annotate emboss_isochore.xml @ 10:d49956b87f7e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1

<tool id="EMBOSS: isochore47" name="isochore" version="5.0.0.1">
  <description>Plots isochores in large DNA sequences</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <command>perl '$__tool_directory__/emboss_single_outputfile_wrapper.pl' isochore -sequence '$input1' -outfile '$ofile2' -goutfile '$ofile1' -graph png -window $window -shift $shift -auto</command>
  <inputs>
    <param name="input1" type="data" format="fasta" label="Sequences" />
    <param name="window" type="integer" value="1000" label="Window size" />
    <param name="shift" type="integer" value="100" label="Shift increment" />
  </inputs>
  <outputs>
    <data name="ofile1" format="png" />
    <data name="ofile2" format="isochore" />
  </outputs>
  <!-- <tests>
    <test>
      <param name="input1" value="2.fasta"/>
      <param name="window" value="1000"/>
      <param name="shift" value="100"/>
      <output name="ofile1" file="emboss_isochore_out.isochore"/>
      <output name="ofile2" file="emboss_isochore_out.isochore"/>
    </test>
         <test>
      <param name="input1" value="2.fasta"/>
      <param name="window" value="1000"/>
      <param name="shift" value="100"/>
      <output name="ofile2" file="emboss_isochore_out.isochore"/>
    </test>
  </tests>-->
  <help>
.. class:: warningmark

The input dataset needs to be sequences.

-----

**Syntax**

This application plots GC content over a sequence. It is intended for large sequences such as complete chromosomes or large genomic contigs, although interesting results can also be obtained from shorter sequences. You can view the original documentation here_.

    .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/isochore.html

- Both **Window size** and **Shift increment** are intergers.

-----

**Example**

- Input sequences::

    >hg18_dna range=chrX:151073054-151073376 5'pad=0 3'pad=0 revComp=FALSE strand=? repeatMasking=none
    TTTATGTCTATAATCCTTACCAAAAGTTACCTTGGAATAAGAAGAAGTCA
    GTAAAAAGAAGGCTGTTGTTCCGTGAAATACTGTCTTTATGCCTCAGATT
    TGGAGTGCTCAGAGCCTCTGCAGCAAAGATTTGGCATGTGTCCTAGGCCT
    GCTCAGAGCAGCAAATCCCACCCTCTTGGAGAATGAGACTCATAGAGGGA
    CAGCTCCCTCCTCAGAGGCTTCTCTAATGGGACTCCAAAGAGCAAACACT
    CAGCCCCATGAGGACTGGCCAGGCCAAGTGGTGTGTGGGAACAGGGAGCA
    GCGGTTTCCAAGAGGATACAGTA

- Output data file::

    Position	Percent G+C 1 .. 323
    80	0.422
    112	0.460
    144	0.509
    176	0.534
    208	0.553
    240	0.553

- Output graphics file:

.. image:: ./static/emboss_icons/isochore.png
  </help>
  <expand macro="citations" />
</tool>