# HG changeset patch
# User yhoogstrate
# Date 1447362536 18000
# Node ID 1efce8a693cab0d6ea8de5b62bb53ce463647661
# Parent  5ef4ac8f2956d842ae7ef901e656e249e978aa4e
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 2a0f8a26551929e52f6aea1d109b8a3bda81af8b-dirty

diff -r 5ef4ac8f2956 -r 1efce8a693ca crossmap.xml
--- a/crossmap.xml	Thu Nov 12 10:42:27 2015 -0500
+++ b/crossmap.xml	Thu Nov 12 16:08:56 2015 -0500
@@ -14,7 +14,8 @@
     
     <version_command>python $CROSSMAP_ROOT_DIR/bin/CrossMap.py 2&gt;&amp;1 | head -n 1 | grep -E --only-matching 'CrossMap.*'</version_command>
     
-    <command><!-- First line of CrossMap has hardcoded "#!/usr/bin/python". This makes use of Galaxy's python: -->
+    <!-- First line of CrossMap has hardcoded "#!/usr/bin/python". This makes use of Galaxy's python: -->
+    <command><![CDATA[
         python \$CROSSMAP_ROOT_DIR/bin/CrossMap.py
             ${multiple.input_format.replace("sam","bam")}
             
@@ -44,16 +45,16 @@
             "$output"
             
             #if $multiple.input_format in ["bam", "sam"]
-                ; mv "${output}.${multiple.input_format}" "$output"
-                ; mv "${output}.unmap.${multiple.input_format}" "$output_unmapped"
+                && mv "${output}.${multiple.input_format}" "$output"
+                && mv "${output}.unmap.${multiple.input_format}" "$output_unmapped"
             #else if $multiple.input_format in ["vcf"]
-                ; mv "${output}" "$output"
-                ; mv "${output}.unmap" "$output_unmapped"
+                && mv "${output}" "$output"
+                && mv "${output}.unmap" "$output_unmapped"
             #else if $multiple.input_format in ["wig", "bigwig"]
-                ; mv "${output}.bw" "$output"
-                ; mv "${output}.sorted.bgr" "$output2"
+                && mv "${output}.bw" "$output"
+                && mv "${output}.sorted.bgr" "$output2"
             #end if
-    </command>
+    ]]></command>
 
     <inputs>
         <conditional name="multiple">
@@ -73,7 +74,7 @@
                         <option value="history">From History</option>
                     </param>
                         <when value="cached">
-                            <param type="data" format="bam" name="input" label="BAM/SAM file">
+                            <param type="data" format="bam" name="input" label="BAM file">
                                 <validator type="unspecified_build" />
                                 <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build." />
                             </param>
@@ -105,7 +106,7 @@
                         <option value="history">From History</option>
                     </param>
                         <when value="cached">
-                            <param type="data" format="sam" name="input" label="BAM/SAM file">
+                            <param type="data" format="sam" name="input" label="SAM file">
                                 <validator type="unspecified_build" />
                                 <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build." />
                             </param>
@@ -334,6 +335,17 @@
     <tests>
     <!-- BAM/SAM -->
         <test>
+            <param name="input_format" value="bam"/>
+            <param name="index_source" value="history"/>
+            <param name="input" value="test_bam_01_input_a.sam" ftype="bam"/>
+            <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
+            <param name="include_fails" value="False"/>
+            
+            <output name="output" file="test_bam_01_output_a.sam" compare="diff" lines_diff="4"/>
+            <output name="output_unmapped" file="test_bam_01_output_a.unmap.sam"/>
+        </test>
+    
+        <test>
             <param name="input_format" value="sam"/>
             <param name="index_source" value="history"/>
             <param name="input" value="test_bam_01_input_a.sam" ftype="sam"/>
diff -r 5ef4ac8f2956 -r 1efce8a693ca test-data/test_bam_01_input_a.bam
Binary file test-data/test_bam_01_input_a.bam has changed
diff -r 5ef4ac8f2956 -r 1efce8a693ca tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Nov 12 10:42:27 2015 -0500
+++ b/tool_dependencies.xml	Thu Nov 12 16:08:56 2015 -0500
@@ -7,6 +7,6 @@
         <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="bbc4d67d6a37" name="package_crossmap_0_2" owner="yhoogstrate" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="dbe83f5bef40" name="package_crossmap_0_2" owner="yhoogstrate" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>