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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
author abims-sbr
date Wed, 27 Sep 2017 10:03:45 -0400
parents 6d930f037fea
children 0464ec48bc3a
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<tool name="ConcatPhyl" id="concatphyl" version="2.0">

	<description>
		Concatenation and phylogeny
	</description>

	<macros>
		<import>macros.xml</import>
	</macros>

	<requirements>
		<expand macro="python_required" />
		<requirement type="package" version="8.2.9">raxml</requirement>
	</requirements>

  	<command><![CDATA[
        #set $infiles_filter_assemblies = ""
        #for $input_filter_assemblie in $input_filter_assemblies
            ln -s '$input_filter_assemblie' '$input_filter_assemblie.element_identifier';
            #set $infiles_filter_assemblies = $infiles_filter_assemblies + $input_filter_assemblie.element_identifier + ","
        #end for
        #set $infiles_filter_assemblies = $infiles_filter_assemblies[:-1]

        #set $infiles_alignments = ""
        #for $input_alignment in $input_alignments
            ln -s '$input_alignment' '$input_alignment.element_identifier';
            #set $infiles_alignments = $infiles_alignments + $input_alignment.element_identifier + ","
        #end for
        #set $infiles_alignments = $infiles_alignments[:-1]

        python $__tool_directory__/scripts/S01_concatenate.py

        $infiles_filter_assemblies

        #if $format.format_run == "nucleic" :
            nucleic
        #elif $format.format_run == "proteic" :
            proteic
        #end if

        $infiles_alignments
        > ${output};

        raxmlHPC -n galaxy_run
        #if $format.format_run == "nucleic" :
            ##-q 05_partitions_gene_NUC
            -s "03_Concatenation_nuc.phy"
            -m $format.base_model
        #elif $format.format_run == "proteic" :
            ##-q 06_partitions_gene_AA
            -s 02_Concatenation_aa.phy
            -m $format.base_model$format.aa_search_matrix
        #end if

        -p $random_seed
        
        #if $number_of_runs !="" and $number_of_runs_bootstop =="":
            -N $number_of_runs
            -x $rapid_bootstrap_random_seed
        #elif ($number_of_runs !="" and $number_of_runs_bootstop !="") or ($number_of_runs =="" and $number_of_runs_bootstop !=""):
            -N $number_of_runs_bootstop
            -x $rapid_bootstrap_random_seed
        #end if

        -f $search_algorithm

        >> ${output};
    ]]>
  	</command>

 	<inputs>

		<param name="input_filter_assemblies" type="data" format="fasta" multiple="true" label="Files from Filter assemblies" />
        <param name="input_alignments" type="data" format="fasta" multiple="true" label="Aligned files without indels" help="nucleic or proteic format according to the analysis you want to do below"/>

		<conditional name="format">
			<param name="format_run" type="select" label="Which format do you want to use for this tool (concatenation and RAxML run) ? ">
				<option value="nucleic">Nucleic format</option>
				<option value="proteic">Proteic format</option>
			</param>

			<when value="nucleic">				
		    	<param name="base_model" type="select" label="Substitution Model">
		        	<option value="GTRCAT">GTRCAT</option>
		        	<option value="GTRCATI">GTRCATI</option>
		        	<option value="GTRGAMMA" selected="true">GTRGAMMA</option>
		        	<option value="GTRGAMMAI">GTRGAMMAI</option>
		   		</param>
			</when>

			<when value="proteic">			
		    	<param name="base_model" type="select" label="Substitution Model (-m)">
					<option value="PROTCAT" selected="true">PROTCAT</option>
					<option value="PROTCATI">PROTCATI</option>
					<option value="PROTGAMMA">PROTGAMMA</option>
			    	<option value="PROTGAMMAI">PROTGAMMAI</option>
		    	</param>
		    	<param name="aa_search_matrix" type="select" label="Matrix">
					<option value="DAYHOFF" selected="true">DAYHOFF</option>
					<option value="JTT">JTT</option>
					<option value="WAG">WAG</option>
					<option value="BLOSUM62">BLOSUM62</option>
			    </param>
			</when>
		</conditional>

		<param name="random_seed" type="integer" value="1234567890" size="12" label="Random seed used for the parsimony inferences" />

