Mercurial > repos > iuc > crossmap_wig

annotate macros.xml @ 4:3cb69f2ecea2 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 2dbcf8154aff86b27a1dd535407d20168c4ef697"
author iuc
date Wed, 11 Sep 2019 19:29:03 -0400
parents 8c26026e7ad9
children e8d84292e510
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0e6f675cea09 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"?>
0e6f675cea09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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2 <macros>
0e6f675cea09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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3 <xml name="requirements">
0e6f675cea09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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4 <requirements>
4
3cb69f2ecea2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 2dbcf8154aff86b27a1dd535407d20168c4ef697"
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5 <requirement type="package" version="@TOOL_VERSION@">crossmap</requirement>
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6 <yield/>
0e6f675cea09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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7 </requirements>
0e6f675cea09 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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3cb69f2ecea2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 2dbcf8154aff86b27a1dd535407d20168c4ef697"
iuc
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9 <token name="@TOOL_VERSION@">0.3.7</token>
3cb69f2ecea2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 2dbcf8154aff86b27a1dd535407d20168c4ef697"
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10 <token name="@WRAPPER_VERSION@">@TOOL_VERSION@</token>
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0e6f675cea09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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11 <xml name="stdio">
0e6f675cea09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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12 <stdio>
0e6f675cea09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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13 <regex match="Aborted (core dumped)" source="stdout" level="fatal"/>
0e6f675cea09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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14 <regex match=".*" source="both" level="log"/>
0e6f675cea09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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15 <exit_code range="1:"/>
0e6f675cea09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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16 </stdio>
0e6f675cea09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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17 </xml>
0e6f675cea09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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18 <xml name="version_command">
1
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19 <version_command><![CDATA[
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20 CrossMap.py 2>&1 | head -n 1 | grep -E --only-matching 'CrossMap.*'
81986a56b281 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
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21 ]]></version_command>
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22 </xml>
0e6f675cea09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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23 <xml name="chain">
0e6f675cea09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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24 <conditional name="chain_source">
0e6f675cea09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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25 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
0e6f675cea09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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26 <option value="cached">Local data (in galaxy)</option>
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27 <option value="history">From History</option>
0e6f675cea09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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28 </param>
0e6f675cea09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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29 <when value="cached">
0e6f675cea09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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30 <param name="input_chain" type="select" label="Lift Over To">
1
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31 <options from_data_table="liftOver">
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32 <filter type="data_meta" ref="input" key="dbkey" column="0"/>
0e6f675cea09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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33 </options>
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34 </param>
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35 </when>
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36 <when value="history">
1
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37 <param name="input_chain" type="data" format="csv" label="LiftOver chain file"/>
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38 </when>
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39 </conditional>
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40 </xml>
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41 <token name="@HELP_GENERAL@">
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42 CrossMap
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43 --------
0e6f675cea09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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44 CrossMap is versatile tool to convert genome coordinates or annotation files between genome
0e6f675cea09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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45 assemblies. It supports mostly commonly used file types, including BAM, BED,BigWig, GFF,
0e6f675cea09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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46 GTF, SAM, Wiggle, and VCF formats. For large plain text file types, such as BED, GFF, GTF
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47 and VCF, reading from remote servers and file compression are supported.
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48 </token>
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49 </macros>