comparison pyCrac_galaxy/pyFasta2tab.xml @ 0:ae088f9b2f2e draft default tip

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0:ae088f9b2f2e

<tool id="pyFasta2Tab" name="pyFasta2Tab">
	  <description>converter</description>
	  <requirements>
        	<requirement type="package">pyCRAC</requirement>
    	  </requirements>
 	  <command interpreter="python">/usr/local/bin/pyFasta2tab.py -f $input -o $output
 	  </command>
	  <version_command>/usr/local/bin/pyFasta2tab.py --version</version_command>
 	  <inputs>
	      <param name="input" type="data" format="fasta" label="Fasta file -f"/>
 	  </inputs>
	  <param name="label" type="text" format="txt" size="30" value="pyFasta2Tab" label="Enter output file label -o" />
 	  <outputs>
	    <data name="output" format="tabular" label="${label.value}.tab"/>
 	  </outputs>
	  <help>

.. class:: infomark

**pyFasta2Tab**

pyFasta2Tab is part of the pyCRAC_ package. Converts fasta to tabular format. Is used to convert your reference sequences in fasta format to the tabular format that pyCRAC uses for almost all tools.

Example::
    
    >sequence1
    ATAGGATACATAACCATATTATGAGACC
    
Is converted into::

    sequence1   ATAGGATACATAACCATATTATGAGACC
    
The pyCRAC package lo
   
.. _pyCRAC: http://sandergranneman.bio.ed.ac.uk/Granneman_Lab/pyCRAC_software.html

-------

**Parameter list**                                                                                                                                         

Options::

  -f fasta_file, --input_file=fasta_file
                        provide the name and path of your fasta input file.
                        Default is standard input.

        

 	  </help>
</tool>