		<!-- ## (-N/#) -->
		<param name="number_of_runs" type="integer" size="8" value="100"
            label="Number of runs" help="Specify the number of
            alternative runs (-N|#) on distinct starting trees In combination
            with the '-b' option will invoke a multiple boostrap analysis.
            You can add the bootstopping criteria by choosing the autoMR,
            autoMRE, autoMRE_IGN, or autoFC value in a menu below instead of
            providing a number here. Bootstopping will only work in
            combination with '-x' or '-b'."
            optional="True" />
		<param name="number_of_runs_bootstop" type="select" label="Use bootstopping criteria for number of runs" optional="True">
	    	<option value="" selected="yes"></option>
	    	<option value="autoMR">autoMR</option>
	    	<option value="autoMRE">autoMRE</option>
	    	<option value="autoMRE_IGN">autoMRE_IGN</option>
	    	<option value="autoFC">autoFC</option>
		</param>

		<!-- ## (-f) -->
   		<param name="search_algorithm" type="select" label="Algorithm to execute" optional="True">
            <option value="a" selected="true">Rapid bootstrap and best ML tree search (a)</option>
            <option value="A">Compute marginal ancestral states (A)</option>
            <option value="b">Draw bipartition information (b)</option>
            <option value="c">Check if the alignment can be read (c)</option>
            <option value="d">Hill-climbing ML Search (d) (default)</option>
            <option value="e">Optimize GAMMA/GAMMAI model/branches (e)</option>
            <option value="g">Compute per-site log likelihoods for -z trees (g)</option>
            <option value="h">Compute log likelihood test for -t / -z trees (h)</option>
            <option value="j">Generate bootstrapped alignment files (j)</option>
            <option value="J">Compute SH-like support values for the -t tree (J)</option>
            <option value="m">Compare bipartitions between -t and -z trees (m)</option>
            <option value="n">Compute log likelihood score for -z trees (n)</option>
            <option value="o">Use old slower search algorithm (o)</option>
            <option value="p">Stepwise MP addition of new sequences (p)</option>
            <option value="q">Fast quartet calculator (q)</option>
            <option value="r">Compute pairwise RF distances in -z trees (r)</option>
            <option value="s">Split a multi-gene alignment (s)</option>
            <option value="S">Compute site-specific placement bias (S)</option>
            <option value="t">Randomized tree searches on a fixed starting tree (t)</option>
            <option value="T">Final optimization of a ML tree from a bootstrap (T)</option>
            <option value="u">Morphological weight calibration using ML on a -t tree (u)</option>
            <option value="v">Classify environmental sequences (v)</option>
            <option value="w">Compute ELW-test on -z trees (w)</option>
            <option value="x">Compute GAMMA model pair-wise ML distances on a tree (x)</option>
            <option value="y">Classify environmental sequences into a reference tree (y)</option>
        </param>

        <!-- ## (-q) -->
	  	<param name="multiple_model" format="txt" type="data" label="Multiple model assignment to alignment partitions" optional="True" help="Specify the file name which contains the assignment of models to alignment partitions for multiple models of substitution. For the syntax of this file please consult the manual." />

	 	<!-- ## (-x) -->
         <param name="rapid_bootstrap_random_seed" type="integer" value='12345' size="7" label="Rapid bootstrapping random seed" optional="True" help="Specify a random seed and turn on rapid bootstrapping. CAUTION: unlike in version 7.0.4 RAxML will conduct rapid BS replicates under the model of rate heterogeneity you specified via '-m' and not by default under CAT." />

		<param name="out" type="select" label="What format of file do you want for your output (concatenation of the sequences) ? ">
			<option value="nothing">No output</option>
			<option value="fasta">Fasta format</option>
			<option value="phylip">Phylip format</option>
			<option value="nexus">Nexus format</option>
		</param>
		
		<param name="raxml1" type="boolean" label="Do you want the output of RAxML : best tree ? " />
		<param name="raxml3" type="boolean" label="Do you want the output of RAxML : bi-partition ? " />
		<param name="raxml4" type="boolean" label="Do you want the output of RAxML : bootstrap ? " help="Only if the option 'rapid bootsptrap' is chosen. When you don't want to choose your options, this output is accessible"/>

	</inputs>

	<outputs>
		<data name="output" format="txt" label="Phylogeny"/>

		<data name="out_fasta_aa" format="fasta" label="Phylogeny_concatenation_fasta_aa" from_work_dir="02_Concatenation_aa.fas">
			<filter>format['format_run'] == "proteic" and out == "fasta"</filter>
		</data>

