--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rearrange_columns/editColumnHeadings.xml	Mon Feb 27 13:05:18 2017 -0500
@@ -0,0 +1,134 @@
+<tool id="edit_rearrange_columns" name="Remove, rearrange and/or rename columns" version="1.1">
+  <description>in txt-converted FCS files.</description>
+  <stdio>
+    <exit_code range="2" level="fatal" description="Please provide a comma separated list of integers for columns you want to keep." />
+    <exit_code range="3" level="fatal" description="Please provide integers for columns you want to keep." />
+    <exit_code range="4" level="fatal" description="List of column headings and list of selected columns must match. For instance for columns 1,3,4: Marker1,,Marker3." />
+  </stdio>
+  <command><![CDATA[
+    python $__tool_directory__/editColumnHeadings.py -o "${output_file}" -i "${input}"
+ #if $columns
+    -c "${columns}"
+ #end if
+ #if $colnames
+    -n "${colnames}"
+ #end if
+  ]]>
+  </command>
+  <inputs>
+    <param format="flowtext" name="input" type="data" label="Text file"/>
+    <param name="columns" type="text" label="Column order:" value="i.e.:1,5,2" optional="true" help="By default, will keep all columns in the same order."/>
+    <param name="colnames" type="text" label="New column headings:" value="i.e.:Marker1,,Marker4" optional="true" help="By default, will not change the column headings. Check below for more details.">
+    </param>
+  </inputs>
+  <outputs>
+    <data format="flowtext" name="output_file" label="Rearranged ${input.name}"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="input" value="input1.txt"/>
+      <param name="columns" value="3,4,5,6"/>
+      <param name="colnames" value="CD4,CCR3,CD8,CCR7"/>
+      <output name="output_file" file="output1.flowtext"/>
+    </test>
+    <test>
+      <param name="input" value="input2.txt"/>
+      <param name="columns" value="2,3,6,1"/>
+      <param name="colnames" value="i.e.:Marker1,,Marker4"/>
+      <output name="output_file" file="output2.flowtext"/>
+    </test>
+    <test>
+      <param name="input" value="input3.txt"/>
+      <param name="columns" value="i.e.:1,5,2"/>
+      <param name="colnames" value="M1,M2,M3,M4,M5,M6"/>
+      <output name="output_file" file="output3.flowtext"/>
+    </test>
+  </tests>
+  <help><![CDATA[
+   This tool enables the removal, rearrangement and/or renaming of text file columns.
+
+-----
+
+**Input files**
+
+This tool requires txt, flowtext or tabular files as input.
+
+**Column order**
+
+Please indicate columns to keep in the order in which they should be (comma-separated list).
+This field is optional.
+
+**Column names**
+
+Please indicate the new columns headings in the order in which they should appear in the ouptut file (comma-separated list). The number of headings should match the number of columns in the output.
+This field is optional.
+
+.. class: warningmark
+
+When providing column order AND new column headings the column count for each must match. See below for an example.
+
+**Output file**
+
+The output flowtext file is a copy of the input file with rearranged and/or renamed columns.
+
+-----
+
+**Examples**
+
+**Input file**::
+
+   Marker1 Marker2 Marker3 Marker4 Marker5
+   4       45      123     1956    62534
+   3       65      104     1254    36576
+   7       26      767     4124    42235
+   4       56      323     7623    74634
+   5       83      532     6256    34763
+   4       15      877     9312    21265
+
+*Example 1*
+
+- Column order: 5,3,2,4
+- Column names: Default
+
+*Output1*::
+
+   Marker5 Marker3 Marker2 Marker4
+   62534   123     45      1956
+   36576   104     65      1254
+   42235   767     26      4124
+   74634   323     56      7623
+   34763   532     83      6256
+   21265   877     15      9312
+
+*Example 2*
+
+- Column order: 5,3,2,4
+- Column names: Mar34,,Mar7,
+
+*Output2*::
+
+   Mar34 Marker3 Mar7 Marker4
+   62534 123     45   1956
+   36576 104     65   1254
+   42235 767     26   4124
+   74634 323     56   7623
+   34763 532     83   6256
+   21265 877     15   9312
+
+*Example 3*
+
+- Column order: Default
+- Column names: Mar23,,,Mar7,Mar8
+
+*Output3*::
+
+   Mar23 Marker2 Marker3 Mar7 Mar8
+   4     45      123     1956 62534
+   3     65      104     1254 36576
+   7     26      767     4124 42235
+   4     56      323     7623 74634
+   5     83      532     6256 34763
+   4     15      877     9312 21265
+  ]]>
+  </help>
+</tool>