annotate pairwise.xml @ 0:90b57ab0bd1d draft default tip

planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty

<tool name="Pairwise" id="pairwise" version="2.1.1">

    <description>
        Find homologous couples by blast with RBH
    </description>

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

    <requirements>
        <expand macro="python_required" />
        <requirement type="package" version="1.65">biopython</requirement>
        <requirement type="package" version="0.9.22">diamond</requirement>
        <requirement type="package" version="2.2.22">blast-legacy</requirement>      
    </requirements>

    <command><![CDATA[
        #set $infiles = ""
        #for $input in $inputs
            ln -s '$input' '$input.element_identifier';
            #set $infiles = $infiles + $input.element_identifier + ","
        #end for
        #set $infiles = $infiles[:-1]
        
        ln -s $__tool_directory__/scripts/S02_04_keep_one_hit_from_blast.py . &&
        ln -s $__tool_directory__/scripts/S03_run_second_blast.py . &&
        ln -s $__tool_directory__/scripts/S05_find_rbh.py . &&        

        python -W ignore $__tool_directory__/scripts/S01_run_first_blast.py $infiles ${e_value} $method
        > ${output};
    ]]></command>

    <inputs>
        <param name="inputs" type="data" format="fasta" multiple="true" label="Input fasta files" />
        <param name="method" type="select" label="Alignment tool to use" help="tblastx is slow and sensitive, diamond is a lot quicker and less sensitive">
            <option value="tblastx">tblastx</option>
            <option value="diamond">Diamond</option>
        </param>
        <param name="e_value" type="float" value="1e-5" label="e_value" help="e-value for blast." />
    </inputs>

    <outputs>
        <data format="txt" name="output" label="Pairwise" />
        <collection name="output_fasta_dna" type="list" label="Pairwise_DNA">
            <discover_datasets pattern="__name_and_ext__" directory="outputs_RBH_dna" />
        </collection>
    </outputs>

    <tests>
        <test>
            <param name="inputs" ftype="fasta" value="inputs_tblastx/AcAcaud_trinity.fasta,inputs_tblastx/AmAmphi_trinity.fasta,inputs_tblastx/ApApomp_trinity.fasta,inputs_tblastx/PfPfiji_trinity.fasta" />
            <param name="e-value" value="1e-5" />
            <param name="method" value="tblastx" />
            <output_collection name="output_fasta_dna" type="list">
                <element name="RBH_AcAcaud_AmAmphi_dna">
                    <assert_contents>
                        <has_text text=">Ac5_1/1_1.000_160"/>
                        <has_text text="GCACCGGGATGCGGATTTGCTGACGATATGGCAAAAGCATTGTCAGCGTGCGGAACCTGTTTATGTCACACCA"/>
                        <has_text text=">Am1_1/1_1.000_160"/>
                        <has_text text=">Ac7_1/1_1.000_160"/>
                        <has_text text="GCACCTAGAATTACCCGAAGTTGCTTGGCAATAGCGACACCTAACGGTCGCCATGATATTTGCAGGAAGAAGG"/>
                        <has_text text=">Am3_1/1_1.000_160"/>
                        <has_text text=">Ac6_1/1_1.000_160"/>
                        <has_text text="CAGCCTACCACTGAGAAGAGATACTTCAACATGTCTTACTGGGGTAGAAGTGGTGGTCGTACAGCGGGTGGTA"/>
                        <has_text text=">Am2_1/1_1.000_160"/>
                    </assert_contents>
                </element>
                <element name="RBH_AcAcaud_PfPfiji_dna">
                    <assert_contents>
                        <has_text text=">Ac8_1/1_1.000_160"/>
                        <has_text text="ATCAAAGAAGAGCAACATCGAGCTACTGGCACTGGCAATGGAATCCTAATTATAGCAGAAACAAGCACTGGTTG"/>
                        <has_text text=">Pf8_1/1_1.000_160"/>
                        <has_text text=">Ac5_1/1_1.000_160"/>
                        <has_text text="GCACCGGGATGCGGATTTGCTGACGATATGGCAAAAGCATTGTCAGCGTGCGGAACCTGTTTATGTCACACCAC"/>
                        <has_text text=">Pf7_1/1_1.000_160"/>
                    </assert_contents>
                </element>
                <element name="RBH_ApApomp_PfPfiji_dna">
                    <assert_contents>
                        <has_text text=">Ap2_1/1_1.000_160"/>
                        <has_text text="ATACTCAGGCACACAGCATTTGTCGTACTAGGCGAGAGAGAGAGAGGAACGACTAATTGCAACCACGATTA"/>
                        <has_text text=">Pf5_1/1_1.000_160"/>
                        <has_text text=">Ap1_1/1_1.000_160"/>
                        <has_text text="GGTCGCCTTATAAAAACCAATCCGAAACAGTTTTCCTTTGAAACGTGCCAAAAACCAAAAACATACTTCAA"/>
                        <has_text text=">Pf4_1/1_1.000_160"/>
                        <has_text text=">Ap4_1/1_1.000_135"/>
                        <has_text text="CGGCCGCGGCGCGTCGTTCTCAGCCAAGCTGACTTCGACTTGAGCCGTCCATTCGCTTATTTACACGACGA"/>
                        <has_text text=">Pf10_1/1_1.000_160"/>
                        <has_text text=">Ap3_1/1_1.000_160"/>
                        <has_text text="GCCATGCAGTACACTGGACTTCTGTTATTCTGTTTGTTTGCCTTGACGGCAGCCAAACCCGCGGAAGACCT"/>
                        <has_text text=">Pf6_1/1_1.000_160"/>
                    </assert_contents>
                </element>
                <element name="RBH_AmAmphi_PfPfiji_dna">
                    <assert_contents>
                        <has_text text=">Am8_1/1_1.000_160"/>
                        <has_text text="GTATTAATAAAAGGACAAGACTATTATTTAATACCAAGAAATCTGGCCTTAATAAGCATGGTTGCTTATATCAT"/>
                        <has_text text=">Pf9_1/1_1.000_160"/>
                        <has_text text=">Am1_1/1_1.000_160"/>
                        <has_text text="GCACCGGGATGCGGATTTGCTGACGATATGGCAAAAGCATTGTCAGCGTGCGGAACCTGTTTATGTCACACCA"/>
                        <has_text text=">Pf7_1/1_1.000_160"/>
                    </assert_contents>
                </element>
            </output_collection>
        </test>

        <test>
            <param name="inputs" ftype="fasta" value="inputs_diamond/AcAcaud_Trinity.fasta,inputs_diamond/AmAmphi_Trinity.fasta,inputs_diamond/ApApomp_Trinity.fasta,inputs_diamond/PfPfiji_Trinity.fasta" />
            <param name="e-value" value="1e-5" />
            <param name="method" value="diamond" />
            <output_collection name="output_fasta_dna" type="list">
                <element name="RBH_AcAcaud_AmAmphi_dna">
                    <assert_contents>
                        <has_text text=">Ac5_1/1_1.000_160"/>
                        <has_text text="GCACCGGGATGCGGATTTGCTGACGATATGGCAAAAGCATTGTCAGCGTGCGGAACCTGTTTATGTCACACCA"/>
                        <has_text text=">Am1_1/1_1.000_160"/>
                        <has_text text=">Ac7_1/1_1.000_160"/>
                        <has_text text="GCACCTAGAATTACCCGAAGTTGCTTGGCAATAGCGACACCTAACGGTCGCCATGATATTTGCAGGAAGAAGG"/>
                        <has_text text=">Am3_1/1_1.000_160"/>
                        <has_text text=">Ac6_1/1_1.000_160"/>
                        <has_text text="CAGCCTACCACTGAGAAGAGATACTTCAACATGTCTTACTGGGGTAGAAGTGGTGGTCGTACAGCGGGTGGTA"/>
                        <has_text text=">Am2_1/1_1.000_160"/>
                    </assert_contents>
                </element>
                <element name="RBH_AcAcaud_ApApomp_dna">
                    <assert_contents>
                        <has_text text=">Ac23_1/1_1.000_366"/>
                        <has_text text="ACTGAGGCTCGAACACAACAAAAAGGTGATGAGCAGTCAGCACTTAATAGAATATTACAGCAAGTAGCCAGTAA"/>
                        <has_text text=">Ap46_1/1_1.000_217"/>
                        <has_text text="CCACAACCAAGTGGCGGGTATAACAGCACCGAGGCTCGAACACAGCAAAAAGGTGATGAGCAGTCAGCTCTTAA"/>
                    </assert_contents>
                </element>
                <element name="RBH_AcAcaud_PfPfiji_dna">
                    <assert_contents>
                        <has_text text=">Ac8_1/1_1.000_160"/>
                        <has_text text="ATCAAAGAAGAGCAACATCGAGCTACTGGCACTGGCAATGGAATCCTAATTATAGCAGAAACAAGCACTGGTTG"/>
                        <has_text text=">Pf8_1/1_1.000_160"/>
                        <has_text text=">Ac5_1/1_1.000_160"/>
                        <has_text text="GCACCGGGATGCGGATTTGCTGACGATATGGCAAAAGCATTGTCAGCGTGCGGAACCTGTTTATGTCACACCAC"/>
                        <has_text text=">Pf7_1/1_1.000_160"/>
                    </assert_contents>
                </element>
                <element name="RBH_AmAmphi_PfPfiji_dna">
                    <assert_contents>
                        <has_text text=">Am8_1/1_1.000_160"/>
                        <has_text text="GTATTAATAAAAGGACAAGACTATTATTTAATACCAAGAAATCTGGCCTTAATAAGCATGGTTGCTTATATCAT"/>
                        <has_text text=">Pf9_1/1_1.000_160"/>
                        <has_text text=">Am1_1/1_1.000_160"/>
                        <has_text text="GCACCGGGATGCGGATTTGCTGACGATATGGCAAAAGCATTGTCAGCGTGCGGAACCTGTTTATGTCACACCA"/>
                        <has_text text=">Pf7_1/1_1.000_160"/>
                    </assert_contents>
                </element>
                <element name="RBH_ApApomp_PfPfiji_dna">
                    <assert_contents>
                        <has_text text=">Ap2_1/1_1.000_160"/>
                        <has_text text="ATACTCAGGCACACAGCATTTGTCGTACTAGGCGAGAGAGAGAGAGGAACGACTAATTGCAACCACGATTA"/>
                        <has_text text=">Pf5_1/1_1.000_160"/>
                        <!--
                        <has_text text=">Ap1_1/1_1.000_160"/>
                        <has_text text="GGTCGCCTTATAAAAACCAATCCGAAACAGTTTTCCTTTGAAACGTGCCAAAAACCAAAAACATACTTCAA"/>
                        <has_text text=">Pf4_1/1_1.000_160"/>
                        <has_text text=">Ap4_1/1_1.000_160"/>
                        <has_text text="CGGCCGCGGCGCGTCGTTCTCAGCCAAGCTGACTTCGACTTGAGCCGTCCATTCGCTTATTTACACGACGA"/>
                        <has_text text=">Pf10_1/1_1.000_160"/>
                        <has_text text=">Ap3_1/1_1.000_160"/>
                        <has_text text="GCCATGCAGTACACTGGACTTCTGTTATTCTGTTTGTTTGCCTTGACGGCAGCCAAACCCGCGGAAGACCT"/>
                        <has_text text=">Pf6_1/1_1.000_160"/>
                        -->
                    </assert_contents>
                </element>
            </output_collection>
        </test>
    </tests>