		<data name="out_phylip_aa" format="phylip" label="Phylogeny_concatenation_phylip_aa" from_work_dir="02_Concatenation_aa.phy">
			<filter>format['format_run'] == "proteic" and out == "phylip"</filter>
		</data>

		<data name="out_nexus_aa" format="nexus" label="Phylogeny_concatenation_nexus_aa" from_work_dir="02_Concatenation_aa.nex">
			<filter>format['format_run'] == "proteic" and out == "nexus"</filter>
		</data>

		<data name="out_fasta_nuc" format="fasta" label="Phylogeny_concatenation_fasta_nuc" from_work_dir="03_Concatenation_nuc.fas">
			<filter>format['format_run'] == "nucleic" and out == "fasta"</filter>
		</data>

		<data name="out_phylip_nuc" format="phylip" label="Phylogeny_concatenation_phylip_nuc" from_work_dir="03_Concatenation_nuc.phy">
			<filter>format['format_run'] == "nucleic" and out == "phylip"</filter>
		</data>

		<data name="out_nexus_nuc" format="nexus" label="Phylogeny_concatenation_nexus_nuc" from_work_dir="03_Concatenation_nuc.nex">
			<filter>format['format_run'] == "nucleic" and out == "nexus"</filter>
		</data>

		<data name="out_raxml1" format="txt" label="Phylogeny_RAxML_BestTree" from_work_dir="RAxML_bestTree.galaxy_run">
			<filter>raxml1 == True</filter>
		</data>

		<data name="out_raxml3" format="txt" label="Phylogeny_RAxML_BiPartition" from_work_dir="RAxML_bipartitions.galaxy_run">
			<filter>raxml3 == True</filter>
		</data>

		<data name="out_raxml4" format="txt" label="Phylogeny_RAxML_BootStrap" from_work_dir="RAxML_bootstrap.galaxy_run">
			<filter>raxml4 == True</filter>
		</data>
	</outputs>

	<tests>
		<test>
            <param name="input_filter_assemblies" ftype="fasta" value="input_filter_assemblies/AcAcaud_trinity.fasta,input_filter_assemblies/AmAmphi_trinity.fasta,input_filter_assemblies/ApApomp_trinity.fasta,input_filter_assemblies/PgPgras_trinity.fasta,input_filter_assemblies/PhPhess_trinity.fasta,input_filter_assemblies/ThThelep_trinity.fasta" />
            <param name="input_alignments" ftype="fasta" value="input_from_CDS_Search/locus17_sp3_sp3.fasta,input_from_CDS_Search/locus147_sp3_sp3.fasta,input_from_CDS_Search/locus183_sp3_sp3.fasta,input_from_CDS_Search/locus334_sp3_sp3.fasta" />
            <conditional name="format">
				<param name="format_run" value="nucleic" />
				<param name="base_model" value="GTRGAMMA" />
			</conditional>
			<param name="random_seed" value="1234567890" />
			<param name="number_of_runs" value="100" />
			<param name="number_of_runs_bootstop" value="" />
			<param name="search_algorithm" value="d" />
			<!-- <param name="multiple_model" value="" /> -->
			<param name="rapid_bootstrap_random_seed" value="123456789" />
			<param name="out" value="nothing" />
			<param name="raxml1" value="True" />
			<param name="raxml3" value="True" />
			<param name="raxml4" value="True" />
			<output name="out_raxml4">
				<assert_contents>
					<has_text text="((Pg,(Am,Th)),(Ph,Ap),Ac);"/>
					<has_text text="((Th,(Pg,Am)),(Ph,Ap),Ac);"/>
					<has_text text="((Ph,Ap),(Am,(Pg,Th)),Ac);"/>
				</assert_contents>
			</output>
		</test>

