Mercurial > repos > yhoogstrate > crossmap
changeset 5:9da7052375b9 draft
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 | 86e9f82dd2b2 |
| children | 5ef4ac8f2956 |
| files | crossmap.xml tool_dependencies.xml |
| diffstat | 2 files changed, 7 insertions(+), 7 deletions(-) [+] |
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--- a/crossmap.xml Wed Nov 04 10:11:58 2015 -0500 +++ b/crossmap.xml Thu Nov 12 09:06:25 2015 -0500 @@ -1,4 +1,4 @@ -<tool id="crossmap" name="CrossMap" version="0.2.c"> +<tool id="crossmap" name="CrossMap" version="0.2.d"> <description>Convert genome coordinates or annotation files between genome assemblies</description> <requirements> @@ -12,10 +12,10 @@ <regex match=".*" source="both" level="log"/> </stdio> - <version_command>CrossMap.py 2>&1 | head -n 1 | grep -E --only-matching 'CrossMap.*'</version_command> + <version_command>python \$CROSSMAP_ROOT_DIR/bin/CrossMap.py 2>&1 | head -n 1 | grep -E --only-matching 'CrossMap.*'</version_command> - <command> - CrossMap.py + <command><!-- First line of CrossMap has hardcoded "#!/usr/bin/python". This makes use of Galaxy's python: --> + python \$CROSSMAP_ROOT_DIR/bin/CrossMap.py ${multiple.input_format.replace("sam","bam")} #if $multiple.input_format == "vcf" and $multiple.seq_source.index_source == "cached"
--- a/tool_dependencies.xml Wed Nov 04 10:11:58 2015 -0500 +++ b/tool_dependencies.xml Thu Nov 12 09:06:25 2015 -0500 @@ -3,10 +3,10 @@ <package name="ucsc_tools" version="312"> <repository changeset_revision="2d6bafd63401" name="package_ucsc_tools_312" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> - <package name="python" version="2.7"> - <repository changeset_revision="eb37ce21eef1" name="package_python_2_7" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + <package name="python" version="2.7.10"> + <repository changeset_revision="73631e818d3d" name="package_python_2_7_10" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="crossmap" version="0.2"> - <repository changeset_revision="e4de7f1284ce" name="package_crossmap_0_2" owner="yhoogstrate" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="bbc4d67d6a37" name="package_crossmap_0_2" owner="yhoogstrate" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency>