comparison pairwise.xml @ 4:6709645eff5d draft

planemo upload for repository https://github.com/abims-sbr/adaptsearch commit cf1b9c905931ca2ca25faa4844d45c908756472f

3:5f68b2fc02c1

            ln -s '$input' '$input.element_identifier';
            #set $infiles = $infiles + $input.element_identifier + ","
        #end for
        #set $infiles = $infiles[:-1]

        ln -s $__tool_directory__/scripts/S02_xxx_patron_pipeline.sh . &&
        ln -s $__tool_directory__/scripts/S03_run_blast_with_k_filter.sh . &&
        ln -s $__tool_directory__/scripts/S04_run_blast2_with_k_filter.sh . &&
        ln -s $__tool_directory__/scripts/S05_script_extract_match_v20_blastx.py . &&
        ln -s $__tool_directory__/scripts/S06_post_processing_of_pairwise.py . &&

            <discover_datasets pattern="__name_and_ext__" directory="outputs_prot" />
        </collection>
	</outputs>

	<tests>
		<test>
            <param name="inputs" ftype="fasta" value="inputs/PfPfiji_Trinity.fasta,inputs/ApApomp_Trinity.fasta,inputs/AmAmphi_Trinity.fasta,inputs/AcAcaud_Trinity.fasta" />
			<param name="e-value" value="1e-5" />
			<output name="output" >
				<assert_contents>

		</test>
	</tests>

	<help>

@HELP_AUTHORS@

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

| This tool takes a 'data collection list' containing nucleic fasta sequence files and searches different homologous genes from pairwise comparaisons.
| There are 3 outputs.
|

--------

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

The choice of parameters is possible :

**-e** :
	|  is the option for the choice of the e-value.
	| By default it's 10.
	|

--------

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

This tool, produces the following files :

**Pairwise**:
	| is the general output. It gives the information about what the tool is doing (for each pairwise).
	|

**Pairwise DNA**:
	| is the output wich contains nucleic sequences (of the pairwise) that are homologues. The sequences are with nucleotides. Shows:
	| the name of the query sequence
	| the part of the sequence in nucleotides
	| the name of the match sequence
	| the part of the sequence in nucleotides
	|

**Pairwise PROT**:
	| is the output wich contains proteic sequences (of the pairwise) that are homologues. The sequences are with protein. Shows:
	| the name of the query sequence (the name of the sequence || the position (Start and End) of the homologous sequences || divergence || number of gaps || real divergence || the length of the homologous sequence)
	| the part of the sequence in protein
	| the name of the match sequence (the name of the sequence || the position (Start and End) of the homologous sequences || divergence || number of gaps || real divergence || the length of the homologous sequence)
	| the part of the sequence in protein

--------

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

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

**Input files**
	| 3 files with 200 nucleic sequences each : Ap.fasta, Ac.fasta et Pp.fasta
	|
**Parameters**
	| e-value = 1e-20
	|

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

**Pairwise**

| -------------------- Pairwise Pp_Ap --------------------
|
| database :  Pp.fasta
| query file :  Ap.fasta
|
| ***** START run BLAST *****
| ***** END run BLAST *****
|
|
| database :  Ap.fasta
| query file : only the sequences of Pp.fasta who matched during the last BLAST
|
| ***** START run BLAST *****
| ***** END run BLAST *****
|
| [3/5] Get pairs of sequences ...
| Get list of fasta name involved in RBH
| Number of pairwises parsed = 15
| Get subset of Alvinella db
| Get subset of Paralvinella db
|
| -------------------- Pairwise Pp_Ac --------------------
|
| database :  Pp.fasta
| query file :  Ac.fasta
|
| ***** START run BLAST *****
| ***** END run BLAST *****
|
|
| database :  Ac.fasta
| query file : only the sequences of Pp.fasta who matched during the last BLAST
|
| ***** START run BLAST *****
| ***** END run BLAST *****
|
| [3/5] Get pairs of sequences ...
| Get list of fasta name involved in RBH
| Number of pairwises parsed = 13
| Get subset of Alvinella db
| Get subset of Paralvinella db
|
|
| -------------------- Pairwise Ap_Ac --------------------
|
| database :  Ap.fasta
| query file :  Ac.fasta
| 
| ***** START run BLAST *****
| ***** END run BLAST *****
|
|
| database :  Ac.fasta
| query file : only the sequences of Ap.fasta who matched during the last BLAST
|
| ***** START run BLAST *****
| ***** END run BLAST *****
|
| [3/5] Get pairs of sequences ...
| Get list of fasta name involved in RBH
| Number of pairwises parsed = 24
| Get subset of Alvinella db
| Get subset of Paralvinella db
|
|