        <test>
            <param name="input_filter_assemblies" ftype="fasta" value="input_filter_assemblies/AcAcaud_trinity.fasta,input_filter_assemblies/AmAmphi_trinity.fasta,input_filter_assemblies/ApApomp_trinity.fasta,input_filter_assemblies/PgPgras_trinity.fasta,input_filter_assemblies/PhPhess_trinity.fasta,input_filter_assemblies/ThThelep_trinity.fasta" />
            <param name="input_alignments" ftype="fasta" value="input_from_CDS_Search/locus17_sp3_sp3.fasta,input_from_CDS_Search/locus147_sp3_sp3.fasta,input_from_CDS_Search/locus183_sp3_sp3.fasta,input_from_CDS_Search/locus334_sp3_sp3.fasta" />
            <conditional name="format">
                <param name="format_run" value="nucleic" />
                <param name="base_model" value="GTRGAMMA" />
            </conditional>
            <param name="random_seed" value="1234567890" />
            <param name="number_of_runs" value="100" />
            <param name="number_of_runs_bootstop" value="" />
            <param name="search_algorithm" value="a" />            
            <param name="rapid_bootstrap_random_seed" value="1234567890" />
            <param name="out" value="nothing" />
            <param name="raxml1" value="True" />
            <param name="raxml3" value="True" />
            <param name="raxml4" value="True" />
            <output name="out_raxml1" value="RAxML_bestTree"/>     
            <output name="out_raxml3" value="RAxML_bipartitions"/>                
        </test>
        
        <test>
            <param name="input_filter_assemblies" ftype="fasta" value="input_filter_assemblies/AcAcaud_trinity.fasta,input_filter_assemblies/AmAmphi_trinity.fasta,input_filter_assemblies/ApApomp_trinity.fasta,input_filter_assemblies/PgPgras_trinity.fasta,input_filter_assemblies/PhPhess_trinity.fasta,input_filter_assemblies/ThThelep_trinity.fasta" />
            <param name="input_alignments" ftype="fasta" value="input_from_CDS_Search/locus17_sp3_sp3.fasta,input_from_CDS_Search/locus147_sp3_sp3.fasta,input_from_CDS_Search/locus183_sp3_sp3.fasta,input_from_CDS_Search/locus334_sp3_sp3.fasta" />
            <conditional name="format">
                <param name="format_run" value="nucleic" />
                <param name="base_model" value="GTRGAMMA" />
            </conditional>
            <param name="random_seed" value="1234567890" />
            <param name="number_of_runs" value="100" />
            <param name="number_of_runs_bootstop" value="autoMR" />
            <param name="search_algorithm" value="a" />            
            <param name="rapid_bootstrap_random_seed" value="1234567890" />
            <param name="out" value="nothing" />
            <param name="raxml1" value="True" />
            <param name="raxml3" value="True" />
            <param name="raxml4" value="True" />
            <output name="out_raxml1" value="RAxML_bestTree_test3"/>     
            <output name="out_raxml3" value="RAxML_bipartitions_test3"/>                
        </test>
	</tests>

	<help>

@HELP_AUTHORS@

============
What it does
============

| This tool takes a 'dataset collection list'  containing nucleic fasta sequence files and searches different homologous genes from pairwise comparisons.

--------

==========
Parameters
==========

| The choice of the format sequences is possible : **proteic** or **nucleic**
|

The choice of parameters for the RAxML run is possible :

**-m** :
	| is the option for the choice of the substitution model.
	| By default it's GTRGAMMA.
	|

**-N** :
	| is the option for the choice of the number of run
	| by default it's 100
	|

**rapid bootstrapping** :
	| is the option to have, in addition to the best tree search, the rapid bootstrapping
	| this translates by : -x 12345 -f a
	| by default, this option is choosen
	|

.. class:: warningmark
| RAxML has some incompatible parameters. 
| The search algorithm compatible with boostrapping and giving a besttree file is the one set by default:
| -f a

| The search algorithm compatible with boostrapping and NOT giving a besttree file are:
| -f d
| -f o
| -f t
--------

======
Inputs
======

--------

=======
Outputs
=======

This tool, produces the following files :

**Phylogeny** :
	| is the general output. It gives the information about the concatenation (statistics) and the RAxML run.
	|

**Phylogeny_concatenation_fasta_aa** :
	| is the output which contains the sequences concatenated in fasta format when you choose the option proteic
	|

**Phylogeny_concatenation_phylip_aa** :
	| is the output which contains the sequences concatenated in phylip format when you choose the option proteic
	|

**Phylogeny_concatenation_nexus_aa** :
	| is the output which contains the sequences concatenated in nexus format when you choose the option proteic
	|

**Phylogeny_concatenation_fasta_nuc** :
	| is the output which contains the sequences concatenated in fasta format when you choose the option nucleic
	|

**Phylogeny_concatenation_phylip_nuc** :
	| is the output which contains the sequences concatenated in phylip format when you choose the option nucleic
	| it's this output which is used for the RAxML run
	|

