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<tool id="phylo-protpars-id" name="Phylogeny Maximum Parsimony" version="0.1.0">
  <description>Gives an option to add a certain informative site (defined by user) for the Maximum Parsimony Tree</description>
   <stdio>
      <!-- Whatever match this, is not an error -->
      <regex match="[Use of uninitialized value*"/>
  </stdio>
  <command interpreter="perl">
  	#if $phylogeny.define
		phylo-protpars.pl $input $phylogeny.numValues $phylogeny.numRepeats
	#else
		phylo-protpars.pl $input
	#end if
  </command>
  <inputs>
    <param format="fasta" name="input" type="data" label="Source file"/>
	<conditional name="phylogeny">
		<param name="define" type="boolean" checked="true" label="Define informative site?"/>

		<when value="true">
			<param name="numValues" type="integer" value="2" min="2" label="Minimum number of different repeated aa. (>1)" />
			<param name="numRepeats" type="integer" value="2" min="2" label="Minimum frequency of the aa. (>1)" />
		</when>
	</conditional>
	</inputs>
	<outputs>
		<data name="output_tree_text" format="txt" label="Tree as text" from_work_dir="treePars.txt"/>
		<data name="output_alignment" format="phylip" label="Alignment from ClustalW" from_work_dir="sequences.aln"/>
		<data name="output_alignment_phy" format="phylip" label="Alignment processed" from_work_dir="sequences.aln.phy">
			<filter>phylogeny['define']</filter>
		</data>
	</outputs>

	<help>
    <!-- This tool computes a Maximum Parsimony Tree with specific values given by the user. -->
    .. class:: infomark
       
**Example 1: without informative sites**
	source file = 'sequences.fasta'

result::

	Tree as text
	(2134442,(((1170853,1172622),1169853),1708266));

	Alignment from ClustalW
	5    376
	1708266    ------MTCQ AFASSDNFVP LNSDSSPSLP LIMHHSAAEC LPVSNHATSV
	2134442    -----MVPNY STEETVKRIH VDCPVSGRHS YIYIMVPTVY SIIFIIGIFG
	1169853    MTLESMMACC LSDEVKESKR INAEIEKQLR RDKRDARREL KLLLLG--TG
	1172622    --------MS NTGASLKGLL LAVLLVSNML LTKEGVTSLP ICSSGSVNCQ
	1170835    ---------- ---------- ---------- ---------- --------MG

	           VSTVPSVLSL IQTPKCSHLH FAMMTSGNVS AGLHYSVPSC HYGNQTSTYG
	           NSLVVIVIYC YMKLKTVASI FLLNLALADL CFLITLPLWA AYTAMEYQWP
	           ESGKSTFIKQ MRIIHGSGYS EEDKKGFTKL VYQNIFTAMQ SMIRAMETLK
	           VSLGELFDRA VRLSHYIHFL SSEIFNEFDE RYAQGRGFIT KAVNGCHTSS
	           GAQVLVLMTL LGTPPVTTGT PPVVVDPSVA VVGPPLGLGG GGRPPCRPIN

**Example 2: with informative sites**
	source file = 'sequences.fasta'

	Minimum number of different repeated aa. (>1) = 2

	Minimum frequency of the aa. (>1) = 2

result::

	Tree as text
	(2134442,(1172622,(1169853,(1170835,1708266))));
	
	Alignment from ClustalW
	5    376
	1708266    ------MTCQ AFASSDNFVP LNSDSSPSLP LIMHHSAAEC LPVSNHATSV
	2134442    -----MVPNY STEETVKRIH VDCPVSGRHS YIYIMVPTVY SIIFIIGIFG
	1169853    MTLESMMACC LSDEVKESKR INAEIEKQLR RDKRDARREL KLLLLG--TG
	1172622    --------MS NTGASLKGLL LAVLLVSNML LTKEGVTSLP ICSSGSVNCQ
	1170835    ---------- ---------- ---------- ---------- --------MG

	           VSTVPSVLSL IQTPKCSHLH FAMMTSGNVS AGLHYSVPSC HYGNQTSTYG
	           NSLVVIVIYC YMKLKTVASI FLLNLALADL CFLITLPLWA AYTAMEYQWP
	           ESGKSTFIKQ MRIIHGSGYS EEDKKGFTKL VYQNIFTAMQ SMIRAMETLK
	           VSLGELFDRA VRLSHYIHFL SSEIFNEFDE RYAQGRGFIT KAVNGCHTSS
	           GAQVLVLMTL LGTPPVTTGT PPVVVDPSVA VVGPPLGLGG GGRPPCRPIN

	Alignment processed
	5 12
	1708266      VKVLQIKRAK QN
	2134442      VKDLVVATFK KP
	1169853      FHKERIKSFR LS
	1172622      FHDEVVASYD KN
	1170835      LPV-RRGRAD QP

   </help>

</tool>