view reorder.xml @ 36:51cd0307fb70

Phylip's extra ouputs are now stored in the job working directory

<tool id="gd_reorder" name="Reorder individuals" version="1.0.0">
  <description>: exchange rows in the above picture</description>

  <command interpreter="python">
    reorder.py '$input' '$output' '$order'
  </command>

  <inputs>
    <param name="input" type="data" format="gd_indivs" label="Individuals dataset" />
    <param name="order" size="40" type="text" value="" label="New order"/>
  </inputs>

  <outputs>
    <data name="output" format="gd_indivs" metadata_source="input"/>
  </outputs>

  <help>
**Dataset formats**

The input and output datasets are in gd_indivs_ format.

.. _gd_indivs: ./static/formatHelp.html#gd_indivs

-----

**What it does**

The user picks a gd_indivs dataset from their history and specifies
a new ordering.  This tool creates a new gd_indivs dataset with the
individuals reordered as specified by the user.

The new ordering is a list of comma separated ranges (e.g **5,6-12,20**).
Ranges can be either a single number (e.g. **3**) or two dash separated
numbers (e.g. **3-5**).  The numbers represent the line number of
gd_indivs dataset.  Line numbers that are not listed will appear on the
output after the specified line numbers in their same relative ordering.

-----

**Example**

Input dataset (six rows)::

   18  McClintock
   22  Peltonen-Palotie
   26  Sager
   30  Franklin
   34  Auerbach
   38  Stevens

new ordering "**1,3-4**" will return::

   18  McClintock
   26  Sager
   30  Franklin
   22  Peltonen-Palotie
   34  Auerbach
   38  Stevens

new ordering "**3,5,1,6**" will return::

   26  Sager
   34  Auerbach
   18  McClintock
   38  Stevens
   22  Peltonen-Palotie
   30  Franklin

new ordering "**3-1,6,4-5**" will return::

   26  Sager
   22  Peltonen-Palotie
   18  McClintock
   38  Stevens
   30  Franklin
   34  Auerbach
  </help>
</tool>