<tool id="PSM.Plot" name="PSM Plotter" version="1.94.2">
  <description>plots data from PSM Prep</description>
  <version_command>perl cpt_psm_1_plot.pl --version</version_command>
  <stdio>
    <exit_code range="1:" level="fatal"/>
  </stdio>
  <requirements>
    <requirement type="package" version="5.22.1">perl</requirement>
    <requirement type="package">perl-bioperl</requirement>
    <requirement type="package">perl-moose</requirement>
    <requirement type="package">perl-ipc-run</requirement>
    <requirement type="package">perl-getopt-long-descriptive</requirement>
  </requirements>
  <command detect_errors="aggressive"><![CDATA[
perl -Mlib='$__tool_directory__/lib' '$__tool_directory__/cpt_psm_1_plot.pl'
--galaxy
--outfile_supporting '$__new_file_path__'
--file "${file}"

--user_ordering "${user_ordering}"

#if $percent_filled and $percent_filled is not "None":
--percent_filled "${percent_filled}"
#end if

#if $ig_dist and $ig_dist is not "None":
--ig_dist "${ig_dist}"
#end if

#if $stroke_thickness and $stroke_thickness is not "None":
--stroke_thickness "${stroke_thickness}"
#end if

#if $every_nth and $every_nth is not "None":
--every_nth "${every_nth}"
#end if

#if $evalue and $evalue is not "None":
--evalue "${evalue}"
#end if

#if $dice and $dice is not "None":
--dice "${dice}"
#end if

#if $mismatch and $mismatch is not "None":
--mismatch "${mismatch}"
#end if

#if $gap_penalty and $gap_penalty is not "None":
--gap_penalty "${gap_penalty}"
#end if

#if $match and $match is not "None":
--match "${match}"
#end if

--output_circos_confs "${output_circos_confs}"

--output_circos_confs_files_path "${output_circos_confs.files_path}"

--output_circos_confs_format "${output_circos_confs_format}"

--output_circos_confs_id "${output_circos_confs.id}"

]]></command>
  <inputs>
    <param name="file" help="PSM2 Data File" optional="False" label="file" type="data"/>
    <param name="user_ordering" help="List of genome IDs used in the analysis, can be comma/space/newline separated." optional="False" label="user_ordering" type="text"/>
    <param min="0.1" value="0.8" max="1.0" name="percent_filled" optional="True" help="Percentage of a whole block that an individual gene is" type="float" label="percent_filled"/>
    <param value="100" name="ig_dist" help="Maximum length of links between genome comparisons" optional="True" label="ig_dist" type="integer"/>
    <param min="1" value="2" max="10" name="stroke_thickness" optional="True" help="Thickness of inter-genome links" type="integer" label="stroke_thickness"/>
    <param value="20" name="every_nth" optional="True" help="Plot every Nth gene a modified version of the main color for that genome" label="every_nth" type="integer"/>
    <param value="0.0001" name="evalue" optional="True" help="Evalue cutoff" label="evalue" type="float"/>
    <param value="50" name="dice" optional="True" help="Dice cutoff" label="dice" type="float"/>
    <param value="-0.1" name="mismatch" optional="True" help="Mismatch Score" label="mismatch" type="float"/>
    <param value="0.0" name="gap_penalty" optional="True" help="Gap Penalty" label="gap_penalty" type="float"/>
    <param value="5" name="match" optional="True" help="Match Score" label="match" type="float"/>
    <param name="output_circos_confs_format" help="Output Circos Conf Object" optional="False" label="Format of output_circos_confs" type="select">
      <option value="zip">zip</option>
    </param>
  </inputs>
  <outputs>
    <data name="output_circos_confs" format="tar.gz">
      <change_format>
        <when input="output_circos_confs_format" value="tar.gz" format="tar.gz"/>
        <when input="output_circos_confs_format" value="zip" format="zip"/>
        <when input="output_circos_confs_format" value="tar" format="tar"/>
      </change_format>
    </data>
  </outputs>
  <help>NAME
====

PSM Plotter

DESCRIPTION
===========

Following the execution of the PSM Prep tool, this tool plots a subset
of those genomes as ciruclar tracks with protein-protein relationships
plotted as links between the boxes representing proteins.

IMPORTANT PARAMETERS
--------------------

-  ``user_ordering``

   This parameter controls the order in which genomes are aligned and
   then plotted. This MUST contain (comma/space) separated values
   listing the order (outside to in) in which you want your genomes to
   appear. In this field, type the name of each genome. The name can be
   found on the first line of the file under "LOCUS NC\_00000001", where
   NC\_00000001 would be the genome's name.

-  ``evalue``, ``dice``

   Adjusting these parameters will affect which links are plotted. Links
   are heatmapped into bins based on dice score as that is the easiest
   measure to work with, and scales nicely from 0 to 100. For example, a
   link with a dice score of 20-29 would be plotted as 20% black
   (grey20), whereas a dice score of 90+ would be plotted as solid black

-  ``mismatch``, ``gap_penalty``, ``match``

   These parameters control the Needleman-Wunsch Multiple Sequence
   Alignment library's scoring scheme. Mismatch scores are generally
   negative and discourage unrelated proteins from being plotted in a
   line together. Match scores encourage related proteins to line up.
   Gap penalty is set at zero as we generally prefer gaps to mismatches
   in this tool; phage genomes are small and gaps are "cheap" to use,
   whereas mismatches can sometimes give an incorrect impression of
   relatedness. That said, how your plots look is completely up to you
   and we encourage experimentation!

-  ``every_nth``

   Every Nth gene in a genome will be plotted a slightly different
   color.

Why Can't I Control Colors?
---------------------------

::

    Brewer colors compose Brewer palettes which have been manually defined by
    Cynthia Brewer for their perceptual properties.

    http://circos.ca/tutorials/lessons/configuration/colors/

Color palette choice is very important to creating an attractive and
easy to read graphic. In the words of Dr. Krzywinski, `Color palettes
matter &lt;http://mkweb.bcgsc.ca/jclub/biovis/brewer/colorpalettes.pdf&gt;`__.
Humans selecting from an RGB/HSV color palette tend to make poor
choices, so we've removed the option in lieu of using the very
attractive `Brewer Palettes &lt;http://colorbrewer2.org/&gt;`__. Specifically,
I've selected the 8 class qualtitative "Accent" color set, which has
produced some very nice maps. If you would like the option of selecting
amongst the other 8-class qualitative color sets, please file a bug
report and let me know.
</help>
  <tests/>
</tool>