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phylo-protpars.xml |
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| 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 |
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| @@ -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> |