Mercurial > repos > iuc > crossmap_gff

annotate macros.xml @ 6:9ca13f08f2f7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447-dirty
author iuc
date Tue, 26 Sep 2017 06:09:26 -0400
parents 567ddd432541
children 1b57bf1bb4ec
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5773a57e91e6 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"?>
5773a57e91e6 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="324">ucsc-wigtobigwig</requirement>
5773a57e91e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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6 <requirement type="package" version="0.2.2">crossmap</requirement>
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7 <yield/>
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8 </requirements>
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9 </xml>
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10 <token name="@WRAPPER_VERSION@">0.2.2</token>
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11 <xml name="stdio">
5773a57e91e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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12 <stdio>
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13 <regex match="Aborted (core dumped)" source="stdout" level="fatal"/>
5773a57e91e6 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"/>
5773a57e91e6 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:"/>
5773a57e91e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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16 </stdio>
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17 </xml>
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18 <xml name="version_command">
5773a57e91e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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19 <version_command>CrossMap.py 2&gt;&amp;1 | head -n 1 | grep -E --only-matching 'CrossMap.*'</version_command>
5773a57e91e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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20 </xml>
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21 <xml name="chain">
5773a57e91e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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22 <conditional name="chain_source">
5773a57e91e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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23 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
5773a57e91e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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24 <option value="cached">Local data (in galaxy)</option>
5773a57e91e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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25 <option value="history">From History</option>
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26 </param>
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27 <when value="cached">
5773a57e91e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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28 <param name="input_chain" type="select" label="Lift Over To">
6
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29 <options from_data_table="liftOver">
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30 <!--
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31 planemo can't update this ?
9ca13f08f2f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447-dirty
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32 <filter type="data_meta" ref="input" key="dbkey"/>
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33 -->
5
567ddd432541 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447-dirty
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34 </options>
0
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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 type="data" format="csv" name="input_chain" 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 <xml name="source">
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43 <param name="index_source" type="select" label="Source for Input Data">
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44 <option value="cached">Local data (in galaxy)</option>
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45 <option value="history">From History</option>
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46 </param>
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47 </xml>
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48 <token name="@HELP_GENERAL@">
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49 CrossMap
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50 --------
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51 CrossMap is versatile tool to convert genome coordinates or annotation files between genome
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52 assemblies. It supports mostly commonly used file types, including BAM, BED,BigWig, GFF,
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53 GTF, SAM, Wiggle, and VCF formats. For large plain text file types, such as BED, GFF, GTF
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54 and VCF, reading from remote servers and file compression are supported.
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55 </token>
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56 </macros>