Mercurial > repos > iuc > crossmap_vcf

annotate macros.xml @ 3:9db73ff23c9f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 23fab16cd40acbd5b0e9d640ed3858040db7a622
author iuc
date Thu, 24 May 2018 19:09:50 -0400
parents 7a3c34157901
children 9d61d74f03a4
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734eedede47c 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"?>
734eedede47c 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">
734eedede47c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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4 <requirements>
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9db73ff23c9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 23fab16cd40acbd5b0e9d640ed3858040db7a622
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5 <requirement type="package" version="0.2.7">crossmap</requirement>
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6 <yield/>
734eedede47c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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7 </requirements>
734eedede47c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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8 </xml>
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9db73ff23c9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 23fab16cd40acbd5b0e9d640ed3858040db7a622
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9 <token name="@WRAPPER_VERSION@">0.2.7</token>
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10 <xml name="stdio">
734eedede47c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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11 <stdio>
734eedede47c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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12 <regex match="Aborted (core dumped)" source="stdout" level="fatal"/>
734eedede47c 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"/>
734eedede47c 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:"/>
734eedede47c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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15 </stdio>
734eedede47c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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16 </xml>
734eedede47c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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17 <xml name="version_command">
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18 <version_command><![CDATA[
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19 CrossMap.py 2>&1 | head -n 1 | grep -E --only-matching 'CrossMap.*'
a40d9af7d058 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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734eedede47c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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21 </xml>
734eedede47c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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22 <xml name="chain">
734eedede47c 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">
734eedede47c 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)">
734eedede47c 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>
734eedede47c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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26 <option value="history">From History</option>
734eedede47c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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27 </param>
734eedede47c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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28 <when value="cached">
734eedede47c 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 <filter type="data_meta" ref="input" key="dbkey" column="0"/>
734eedede47c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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32 </options>
734eedede47c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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33 </param>
734eedede47c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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34 </when>
734eedede47c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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35 <when value="history">
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a40d9af7d058 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
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36 <param name="input_chain" type="data" format="csv" label="LiftOver chain file"/>
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37 </when>
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38 </conditional>
734eedede47c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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39 </xml>
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40 <token name="@HELP_GENERAL@">
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41 CrossMap
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42 --------
734eedede47c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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43 CrossMap is versatile tool to convert genome coordinates or annotation files between genome
734eedede47c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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44 assemblies. It supports mostly commonly used file types, including BAM, BED,BigWig, GFF,
734eedede47c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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45 GTF, SAM, Wiggle, and VCF formats. For large plain text file types, such as BED, GFF, GTF
734eedede47c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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46 and VCF, reading from remote servers and file compression are supported.
734eedede47c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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47 </token>
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48 </macros>