143ec4d1c8f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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24 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
143ec4d1c8f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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25 <option value="cached">Local data (in galaxy)</option>
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26 <option value="history">From History</option>
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27 </param>
143ec4d1c8f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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28 <when value="cached">
143ec4d1c8f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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29 <param name="input_chain" type="select" label="Lift Over To">
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30 <options from_data_table="liftOver">
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31 <!--
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32 <filter type="data_meta" ref="input" key="dbkey" column="0"/>
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33 -->
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34 </options>
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35 </param>
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36 </when>
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37 <when value="history">
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38 <param name="input_chain" type="data" format="csv" label="LiftOver chain file"/>
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39 </when>
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40 </conditional>
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41 </xml>
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42 <token name="@HELP_GENERAL@">
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43 CrossMap
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44 --------
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45 CrossMap is versatile tool to convert genome coordinates or annotation files between genome
143ec4d1c8f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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46 assemblies. It supports mostly commonly used file types, including BAM, BED,BigWig, GFF,
143ec4d1c8f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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47 GTF, SAM, Wiggle, and VCF formats. For large plain text file types, such as BED, GFF, GTF
143ec4d1c8f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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48 and VCF, reading from remote servers and file compression are supported.
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49 </token>
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50 </macros>