**Pairwise_output_file_PROT**

| For example the 4 last sequences of the file 19_ReciprocalBestHits_Pp_Ap.fasta
|
| &gt;Ap123_1/1_1.000_748||254...478||[[1/1]][[1/6]]||29.3333333333||0||29.3333333333||75.0
| FVRITVGDEMSRRPKFAMITWVGPEVSPMKRAKVSTDKAFVKQIFQNFAKEIQTSERSELEEEYVRQEVMKAGGA
| &gt;Pp_146_1/2_1.000_713||259...483||[[1/1]][[1/6]]||29.3333333333||0||29.3333333333||75.0
| FAYIRCTNEESKRSKFAMITWIGQGVEAMKRAKVSMDKQFLKEIFQNFAREFQTSEKSELDEVCIKHALAIDDGA
| &gt;Ap66_1/1_1.000_400||192...398||[[1/1]][[1/6]]||21.7391304348||0||21.7391304348||69.0
| LSTSLLNWRKHTLCF*GMKLILIILLISFIIPAILFLLSIFTTMRMPESREKFRPYECGFDPNHSARTP
| &gt;Pp_201_2/2_1.000_691||14...220||[[1/1]][[1/6]]||21.7391304348||0||21.7391304348||69.0
| LSTSLLN*RKQPFASEEMKLLILLLFISALIPRILIILSIFTSIRTPKNREKSSPYECGFDPNHSARTP
|
|

**Pairwise_output_file_DNA**

| For example the 4 last sequences of the file 25_DNAalignement_corresponding_to_protein_from_19_RBH_Pp_Ap.fasta
|
| &gt;Ap123_1/1_1.000_748
| CCAGTAACAAGCCGCCACGGGTCCGTCGTGTCTTCTCTTCAAGGAAAGGTTGACAGATTCTCGTACGCTAGACGTCGCCACCTACTCGTCCTGGACTCCGGTGCCGTAGGTGGCGCCACCTGCTTTCATCACTTCCTGCCTA
| ACGTACTCCTCTTCTAGCTCCGATCTCTCGCTCGTCTGGATCTCTTTGGCAAAGTTCTGGAATATCTGCTTGACGAACGCCTTGTCCGTGCTGACTTTGGCGCGCTTCATTGGGCTCACTTCCGGTCCGACCCACGTGATCA
| TGGCGAACTTCGGTCTTCTGCTCATTTCGTCCCCGACGGTAATACGGACAAAGGCGAACGCCCGCTGGTCATCTTGTAGTTTTGATAACAGATCCTCGTATTCGGTTCCTGTAGAGTCCAGTATAATATTGTCGCCATCATA
| CGTCACAAACGCCCAGTTTGTCTCCGTCGCGTCGCTCCTGACGTCTTCGTAAGCCTGTCCGATAGCCTCTCTGTCGATGTCTGCCATGCTGCTGGTCCCGCTCTCGACGCTAATGAGCCAATCACGACTTCTGACAGACGAG
| TAGACATGCAGACAGCCAGACGGACTGACGGACTGACG
| &gt;Pp_146_1/2_1.000_713
| CATTAATTGTGTGTCTGGTTGTGGGTGTGTGTTATAAGAGACATCACTTAGTGTATACTGATGTCCACGTGGTAGTTGACCAGCATGTCGAATATGGATAGGGACTCGATCTTGAATGGCTATGAGGAGGTTCGCAACGACGA
| CTCGGACATTAACTGGGCTTTCGTAACGTATTCACCTGACAACAAACTAGTACTTGATTCAACTGGCACAGACTACTTCCAGCTCCAGGAGAAATATCAAGATGATATGCGAGGATTTGCTTACATCCGGTGCACTAACGAGG
| AGAGTAAACGTTCTAAATTTGCCATGATTACCTGGATTGGACAAGGAGTGGAAGCAATGAAGCGTGCCAAGGTCAGCATGGACAAACAGTTCCTAAAGGAAATCTTCCAGAATTTCGCAAGAGAATTTCAGACGAGTGAAAAG
| TCAGAGCTTGATGAGGTCTGTATTAAACACGCGCTTGCCATTGACGATGGAGCTGGTTGCAAAGTGGAAAGCGAGGACACGAGAAAAGGGGCCTTTCTCAGGAAAGAGGATGACACTGAAGTGGAAAGGGAAACTAATGTCAA
| CAATGTCTCCGGTGTCGTGGAAGAAGATGATGACGCAAAAAATGCAAATGATTTTAATTACGAAGAGGACTGTAACAATGAATAGGTGCATGTCGATGATTTATATAGAGAACTAGACTTCGCACTCGCTAGGTGGTTGAT
| &gt;Ap66_1/1_1.000_400
| TGATCGTCTTATAAACCTAACTTGAAAAACCTTCCTACCATTTAGGGCTAGCAGCCCTATTAATTATCACACCTATCGCAGCGCTCTCACTATAATTATAAGTATTGCGCCGGGTTTGAACGGATAGCTCTGATGCTGCTAATT
| ACGGGACCTAATAATCCCCAATACTTTATCCTTAGAGAGCTGTACCTCTTAGCACCAGTCTTTTAAACTGGCGAAAGCACACTTTATGCTTCTAAGGAATGAAACTAATTCTTATAATCCTACTAATCTCTTTTATCATCCCCG
| CCATTCTATTTTTACTCTCGATCTTTACTACTATGCGCATGCCAGAGAGCCGTGAAAAATTTAGGCCCTACGAGTGCGGGTTTGACCCCAATCACTCGGCCCGAACCCCATT
| &gt;Pp_201_2/2_1.000_691
| ATCGTAGGGAAAAAGGTGTTCGTGCAGAATGATTGGGGTCAAATCCACATTCGTAGGGGCTAGATTTTTCACGGTTTTTAGGTGTACGAATAGAGGTGAAGATTGATAGGATGATTAAAATTCTTGGGATTAATGCTGAAATAAA
| GAGAAGTAGGATTAAAAGTTTCATTTCCTCAGAAGCAAAGGGTTGCTTTCGTCAGTTTAAAAGACTGGTGCTAAGTAGGTACAGCTCTCTAAGGG

