# HG changeset patch
# User galaxyp
# Date 1493311464 14400
# Node ID 1d5f2947f3f951f9d318641bef5a874f5f57708c
# Parent  22e8523066d572f690aec3a4fce7343f47831dee
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 50c26f7fbe8a2bd1347c860d7a62480865efc254

diff -r 22e8523066d5 -r 1d5f2947f3f9 readme.md
--- a/readme.md	Tue Apr 18 15:27:28 2017 -0400
+++ b/readme.md	Thu Apr 27 12:44:24 2017 -0400
@@ -102,10 +102,32 @@
     [...]
     ]]>
     ```
+    
+ * In `IDFileConverter.xml` the following is needed in the command section at the beginning (check your file to know what to copy where):
+ 
+   ```
+    <command><![CDATA[
+   
+      ## check input file type
+      #set $in_type = $param_in.ext
 
- * In `FileConverter.xml` add `auto_format="true"` to the output, e.g.:
+      ## create the symlinks to set the proper file extension, since IDFileConverter uses them to choose how to handle the input files
+      ln -s '$param_in' 'param_in.${in_type}' &&
+
+      IDFileConverter
+
+      #if $param_in:
+        -in 'param_in.${in_type}'
+      #end if
+
+        [...]
+        ]]>
+    ```
+
+ * In `IDFileConverter.xml` and `FileConverter.xml` add `auto_format="true"` to the output, e.g.:
  
-        <data name="param_out" metadata_source="param_in" auto_format="true"/>
+   - `<data name="param_out" auto_format="true"/>`
+   - `<data name="param_out" metadata_source="param_in" auto_format="true"/>`
         
  * To add an example test case to `DecoyDatabase.xml` add the following after the output section. If standard settings change you might have to adjust the options and/or the test files.