modified mergeCols to take advantage of repeat tag. Looks foolproof now.

tools/filters/mergeCols.py

@@ -5,9 +5,19 @@ def stop_err( msg ):
     sys.exit()
 
 def __main__():
-    infile =  open ( sys.argv[1], 'r')
-    cols   =  ( re.sub( '\s*','',sys.argv[2] ) ).split( ',' )
-    outfile = open ( sys.argv[3], 'w')        
+    try:
+        infile =  open ( sys.argv[1], 'r')
+#    cols   =  ( re.sub( '\s*','',sys.argv[2] ) ).split( ',' )
+        outfile = open ( sys.argv[2], 'w')
+    except:
+        stop_err( 'Cannot open or create a file\n' )
+        
+    if len( sys.argv ) < 4:
+        stop_err( 'No columns to merge' )
+    else:
+        cols = sys.argv[3:]        
+
+    skipped_lines = 0
 
     for line in infile:
         line = line.rstrip( '\r\n' )
@@ -16,10 +26,13 @@ def __main__():
             line += '\t'
             for col in cols:
                 try:
-                    line += fields[ int( col.lstrip( 'c' ) ) -1 ]
+                    line += fields[ int( col ) -1 ]
                 except:
-                    stop_err( 'Column %s does not appear in the input file' % str( col ) )
+                    skipped_lines += 1
+                    
             print >>outfile, line
             
+    if skipped_lines > 0:
+        print 'Skipped %d invalid lines' % skipped_lines
             
 if __name__ == "__main__" : __main__()

tools/filters/mergeCols.xml

@@ -1,29 +1,46 @@
-<tool id="mergeCols1" name="Merge columns">
-  <description>together</description>
-  <command interpreter="python">mergeCols.py $input "$columnList" $out_file1</command>
-  <inputs>
-    <param name="columnList" size="10" type="text" value="c1,c2" label="Merge columns"/>
-    <param format="tabular" name="input" type="data" label="In"/>
-  </inputs>
-  <outputs>
-    <data format="tabular" name="out_file1" />
-  </outputs>
-<tests>
+<tool id="mergeCols1" name="Merge Columns" version="1.0.1">
+  <description>together</description>
+  <command interpreter="python">
+   mergeCols.py 
+      $input1
+      $out_file1
+      $col1
+      $col2
+      #for $col in $columns
+        ${col.datacol}
+      #end for
+  </command>
+  <inputs>
+    <param format="tabular" name="input1" type="data" label="Select data" help="Query missing? See TIP below."/>
+    <param name="col1" label="Merge column" type="data_column" data_ref="input1" />
+    <param name="col2" label="with column" type="data_column" data_ref="input1" help="Need to add more columns? Use controls below."/>
+    <repeat name="columns" title="Columns">
+      <param name="datacol" label="Add column" type="data_column" data_ref="input1" />
+    </repeat>
+  </inputs>
+  <outputs>
+    <data format="tabular" name="out_file1" />
+  </outputs>
+  <tests>
     <test>
-      <param name="columnList" value="c4, c1"/>
-      <param name="input" value="1.bed"/>
+      <param name="input1" value="1.bed"/>
+      <param name="col1" value="4" />
+      <param name="col2" value="1" />
+      <param name="datacol" value="6" />
       <output name="out_file1" file="mergeCols.dat"/>
     </test>
   </tests>
-<help>
-
+<help>
+
+.. class:: infomark
+
+**TIP:** If your data is not TAB delimited, use *Text Manipulation-&gt;Convert*
+
+-----
+
 **What it does**
 
-This tool merges columns together
-
-- Columns are specified as **c1**, **c2**, and so on. Column count begins with **1**
-- Columns can be specified in any order (e.g., **c2,c1,c6**)
-
+This tool merges columns together. Any number of valid columns can be merged in any order.
 
 -----
 
@@ -39,9 +56,8 @@ merging columns "**c5,c1**" will return::
    1 10   1000  gene1 chr chr1
    2 100  1500  gene2 chr chr2
 
-.. class:: infomark
+.. class:: warningmark
    
 Note that all original columns are preserved and the result of merge is added as the rightmost column.
-
-</help>
-</tool>
+  </help>
+</tool>