**Phylogeny_concatenation_nexus_nuc** :
	| is the output which contains the sequences concatenated in nexus format when you choose the option nucleic
	|

**Phylogeny_RAxML_BestTree** :
	| is the output of RAxML run which contains the Best Tree found
	|

**Phylogeny_RAxML_BiPartitionBranchLabel** :
	| is the output of RAxML run which contains the Best Tree found with supported values as branch labels
	|

**Phylogeny_RAxML_BiPartition** :
	| is the output of RAxML run which contains the Best Tree found with supported values
	|

**Phylogeny_RAxML_BootStrap** :
	| is the output of RAxML run which contains all the boostrapped trees
	| the number of boostraped trees depending of the option -N (number of run)
	|

--------

===============
Working Example
===============

---------------------------
The input files and options
---------------------------

**Input files**
	| 6 files with 200 nucleic sequences each
	| a 'dataset collection list' containing 2 locus aligned without indel (in nucleic format)
	|
**Parameters**
	| option : nucleic
	| no option for the RAxML run, so by default it's : -m GTRGAMMA -N 100 -f a -x 12345
	|

----------------
The output files
----------------

**Phylogeny** :

| ******************** CONCATENATION ********************
|
| Process nucleotides concatenation:
| Number of taxa aligned = 6
| Number of loci concatenated = 2
|
| Total length of the concatenated sequences [All codon positions] = 504
| Total length of the concatenated sequences [Codon positions 1 and 2] = 336
| Total length of the concatenated sequences [Codon position 3] = 168
|
|
| 
| ******************** RAxML RUN ********************
| 

the informations of the RAxML run

| 

**Phylogeny_concatenation_fasta_nuc** :

| &gt;Ps

cgcagttcctcggtgaggcgttgtagttcggcgttcagacggtcagctctctcctcggctgccctgcgagcattcagtgcctcatccatgtcagcttgcatggcggcaatgtctccctccatacggcgcttatctccagtcaaagtggtcacggtgatgttcagctcgttaacacgggatacagcatcgtgcagttcgttttcggcattcttacgagctctctcagatgtctcca
gaagagatcgaacgtcctccagctccgtttgtagagcgatcctcttcctctcgagtacggtaaccgccgaacgggcttcctcagcactacggcgctcctcctcaatggcaatctccagctccttgaccttggcactgagtcccttgttggccttagatagttcgttgtttgccctcaatgtctcgaccataatccttaacaacaacacactacagccaacaaccttccttgctt
taccctctttgtctatcttgcataatccagcccat

| Ac

cgcagttcctcggtgacgcggtgcagctcggcggcgaggcggtctgccctctcctcggccgccctgcgggcgttcagggcctcgtccagatcggcctgcatggcggcgatgtcgccctccatgcggcgcttgtcgccagtcagcgtcgtcaccgtgatgttcagctcgttgacgcgagccgtggcgtcgtgcaactcgttctcggcattcttacgagctcgttcggc
ggtctccagtagagatctaacatcctccagctctgtttgcaatgcaatcctcttcctctcgagtacagttacagcggaacgggcttcctcagcactgcggtgctcctcctcaatggcaatttccagctccttgaccttggcactaagtcccttgttggccttggacagctcgttgttggctctaagtgtctccacc---------------------------------------------------------
------------------------

| &gt;Pp
| ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
| ------------------------------------------------------------------------------------------------ataatccttgacgaccacacactgcatccaacaacttttctggccttgccttccttgtctattttacacaaaccagcccat

| &gt;Ap

cgcagctcctcggtgacgcggtgcagctcggcggcgaggcgatcggctctctcctcggctgccctgcgggcgttcagggcctcatcaaggtcggcctgcatggcggcgatgtcgccctccatgcggcgcttgtcgccggtcagagtcgtcaccgtgatgttcagctcgttgacgcgagccgtggcgtcgtgtagctcgttctcggcattcttacgagctcgttcggc
ggtctccagtagggatctaacatcctccagctccgtttgcaatgcaatcctcttcctctcgagtacagttacagcggaacgggcttcctcagcactgcggcgctcctcctcaatggcaatttccagctccttgaccttcgcactaagtcccttgttggccttggacagttcgttgttggctctaagtgtctccactataatccttaacaacaacacactgcaaccaacaacctt
ccgggccttgccttccttgtctatcttgcaaagaccagcccat

