Mercurial > repos > iuc > crossmap_region
comparison macros.xml @ 0:067f3a52abd6 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit f436317e2f8d451621e297cfc474e43c20d60bb7"
| author | iuc |
|---|---|
| date | Thu, 15 Jul 2021 16:15:32 +0000 |
| parents | |
| children | 08209a7c4cb7 |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:067f3a52abd6 |
|---|---|
| 1 <?xml version="1.0"?> | |
| 2 <macros> | |
| 3 <xml name="requirements"> | |
| 4 <requirements> | |
| 5 <requirement type="package" version="@TOOL_VERSION@">crossmap</requirement> | |
| 6 <yield/> | |
| 7 </requirements> | |
| 8 </xml> | |
| 9 <token name="@TOOL_VERSION@">0.5.2</token> | |
| 10 <token name="@VERSION_SUFFIX@">0</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><![CDATA[ | |
| 20 CrossMap.py 2>&1 | head -n 1 | grep -E --only-matching 'CrossMap.*' | |
| 21 ]]></version_command> | |
| 22 </xml> | |
| 23 <xml name="chain"> | |
| 24 <conditional name="chain_source"> | |
| 25 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)"> | |
| 26 <option value="cached">Local data (in galaxy)</option> | |
| 27 <option value="history">From History</option> | |
| 28 </param> | |
| 29 <when value="cached"> | |
| 30 <param name="input_chain" type="select" label="Lift Over To"> | |
| 31 <options from_data_table="liftOver"> | |
| 32 <filter type="data_meta" ref="input" key="dbkey" column="dbkey"/> | |
| 33 </options> | |
| 34 </param> | |
| 35 </when> | |
| 36 <when value="history"> | |
| 37 <param name="input_chain" type="data" format="txt" label="LiftOver chain file"/> | |
| 38 </when> | |
| 39 </conditional> | |
| 40 </xml> | |
| 41 <token name="@HELP_GENERAL@"> | |
| 42 CrossMap | |
| 43 -------- | |
| 44 CrossMap is versatile tool to convert genome coordinates or annotation files between genome | |
| 45 assemblies. It supports mostly commonly used file types, including BAM, BED,BigWig, GFF, | |
| 46 GTF, SAM, Wiggle, and VCF formats. For large plain text file types, such as BED, GFF, GTF | |
| 47 and VCF, reading from remote servers and file compression are supported. | |
| 48 </token> | |
| 49 </macros> |