--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/columnArrange.xml	Fri Oct 16 14:31:13 2015 -0400
@@ -0,0 +1,83 @@
+<tool id="bg_column_arrange_by_header" name="Column arrange" version="0.1">
+    <description>by header name</description>
+    <requirements>
+        <requirement type="package" version="0.14.1">pandas</requirement>
+    </requirements>
+    <command interpreter="python">
+    <![CDATA[
+        column_arrange.py
+          --columns
+        #for token in $rep_param_columns:
+            "$token.param_column"
+        #end for
+        --in $param_input
+        --out $output
+    ]]>
+    </command>
+    <inputs>
+        <param format="tabular" name="param_input" type="data" label="file to rearrange" />
+        <repeat name ="rep_param_columns" min="1" title="Specify the first few columns by name">
+            <param name="param_column" type="text" value="" label="column">
+                <sanitizer>
+                    <valid initial="string.printable">
+                        <remove value="&apos;"/>
+                    </valid>
+                </sanitizer>
+            </param>
+        </repeat>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="output" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="param_input" value="columnarrange_input1.tab"/>
+            <repeat name="rep_param_columns">
+                <param name="param_column" value="fname"/>
+            </repeat>
+            <repeat name="rep_param_columns">
+                <param name="param_column" value="age"/>
+            </repeat>
+            <output name="out" file="columnarrange_result1.tab"/>
+        </test>
+        <test>
+            <param name="param_input" value="columnarrange_input2.tab"/>
+            <repeat name="rep_param_columns">
+                <param name="param_column" value="first name"/>
+            </repeat>
+            <repeat name="rep_param_columns">
+                <param name="param_column" value="nationality"/>
+            </repeat>
+            <output name="out" file="columnarrange_result2.tab"/>
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+With this tool you can specify (by naming the header) which columns need to be leftmost.
+The columns which are not specified will be ordered as before, right of the columns which were specified.
+
+Input file::
+
+    AHeader BHeader CHeader DHeader
+    a       b       c       d
+    a       b       c       d
+
+Specifying **CHeader** and **BHeader**, as the columns that should be leftmost, generates::
+
+    CHeader BHeader AHeader DHeader
+    c       b       a       d
+    c       b       a       d
+
+    </help>
+    <citations>
+        <citation type="bibtex">
+            @ARTICLE{bgruening_galaxytools,
+                Author = {Björn Grüning, Cameron Smith, Torsten Houwaart, Nicola Soranzo, Eric Rasche},
+                keywords = {bioinformatics, ngs, galaxy, cheminformatics, rna},
+                title = {{Galaxy Tools - A collection of bioinformatics and cheminformatics tools for the Galaxy environment}},
+                url = {https://github.com/bgruening/galaxytools}
+            }
+        </citation>
+    </citations>
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/column_arrange.py	Fri Oct 16 14:31:13 2015 -0400
@@ -0,0 +1,18 @@
+#!/usr/bin/env python 
+import pandas as pd
+import argparse
+
+parser = argparse.ArgumentParser()
+parser.add_argument('-i', '--input', help='Tabular Input File Name')
+parser.add_argument('-o','--output', help='Tabular Output File')
+parser.add_argument('-c', '--columns', nargs='+', help='Column Headers to Sort By')
+args=parser.parse_args()
+
+cols = args.columns
+table = pd.read_csv(args.input, sep='\t')
+blist = list(table.columns)
+for token in cols:
+    blist.remove(token)
+sorted_table = table[args.columns + blist]
+# write without index, seperated by tabs
+sorted_table.to_csv(args.output, sep='\t', index=False)

Binary file column_arrange_by_header.tar.gz has changed

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/columnarrange_input1.tab	Fri Oct 16 14:31:13 2015 -0400
@@ -0,0 +1,5 @@
+name	fname	age	nationality
+Woryt	Heiko	22	german
+Humte	Alfons	49	austrian
+Witz	Gerald	12	french
+Koulibaly	Ansgard	33	nigerian

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/columnarrange_input2.tab	Fri Oct 16 14:31:13 2015 -0400
@@ -0,0 +1,5 @@
+second name	age	nationality	first name
+Woryt	22	german	Heiko
+Humte	49	austrian	Alfons
+Witz	12	french	Gerald
+Koulibaly	33	nigerian	Ansgard

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/columnarrange_result1.tab	Fri Oct 16 14:31:13 2015 -0400
@@ -0,0 +1,5 @@
+fname	age	name	nationality
+Heiko	22	Woryt	german
+Alfons	49	Humte	austrian
+Gerald	12	Witz	french
+Ansgard	33	Koulibaly	nigerian

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/columnarrange_result2.tab	Fri Oct 16 14:31:13 2015 -0400
@@ -0,0 +1,5 @@
+first name	nationality	second name	age
+Heiko	german	Woryt	22
+Alfons	austrian	Humte	49
+Gerald	french	Witz	12
+Ansgard	nigerian	Koulibaly	33

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Fri Oct 16 14:31:13 2015 -0400
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="pandas" version="0.14.1">
+        <repository changeset_revision="ac9f317487a9" name="package_pandas_0_14" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>