# HG changeset patch
# User yhoogstrate
# Date 1447337031 18000
# Node ID f1fa5c4eba47285299c5990fe9ebd6e4269ce5e2
# Parent  83c9c6bec8e91bf8d4bf8efb9d427386433a02e9
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3d455a19e1a217e8a8f07784892d4a521c18fc10-dirty

diff -r 83c9c6bec8e9 -r f1fa5c4eba47 crossmap.xml
--- a/crossmap.xml	Wed Nov 04 10:10:53 2015 -0500
+++ b/crossmap.xml	Thu Nov 12 09:03:51 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&gt;&amp;1 | head -n 1 | grep -E --only-matching 'CrossMap.*'</version_command>
+    <version_command>python \$CROSSMAP_ROOT_DIR/bin/CrossMap.py 2&gt;&amp;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"
diff -r 83c9c6bec8e9 -r f1fa5c4eba47 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Nov 04 10:10:53 2015 -0500
+++ b/tool_dependencies.xml	Thu Nov 12 09:03:51 2015 -0500
@@ -3,10 +3,10 @@
     <package name="ucsc_tools" version="312">
         <repository changeset_revision="ceda74761368" name="package_ucsc_tools_312" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
-    <package name="python" version="2.7">
-        <repository changeset_revision="9cdf46934080" name="package_python_2_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <package name="python" version="2.7.10">
+        <repository changeset_revision="2f32acbaf21a" name="package_python_2_7_10" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="crossmap" version="0.2">
-        <repository changeset_revision="b38e4886f937" name="package_crossmap_0_2" owner="yhoogstrate" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="58c2f3e6f23a" name="package_crossmap_0_2" owner="yhoogstrate" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>