    <help>

 @HELP_AUTHORS@
 
<![CDATA[

**Description**

This tool searches for different homologous genes from pairwise comparisons between a set of fasta files (one file per species).
 
--------

**Parameters**

    - 'Input files' : a collection of fasta files (one file per species)
    - 'e_value' : the blast e-value. By default it's 1e-5.
    - 'Alignment tool' : choose the sequences alignment tool between tblastx and Diamond. tblastx is more sensitive and Diamond is much faster.

--------

**Outputs**

    - 'Pairwise' : the general output. It gives the information about what the tool has done for each pairwise.

    - 'Pairwise_DNA' : the output which contains nucleic sequences (of the pairwise) that are homologous. The sequences are in nucleic format. There are one file per couple of species, and homologous pairs are written by sets of 4 lines : 

Exemple for two homologous pairs for the output file for species X/Y :

| >Gene_A_species_X_homologous_to_Gene_B_species_Y
| Nucleic_sequence_from_filter_assemblies
| >Gene_B_species_Y_homologous_to_Gene_A_species_X
| Nucleic_sequence_from_filter_assemblies
| >Gene_C_species_X_homologous_to_Gene_D_species_Y
| Nucleic_sequence_from_filter_assemblies
| >Gene_D_species_Y_homologous_to_Gene_C_species_X
| Nucleic_sequence_from_filter_assemblies


--------

**The AdaptSearch Pipeline**

.. image:: adaptsearch_picture_helps.png

---------

Changelog
---------

**Version 2.1 - 03/07/2018**

 - Add the possibility to use Diamond instead of tblastx

**Version 2.0 - 18/04/2017**

 - NEW: Replace the zip between tools by Dataset Collection


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

 - TEST: Add functional test with planemo

 - IMPROVEMENT: Use conda dependencies for blast, samtools and python

    ]]>
    </help>

</tool>