diff multi_join_serial.xml @ 3:0aa0ebcd307c draft

Uploaded

--- a/multi_join_serial.xml	Wed Apr 15 14:43:04 2015 -0400
+++ b/multi_join_serial.xml	Wed Apr 15 16:31:04 2015 -0400
@@ -7,7 +7,7 @@
 	#end for
 
 	#for $i, $s in enumerate( $Files )
-	   /opt/galaxy/galaxy-dist/tools/ngs_rna/Unreleased/run-multi_join_serial.pl --join_file $s.joinMe --join_col $s.joinCol --iteration $i --totalfiles $j --with_header $headerYes --resultsfile $Joined_all --log $log
+	   /opt/galaxy/galaxy-dist/tools/ngs_rna/Unreleased/run-multi_join_serial.pl --join_file $s.joinMe --join_col $s.joinCol --iteration $i --totalfiles $j --with_header $headerYes --resultsfile $Joined_all
 	  ##print "loop iteration $i.\n";
           ;
         #end for
@@ -24,7 +24,6 @@
   </inputs>
   <outputs>
     	<data format="tabular" name="Joined_all" label="Multi-Join result"/>
-	<data format="txt" name="log" label="debug_info"/>
   </outputs>
   <tests>
      <test>
@@ -36,18 +35,12 @@
 	<param name="Files_2joinCol" value="2"/>
 	<param name="headerYes" value="yes"/>
 	<output name="Joined_all" value="multi_join_serial_out.tab" ftype="tabular"/>
-	<output name="log" value="multi_join_serial_debug.txt" ftype="tabular"/>
      <test/>
   <tests/>
   <help>
 
 This tool performs a left-outer join on multiple (at least two) files using a perl script that Ron wrote (thanks, Ron!). The resulting joined file will have the same number of rows as the first file chosen and subsequent files' matches will be shown if present. Rows in the first file without matches in the other files will have empty cells. If none of the input files have a header present, a simple column number header will be added to the output file to denote the start of each set of matches (from each file, start denoted by "C1").
 
-To convert from left-outer join result to inner join result (only include rows in common to all datasets), run Filter out rows and columns with non-numeric values tool with the following options selected (last 3 options, all are drop-down select menus):
-	1. Replace/remove: Empty only
-	2. Remove entire column or row (leave default)
-	3. Remove non-numeric/empty cell-containing ROWS from dataset
-
 
 .. class:: warningmark
 
@@ -58,7 +51,6 @@
 	1. Click Add new File for each tab-delimited file you'd like to add and the column you want to join on.
 	2. After adding all files to join, select whether the headers should all be preserved (this should be Yes if all input datasets have headers).
 	3. Click Execute.
-	4. Please report any issues and/or suggestions to Christy.
 
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