| &gt;Pf

ctgagctcctcggtgaggcgctggagctcggagttcaggcggtcggctcgttcctcggcggcgcggcgagcgttcagcgcctcgtccatgtcggcctgcatggcggcgatgtccgcttccatgcggcgcttgtcgcccgtcagagtggtgaccgtgatgttcagctcgttgacacgggccacggcgtcgtgcagctcgttctcggcgttcttgcgagctctctccga
cgtctccagaagagatcggacgtcctcgagttccgtctgcagggcgatcctcttcctctcgagcacggtaacagcagaacgggcttcctcggcgctacggcgctcttcctcgatggcgatctccagttccttgacctttgcactgagtcccttgttggccttggatagttcgttgttagccctcagtgtctccaccataatccttaacaacaacacactacagccgacaac
cttccttgctttcccttctttgtcaatcttgcataatccggcccat

| &gt;Pg

cgcagctcctcggtgagacgctgcagttcggaattcaggcggtccgccctctcttcggcagccctgcgggcgttcagcgcctcgtccatgtcggcctgcatggcggcgatgtcgccctccatgcggcgcttgtcgccggtcagcgtggtcacggtgatgttcagctcgttgacgcgagaaacggcgtcgtgcatctcgttttcggcattcttgcgagctctctccgacg
tctcaagaagggatcgtacatcctcgagttctgtctggagggcgatcctctttctctcaagcatggtaaccgcggagcgggcttcctcgccactgcggcgttcttcctcgatggtgatctccagttccttaaccttagtactcagtcccttgttggctttggacagttcgttgttcgctcttagtgtctccactataatccttaaccacaacacactacaaccaacaacctttcttgc
cttgccttccttgtctatcttacacaagccagcccat

.. class:: infomark

| If you choose the option proteic : you obtain a file with proteic sequences
|
| 


**Phylogeny_concatenation_phylip_nuc** :

|    6 504
| Ps

cgcagttcctcggtgaggcgttgtagttcggcgttcagacggtcagctctctcctcggctgccctgcgagcattcagtgcctcatccatgtcagcttgcatggcggcaatgtctccctccatacggcgcttatctccagtcaaagtggtcacggtgatgttcagctcgttaacacgggatacagcatcgtgcagttcgttttcggcattcttacgagctctctcagatgtctcca
gaagagatcgaacgtcctccagctccgtttgtagagcgatcctcttcctctcgagtacggtaaccgccgaacgggcttcctcagcactacggcgctcctcctcaatggcaatctccagctccttgaccttggcactgagtcccttgttggccttagatagttcgttgtttgccctcaatgtctcgaccataatccttaacaacaacacactacagccaacaaccttccttgctt
taccctctttgtctatcttgcataatccagcccat

| Ac

cgcagttcctcggtgacgcggtgcagctcggcggcgaggcggtctgccctctcctcggccgccctgcgggcgttcagggcctcgtccagatcggcctgcatggcggcgatgtcgccctccatgcggcgcttgtcgccagtcagcgtcgtcaccgtgatgttcagctcgttgacgcgagccgtggcgtcgtgcaactcgttctcggcattcttacgagctcgttcggc
ggtctccagtagagatctaacatcctccagctctgtttgcaatgcaatcctcttcctctcgagtacagttacagcggaacgggcttcctcagcactgcggtgctcctcctcaatggcaatttccagctccttgaccttggcactaagtcccttgttggccttggacagctcgttgttggctctaagtgtctccacc---------------------------------------------------------
------------------------

| Pp
| ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
| ------------------------------------------------------------------------------------------------ataatccttgacgaccacacactgcatccaacaacttttctggccttgccttccttgtctattttacacaaaccagcccat
|
| Ap

cgcagctcctcggtgacgcggtgcagctcggcggcgaggcgatcggctctctcctcggctgccctgcgggcgttcagggcctcatcaaggtcggcctgcatggcggcgatgtcgccctccatgcggcgcttgtcgccggtcagagtcgtcaccgtgatgttcagctcgttgacgcgagccgtggcgtcgtgtagctcgttctcggcattcttacgagctcgttcggc
ggtctccagtagggatctaacatcctccagctccgtttgcaatgcaatcctcttcctctcgagtacagttacagcggaacgggcttcctcagcactgcggcgctcctcctcaatggcaatttccagctccttgaccttcgcactaagtcccttgttggccttggacagttcgttgttggctctaagtgtctccactataatccttaacaacaacacactgcaaccaacaacctt
ccgggccttgccttccttgtctatcttgcaaagaccagcccat

