<tool id="PSM.Comp" name="PSM Comparison Table" version="1.94">
  <description>aligns and lists data from PSM Prep</description>
  <version_command>perl cpt_psm_2_gentable.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_2_gentable.pl'
--galaxy
--outfile_supporting '$__new_file_path__'
--file "${file}"

#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

--diff_table "${diff_table}"
--diff_table_files_path "${diff_table.files_path}"
--diff_table_format TSV_U
--diff_table_id "${diff_table.id}"

--blastclust "${blastclust}"
--blastclust_files_path "${blastclust.files_path}"
--blastclust_format TSV_U
--blastclust_id "${blastclust.id}"

]]></command>
  <inputs>
    <param name="file" help="PSM2 Data File" optional="False" label="file" type="data"/>
    <param value="0.0001" name="evalue" help="Evalue cutoff" optional="True" label="evalue" type="float"/>
    <param value="50" name="dice" help="Dice cutoff" optional="True" label="dice" type="float"/>
    <param value="-1" name="mismatch" help="Mismatch Score" optional="True" label="mismatch" type="float"/>
    <param value="0.0" name="gap_penalty" help="Gap Penalty" optional="True" label="gap_penalty" type="float"/>
    <param value="5" name="match" help="Match Score" optional="True" label="match" type="float"/>
  </inputs>
  <outputs>
    <data name="diff_table" format="tabular">
    </data>
    <data name="blastclust" format="tabular">
    </data>
  </outputs>
  <help>DESCRIPTION
===========

Following the execution of the PSM Prep tool, this tool simply aligns
the genomes and generates a table comparison the positions of all
proteins. It can be very useful to figure out which genes are missing in
which genomes.

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

-  ``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!


</help>
  <tests/>
</tool>