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

Changelog
---------

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

 - NEW: Replace the zip between tools by Dataset Collection


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

 - TEST: Add funtional test with planemo

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

    </help>

    <expand macro="citations" />

</tool>

4:6709645eff5d

            ln -s '$input' '$input.element_identifier';
            #set $infiles = $infiles + $input.element_identifier + ","
        #end for
        #set $infiles = $infiles[:-1]

        ln -s $__tool_directory__/scripts/functions.py . &&
        ln -s $__tool_directory__/scripts/S02_xxx_patron_pipeline.sh . &&
        ln -s $__tool_directory__/scripts/S03_run_blast_with_k_filter.sh . &&
        ln -s $__tool_directory__/scripts/S04_run_blast2_with_k_filter.sh . &&
        ln -s $__tool_directory__/scripts/S05_script_extract_match_v20_blastx.py . &&
        ln -s $__tool_directory__/scripts/S06_post_processing_of_pairwise.py . &&

            <discover_datasets pattern="__name_and_ext__" directory="outputs_prot" />
        </collection>
	</outputs>

	<tests>
        <test>
            <param name="inputs" ftype="fasta" value="inputs2/PfPfiji_trinity.fasta,inputs2/ApApomp_trinity.fasta,inputs2/AmAmphi_trinity.fasta,inputs2/AcAcaud_trinity.fasta" />
            <param name="e-value" value="1e-5" />
            <output_collection name="output_fasta_dna" type="list">
                <element name="DNAalignment_corresponding_to_protein_from_RBH_AmAmphi_AcAcaud" value="outputs_dna2/DNAalignment_corresponding_to_protein_from_RBH_AmAmphi_AcAcaud.fasta" />                
                <element name="DNAalignment_corresponding_to_protein_from_RBH_PfPfiji_AcAcaud" value="outputs_dna2/DNAalignment_corresponding_to_protein_from_RBH_PfPfiji_AcAcaud.fasta" />                
                <element name="DNAalignment_corresponding_to_protein_from_RBH_PfPfiji_AmAmphi" value="outputs_dna2/DNAalignment_corresponding_to_protein_from_RBH_PfPfiji_AmAmphi.fasta" />
                <element name="DNAalignment_corresponding_to_protein_from_RBH_PfPfiji_ApApomp" value="outputs_dna2/DNAalignment_corresponding_to_protein_from_RBH_PfPfiji_ApApomp.fasta" />
            </output_collection>
        </test>
		<test>
            <param name="inputs" ftype="fasta" value="inputs/PfPfiji_Trinity.fasta,inputs/ApApomp_Trinity.fasta,inputs/AmAmphi_Trinity.fasta,inputs/AcAcaud_Trinity.fasta" />
			<param name="e-value" value="1e-5" />
			<output name="output" >
				<assert_contents>

		</test>
	</tests>

	<help>

 @HELPAUTHORS@
 
<![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.

--------

**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 with nucleotides. It shows for both the query and match :
        the name        
        the sequence in nucleotides
   
    - 'Pairwise_PROT' : the output which contains proteic sequences (of the pairwise) that are homologous. The sequences are with protein. It shows :
        Name, position, length, and part of the sequence in protein for query and match sequences
        Divergence
        Number of gaps 
        Real divergence

--------

**The AdaptSearch Pipeline**

.. image:: ../../adaptsearch_picture_helps.png :heigth: 593 :width: 852

---------

Changelog
---------

**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>

    <expand macro="citations" />

</tool>