Mercurial > repos > yhoogstrate > crossmap

comparison crossmap.xml @ 5:9da7052375b9 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1
author yhoogstrate
date Thu, 12 Nov 2015 09:06:25 -0500
parents 0e0294f5ab3a
children 5ef4ac8f2956
comparison
equal deleted inserted replaced
4:86e9f82dd2b2 5:9da7052375b9
1 <tool id="crossmap" name="CrossMap" version="0.2.c"> 1 <tool id="crossmap" name="CrossMap" version="0.2.d">
2 <description>Convert genome coordinates or annotation files between genome assemblies</description> 2 <description>Convert genome coordinates or annotation files between genome assemblies</description>
3 3
4 <requirements> 4 <requirements>
5 <requirement type="package" version="312">ucsc_tools</requirement> 5 <requirement type="package" version="312">ucsc_tools</requirement>
6 <requirement type="package" version="2.7">python</requirement> 6 <requirement type="package" version="2.7">python</requirement>
10 <stdio> 10 <stdio>
11 <regex match="Usage: CrossMap.py" source="stdout" level="fatal"/> 11 <regex match="Usage: CrossMap.py" source="stdout" level="fatal"/>
12 <regex match=".*" source="both" level="log"/> 12 <regex match=".*" source="both" level="log"/>
13 </stdio> 13 </stdio>
14 14
15 <version_command>CrossMap.py 2&gt;&amp;1 | head -n 1 | grep -E --only-matching 'CrossMap.*'</version_command> 15 <version_command>python \$CROSSMAP_ROOT_DIR/bin/CrossMap.py 2&gt;&amp;1 | head -n 1 | grep -E --only-matching 'CrossMap.*'</version_command>
16 16
17 <command> 17 <command><!-- First line of CrossMap has hardcoded "#!/usr/bin/python". This makes use of Galaxy's python: -->
18 CrossMap.py 18 python \$CROSSMAP_ROOT_DIR/bin/CrossMap.py
19 ${multiple.input_format.replace("sam","bam")} 19 ${multiple.input_format.replace("sam","bam")}
20 20
21 #if $multiple.input_format == "vcf" and $multiple.seq_source.index_source == "cached" 21 #if $multiple.input_format == "vcf" and $multiple.seq_source.index_source == "cached"
22 <!-- This is the 2nd dbkey, and the corresponding value has to be looked up --> 22 <!-- This is the 2nd dbkey, and the corresponding value has to be looked up -->
23 "${filter(lambda x: str( x[1] ) == str($multiple.seq_source.input_chain ), $__app__.tool_data_tables['liftOver'].get_fields())[0][2] }" 23 "${filter(lambda x: str( x[1] ) == str($multiple.seq_source.input_chain ), $__app__.tool_data_tables['liftOver'].get_fields())[0][2] }"