Pf
ctgagctcctcggtgaggcgctggagctcggagttcaggcggtcggctcgttcctcggcggcgcggcgagcgttcagcgcctcgtccatgtcggcctgcatggcggcgatgtccgcttccatgcggcgcttgtcgcccgtcagagtggtgaccgtgatgttcagctcgttgacacgggccacggcgtcgtgcagctcgttctcggcgttcttgcgagctctctccga
cgtctccagaagagatcggacgtcctcgagttccgtctgcagggcgatcctcttcctctcgagcacggtaacagcagaacgggcttcctcggcgctacggcgctcttcctcgatggcgatctccagttccttgacctttgcactgagtcccttgttggccttggatagttcgttgttagccctcagtgtctccaccataatccttaacaacaacacactacagccgacaac
cttccttgctttcccttctttgtcaatcttgcataatccggcccat

Pg
cgcagctcctcggtgagacgctgcagttcggaattcaggcggtccgccctctcttcggcagccctgcgggcgttcagcgcctcgtccatgtcggcctgcatggcggcgatgtcgccctccatgcggcgcttgtcgccggtcagcgtggtcacggtgatgttcagctcgttgacgcgagaaacggcgtcgtgcatctcgttttcggcattcttgcgagctctctccgacg
tctcaagaagggatcgtacatcctcgagttctgtctggagggcgatcctctttctctcaagcatggtaaccgcggagcgggcttcctcgccactgcggcgttcttcctcgatggtgatctccagttccttaaccttagtactcagtcccttgttggctttggacagttcgttgttcgctcttagtgtctccactataatccttaaccacaacacactacaaccaacaacctttcttgc
cttgccttccttgtctatcttacacaagccagcccat

.. class:: infomark

| If you choose the option proteic : you obtain a file with proteic sequences
|
| 

**Phylogeny_concatenation_nexus_nuc** :

#NEXUS

| Begin data;
| Dimensions ntax=6 nchar=504;
| Format datatype=dna gap=-;

Matrix

Ps      cgcagttcctcggtgaggcgttgtagttcggcgttcagacggtcagctctctcctcggctgccctgcgagcattcagtgcctcatccatgtcagcttgcatggcggcaatgtctccctccatacggcgcttatctccagtcaaagtggtcacggtgatgttcagctcgttaacacgggatacagcatcgtgcagttcgttttcggcattcttacgagctctctcagatgtct
ccagaagagatcgaacgtcctccagctccgtttgtagagcgatcctcttcctctcgagtacggtaaccgccgaacgggcttcctcagcactacggcgctcctcctcaatggcaatctccagctccttgaccttggcactgagtcccttgttggccttagatagttcgttgtttgccctcaatgtctcgaccataatccttaacaacaacacactacagccaacaaccttcct
tgctttaccctctttgtctatcttgcataatccagcccat

Ac      cgcagttcctcggtgacgcggtgcagctcggcggcgaggcggtctgccctctcctcggccgccctgcgggcgttcagggcctcgtccagatcggcctgcatggcggcgatgtcgccctccatgcggcgcttgtcgccagtcagcgtcgtcaccgtgatgttcagctcgttgacgcgagccgtggcgtcgtgcaactcgttctcggcattcttacgagctcgttc
ggcggtctccagtagagatctaacatcctccagctctgtttgcaatgcaatcctcttcctctcgagtacagttacagcggaacgggcttcctcagcactgcggtgctcctcctcaatggcaatttccagctccttgaccttggcactaagtcccttgttggccttggacagctcgttgttggctctaagtgtctccacc---------------------------------------------------
------------------------------

Pp      ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
-----------------------------------------------------------------------------------------------------ataatccttgacgaccacacactgcatccaacaacttttctggccttgccttccttgtctattttacacaaaccagcccat

Ap      cgcagctcctcggtgacgcggtgcagctcggcggcgaggcgatcggctctctcctcggctgccctgcgggcgttcagggcctcatcaaggtcggcctgcatggcggcgatgtcgccctccatgcggcgcttgtcgccggtcagagtcgtcaccgtgatgttcagctcgttgacgcgagccgtggcgtcgtgtagctcgttctcggcattcttacgagctcgttc
ggcggtctccagtagggatctaacatcctccagctccgtttgcaatgcaatcctcttcctctcgagtacagttacagcggaacgggcttcctcagcactgcggcgctcctcctcaatggcaatttccagctccttgaccttcgcactaagtcccttgttggccttggacagttcgttgttggctctaagtgtctccactataatccttaacaacaacacactgcaaccaacaa
ccttccgggccttgccttccttgtctatcttgcaaagaccagcccat

