Mercurial > repos > iuc > crossmap_vcf

annotate macros.xml @ 5:1cf119db73cb 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 19:26:15 -0400
parents 69349b98b727
children 36c43ac33aac
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3fc985b6afdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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1 <?xml version="1.0"?>
3fc985b6afdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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2 <macros>
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3 <xml name="requirements">
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4 <requirements>
5
1cf119db73cb "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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3fc985b6afdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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6 <yield/>
3fc985b6afdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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7 </requirements>
3fc985b6afdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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8 </xml>
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1cf119db73cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 2dbcf8154aff86b27a1dd535407d20168c4ef697"
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9 <token name="@TOOL_VERSION@">0.3.7</token>
1cf119db73cb "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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11 <xml name="stdio">
3fc985b6afdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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12 <stdio>
3fc985b6afdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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13 <regex match="Aborted (core dumped)" source="stdout" level="fatal"/>
3fc985b6afdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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14 <regex match=".*" source="both" level="log"/>
3fc985b6afdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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15 <exit_code range="1:"/>
3fc985b6afdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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16 </stdio>
3fc985b6afdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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17 </xml>
3fc985b6afdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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18 <xml name="version_command">
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19 <version_command><![CDATA[
37c8b1afc814 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
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20 CrossMap.py 2>&1 | head -n 1 | grep -E --only-matching 'CrossMap.*'
37c8b1afc814 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
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21 ]]></version_command>
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22 </xml>
3fc985b6afdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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23 <xml name="chain">
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24 <conditional name="chain_source">
3fc985b6afdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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25 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
3fc985b6afdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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26 <option value="cached">Local data (in galaxy)</option>
3fc985b6afdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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27 <option value="history">From History</option>
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28 </param>
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29 <when value="cached">
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30 <param name="input_chain" type="select" label="Lift Over To">
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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"/>
3fc985b6afdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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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">
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37 <param name="input_chain" type="data" format="csv" label="LiftOver chain file"/>
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38 </when>
3fc985b6afdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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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 --------
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44 CrossMap is versatile tool to convert genome coordinates or annotation files between genome
3fc985b6afdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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45 assemblies. It supports mostly commonly used file types, including BAM, BED,BigWig, GFF,
3fc985b6afdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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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>