# HG changeset patch
# User jjv_bioinformaticians
# Date 1491417099 14400
# Node ID 6ab618072d5c2c6747ff95a98cfeb47e3dfd5017
# Parent  e3f75a7a950ca3f9ea421accfaf0b6790f682904
Uploaded

diff -r e3f75a7a950c -r 6ab618072d5c phylo-protpars.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phylo-protpars.xml	Wed Apr 05 14:31:39 2017 -0400
@@ -0,0 +1,95 @@
+<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>