Pf      ctgagctcctcggtgaggcgctggagctcggagttcaggcggtcggctcgttcctcggcggcgcggcgagcgttcagcgcctcgtccatgtcggcctgcatggcggcgatgtccgcttccatgcggcgcttgtcgcccgtcagagtggtgaccgtgatgttcagctcgttgacacgggccacggcgtcgtgcagctcgttctcggcgttcttgcgagctctctcc
gacgtctccagaagagatcggacgtcctcgagttccgtctgcagggcgatcctcttcctctcgagcacggtaacagcagaacgggcttcctcggcgctacggcgctcttcctcgatggcgatctccagttccttgacctttgcactgagtcccttgttggccttggatagttcgttgttagccctcagtgtctccaccataatccttaacaacaacacactacagccgaca
accttccttgctttcccttctttgtcaatcttgcataatccggcccat

Pg      cgcagctcctcggtgagacgctgcagttcggaattcaggcggtccgccctctcttcggcagccctgcgggcgttcagcgcctcgtccatgtcggcctgcatggcggcgatgtcgccctccatgcggcgcttgtcgccggtcagcgtggtcacggtgatgttcagctcgttgacgcgagaaacggcgtcgtgcatctcgttttcggcattcttgcgagctctctccg
acgtctcaagaagggatcgtacatcctcgagttctgtctggagggcgatcctctttctctcaagcatggtaaccgcggagcgggcttcctcgccactgcggcgttcttcctcgatggtgatctccagttccttaaccttagtactcagtcccttgttggctttggacagttcgttgttcgctcttagtgtctccactataatccttaaccacaacacactacaaccaacaacctttc
ttgccttgccttccttgtctatcttacacaagccagcccat

| 	;
| End;
|

.. class:: infomark

| If you choose the option proteic : you obtain a file with proteic sequences
|
| 

**Phylogeny_RAxML_BestTree** :

| ((Ac:0.02889451913999640381,Ap:0.01674414484251282934):0.17730049470177636217,
| ((Pp:0.23405795780876006984,Pg:0.02012322210145659623):0.14429203507314311561,Pf:0.09977363663005259231):0.04320803212100913365,Ps:0.08351583721596630983):0.0;
|
| 


**Phylogeny_RAxML_BiPartitionBranchLabel** :

| (Pg:0.02012322210145659623,(Pf:0.09977363663005259231,(Ps:0.08351583721596630983,
| (Ac:0.02889451913999640381,Ap:0.01674414484251282934):0.17730049470177636217[89]):0.04320803212100913365[42]):0.14429203507314311561[70],Pp:0.23405795780876006984);
|
|


**Phylogeny_RAxML_BiPartition** :

(Pg:0.02012322210145659623,(Pf:0.09977363663005259231,(Ps:0.08351583721596630983,
(Ac:0.02889451913999640381,Ap:0.01674414484251282934)89:0.17730049470177636217)42:0.04320803212100913365)70:0.14429203507314311561,Pp:0.23405795780876006984);

|
|

**Phylogeny_RAxML_BootStrap** :

| ((Ap,Ac),((Pp,Pg),Pf),Ps);
| ((Ap,Ac),((Pp,Pg),Pf),Ps);
| (Pf,((Ap,Ac),(Pp,Pg)),Ps);
| ((Ap,Ac),((Pp,Pg),Pf),Ps);
| ((Ap,Ac),((Pp,Pg),Pf),Ps);
| ((Ap,Ac),((Pp,Pg),Pf),Ps);
| ((Pp,Pg),(Pf,(Ap,Ac)),Ps);

...

---------------------------------------------------

Changelog
---------

**Version 2.0 - 06/07/2017**

 - NEW: Replace the zip between tools by Dataset Collection
 - Corrected bug : output files were empty due to errors in the command section (incompatible parameters set by default instead of the ones mentioned in the help)


**Version 1.0 - 13/04/2017**

 - Add funtional test with planemo

 - Planemo test with conda dependencies for raxml and python

 - Scripts renamed + symlinks to the directory 'scripts'

	</help>

	<expand macro="citations" />

</tool>