Mercurial > repos > yhoogstrate > crossmap

diff crossmap.xml @ 6:5ef4ac8f2956 draft

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 7ab6217b10b7483a03140eddc9c0567551b41b62
author yhoogstrate
date Thu, 12 Nov 2015 10:42:27 -0500
parents 9da7052375b9
children 1efce8a693ca
line wrap: on
line diff
--- a/crossmap.xml	Thu Nov 12 09:06:25 2015 -0500
+++ b/crossmap.xml	Thu Nov 12 10:42:27 2015 -0500
@@ -12,7 +12,7 @@
         <regex match=".*" source="both" level="log"/>
     </stdio>
     
-    <version_command>python \$CROSSMAP_ROOT_DIR/bin/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><!-- First line of CrossMap has hardcoded "#!/usr/bin/python". This makes use of Galaxy's python: -->
         python \$CROSSMAP_ROOT_DIR/bin/CrossMap.py
@@ -304,7 +304,7 @@
     </inputs>
     
     <outputs>
-        <data format="text" name="output" label="${tool.name} on ">
+        <data format="text" name="output" label="${tool.name} on ${on_string}">
             <change_format>
                 <when input="multiple.input_format" value="bam" format="bam" />
                 <when input="multiple.input_format" value="sam" format="sam" />
@@ -312,19 +312,19 @@
                 <when input="multiple.input_format" value="bigwig" format="bigwig" />
                 <when input="multiple.input_format" value="gff" format="gff" />
                 <when input="multiple.input_format" value="vcf" format="vcf" />
-                <when input="imultiple.nput_format" value="wig" format="bigwig" />
+                <when input="multiple.input_format" value="wig" format="bigwig" />
             </change_format>
         </data>
         
-        <data format="text" name="output_unmapped" label="${tool.name} unmapped on ">
-            <filter>input_format in ["bam" , "vcf"]</filter>
+        <data format="text" name="output_unmapped" label="${tool.name} (unmapped) on ${on_string}">
+            <filter>multiple['input_format'] in ["bam" , "vcf"]</filter>
             <change_format>
                 <when input="multiple.input_format" value="bam" format="bam" />
                 <when input="multiple.input_format" value="vcf" format="vcf" />
             </change_format>
         </data>
-        <data format="text" name="output2" label="${tool.name} on ">
-            <filter>input_format in ["wig"]</filter>
+        <data format="text" name="output2" label="${tool.name} (bedgraph) on ${on_string}">
+            <filter>multiple['input_format'] in ["wig"]</filter>
             <change_format>
                 <when input="multiple.input_format" value="wig" format="bedgraph" />
             </change_format>