Mercurial > repos > iuc > crossmap_bam
comparison macros.xml @ 0:d04d5afec2e0 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
| author | iuc |
|---|---|
| date | Tue, 26 Sep 2017 05:44:53 -0400 |
| parents | |
| children | 8e5feca6a518 |
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| -1:000000000000 | 0:d04d5afec2e0 |
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| 1 <?xml version="1.0"?> | |
| 2 <macros> | |
| 3 <xml name="requirements"> | |
| 4 <requirements> | |
| 5 <requirement type="package" version="324">ucsc-wigtobigwig</requirement> | |
| 6 <requirement type="package" version="0.2.2">crossmap</requirement> | |
| 7 <yield/> | |
| 8 </requirements> | |
| 9 </xml> | |
| 10 <token name="@WRAPPER_VERSION@">0.2.2</token> | |
| 11 <xml name="stdio"> | |
| 12 <stdio> | |
| 13 <regex match="Aborted (core dumped)" source="stdout" level="fatal"/> | |
| 14 <regex match=".*" source="both" level="log"/> | |
| 15 <exit_code range="1:"/> | |
| 16 </stdio> | |
| 17 </xml> | |
| 18 <xml name="version_command"> | |
| 19 <version_command>CrossMap.py 2>&1 | head -n 1 | grep -E --only-matching 'CrossMap.*'</version_command> | |
| 20 </xml> | |
| 21 <xml name="chain"> | |
| 22 <conditional name="chain_source"> | |
| 23 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)"> | |
| 24 <option value="cached">Local data (in galaxy)</option> | |
| 25 <option value="history">From History</option> | |
| 26 </param> | |
| 27 <when value="cached"> | |
| 28 <param name="input_chain" type="select" label="Lift Over To"> | |
| 29 <options from_file="liftOver.loc"> | |
| 30 <column name="dbkey" index="0"/><!-- species/build 'from' --> | |
| 31 <column name="name" index="1"/><!-- species/build 'to' --> | |
| 32 <column name="value" index="2"/><!-- path of chain file --> | |
| 33 <filter type="data_meta" ref="input" key="dbkey" column="0"/> | |
| 34 </options> | |
| 35 </param> | |
| 36 </when> | |
| 37 <when value="history"> | |
| 38 <param type="data" format="csv" name="input_chain" label="LiftOver chain file"/> | |
| 39 </when> | |
| 40 </conditional> | |
| 41 </xml> | |
| 42 <xml name="source"> | |
| 43 <param name="index_source" type="select" label="Source for Input Data"> | |
| 44 <option value="cached">Local data (in galaxy)</option> | |
| 45 <option value="history">From History</option> | |
| 46 </param> | |
| 47 </xml> | |
| 48 <token name="@HELP_GENERAL@"> | |
| 49 CrossMap | |
| 50 -------- | |
| 51 CrossMap is versatile tool to convert genome coordinates or annotation files between genome | |
| 52 assemblies. It supports mostly commonly used file types, including BAM, BED,BigWig, GFF, | |
| 53 GTF, SAM, Wiggle, and VCF formats. For large plain text file types, such as BED, GFF, GTF | |
| 54 and VCF, reading from remote servers and file compression are supported. | |
| 55 </token> | |
| 56 </macros> |