# HG changeset patch
# User bgruening
# Date 1425308372 18000
# Node ID b84c81b7d762d91e92c3d89c89db44cb2ba92283

Uploaded

diff -r 000000000000 -r b84c81b7d762 columnArrange.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/columnArrange.xml	Mon Mar 02 09:59:32 2015 -0500
@@ -0,0 +1,78 @@
+<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>
+  <!--<code file="column_sort_tab_options.py"/>-->
+  <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" size="50" value="" label="column">
+        <sanitizer>
+            <valid initial="string.printable">
+                <remove value="&apos;"/>
+            </valid>
+        </sanitizer>
+      </param>
+      
+    </repeat>
+    <!--<param name="param_columns_dummy" type="select" optional="true" multiple="true" label="Columns" dynamic_options="get_options(param_input.file_name)" help="Do not select columns here, this field just shows possible columns."/>-->
+  </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>
+</tool>
diff -r 000000000000 -r b84c81b7d762 column_arrange.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/column_arrange.py	Mon Mar 02 09:59:32 2015 -0500
@@ -0,0 +1,20 @@
+#!/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)
+
diff -r 000000000000 -r b84c81b7d762 test-data/columnarrange_input1.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/columnarrange_input1.tab	Mon Mar 02 09:59:32 2015 -0500
@@ -0,0 +1,5 @@
+name	fname	age	nationality
+Woryt	Heiko	22	german
+Humte	Alfons	49	austrian
+Witz	Gerald	12	french
+Koulibaly	Ansgard	33	nigerian
diff -r 000000000000 -r b84c81b7d762 test-data/columnarrange_input2.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/columnarrange_input2.tab	Mon Mar 02 09:59:32 2015 -0500
@@ -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
diff -r 000000000000 -r b84c81b7d762 test-data/columnarrange_result1.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/columnarrange_result1.tab	Mon Mar 02 09:59:32 2015 -0500
@@ -0,0 +1,5 @@
+fname	age	name	nationality
+Heiko	22	Woryt	german
+Alfons	49	Humte	austrian
+Gerald	12	Witz	french
+Ansgard	33	Koulibaly	nigerian
diff -r 000000000000 -r b84c81b7d762 test-data/columnarrange_result2.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/columnarrange_result2.tab	Mon Mar 02 09:59:32 2015 -0500
@@ -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
diff -r 000000000000 -r b84c81b7d762 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Mon Mar 02 09:59:32 2015 -0500
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="pandas" version="0.14.1">
+        <repository changeset_revision="ef98e20431a7" name="package_pandas_0_14" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>