# HG changeset patch
# User yhoogstrate
# Date 1447353472 18000
# Node ID 5500eeb6560529273fdb1fcfea8599d0a30cf633
# Parent  00a4682c94bc66b464cf88151b5b315fdfff519d
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit dc4deb40aeefdf8b20f496626fe0ba28cbe248ed

diff -r 00a4682c94bc -r 5500eeb65605 crossmap.xml
--- a/crossmap.xml	Thu Nov 12 10:37:25 2015 -0500
+++ b/crossmap.xml	Thu Nov 12 13:37:52 2015 -0500
@@ -44,14 +44,14 @@
             "$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>
 
@@ -73,7 +73,7 @@
                         <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 +105,7 @@
                         <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 +334,17 @@
     <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 00a4682c94bc -r 5500eeb65605 test-data/test_bam_01_input_a.bam
Binary file test-data/test_bam_01_input_a.bam has changed