Mercurial > repos > iuc > crossmap_bam
annotate macros.xml @ 10:5e3b182af35c draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e10d34b547557b2bd4f0be69e31204bd5703e422"
author | iuc |
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date | Thu, 20 Jan 2022 04:29:28 +0000 |
parents | acd53aae2d46 |
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9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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1 <?xml version="1.0"?> |
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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2 <macros> |
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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3 <xml name="requirements"> |
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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4 <requirements> |
5
c76b5389bb34
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 2dbcf8154aff86b27a1dd535407d20168c4ef697"
iuc
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5 <requirement type="package" version="@TOOL_VERSION@">crossmap</requirement> |
0
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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6 <yield/> |
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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7 </requirements> |
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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8 </xml> |
10
5e3b182af35c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e10d34b547557b2bd4f0be69e31204bd5703e422"
iuc
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9 <token name="@TOOL_VERSION@">0.6.1</token> |
8
acd53aae2d46
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit f436317e2f8d451621e297cfc474e43c20d60bb7"
iuc
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10 <token name="@VERSION_SUFFIX@">0</token> |
0
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
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changeset
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11 <xml name="stdio"> |
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff
changeset
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12 <stdio> |
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
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13 <regex match="Aborted (core dumped)" source="stdout" level="fatal"/> |
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff
changeset
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14 <regex match=".*" source="both" level="log"/> |
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff
changeset
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15 <exit_code range="1:"/> |
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff
changeset
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16 </stdio> |
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff
changeset
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17 </xml> |
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
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18 <xml name="version_command"> |
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6463cf32d733
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
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19 <version_command><![CDATA[ |
6463cf32d733
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
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20 CrossMap.py 2>&1 | head -n 1 | grep -E --only-matching 'CrossMap.*' |
6463cf32d733
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
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21 ]]></version_command> |
0
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff
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22 </xml> |
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff
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23 <xml name="chain"> |
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
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24 <conditional name="chain_source"> |
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff
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25 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)"> |
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
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26 <option value="cached">Local data (in galaxy)</option> |
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
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27 <option value="history">From History</option> |
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
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28 </param> |
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff
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29 <when value="cached"> |
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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diff
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30 <param name="input_chain" type="select" label="Lift Over To"> |
2
6463cf32d733
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
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31 <options from_data_table="liftOver"> |
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8c275847f3fa
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 95fe80d08fb14c4c344da4979290e72261e31ae5"
iuc
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32 <filter type="data_meta" ref="input" key="dbkey" column="dbkey"/> |
0
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
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33 </options> |
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
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34 </param> |
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
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35 </when> |
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
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36 <when value="history"> |
7
d38efcdbfa38
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit ce9efed8c15240a269107ff356aeb18b52eb383f"
iuc
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37 <param name="input_chain" type="data" format="txt" label="LiftOver chain file"/> |
0
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
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38 </when> |
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
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39 </conditional> |
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
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40 </xml> |
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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41 <token name="@HELP_GENERAL@"> |
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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42 CrossMap |
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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43 -------- |
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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44 CrossMap is versatile tool to convert genome coordinates or annotation files between genome |
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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45 assemblies. It supports mostly commonly used file types, including BAM, BED,BigWig, GFF, |
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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46 GTF, SAM, Wiggle, and VCF formats. For large plain text file types, such as BED, GFF, GTF |
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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47 and VCF, reading from remote servers and file compression are supported. |
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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48 </token> |
9bcfe0aabf5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
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49 </macros> |