view BlastAlign.xml @ 2:92615a423389 draft

planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b

<tool name="BlastAlign" id="blastalign" version="2.0">

    <description>
        Align the nucleic acid sequences using BLASTN
    </description>

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

    <requirements>
        <expand macro="python_required" />
        <requirement type="package" version="1.4">blastalign</requirement>
    </requirements>

    <stdio>
        <exit_code range="1:" level="fatal" />
    </stdio>

    <command><![CDATA[
        ln -s '$input' '$input.element_identifier'".fasta" &&

        BlastAlign -i '$input.element_identifier'".fasta"
        -m $advanced_option.m
        #if $advanced_option.r != ""
            -r $advanced_option.r
        #end if
        #if $advanced_option.x != ""
            -x $advanced_option.x
        #end if
        -n $advanced_option.n
        #if $advanced_option.s != 0
            -s $advanced_option.s
        #end if
        &&
        ln -s '$input.element_identifier'".fasta.phy" out.phy &&
        ln -s '$input.element_identifier'".fasta.nxs" out.nxs &&
        #if $fasta_out.value == True
            python $__tool_directory__/scripts/S01_phylip2fasta.py out.phy out.fasta
        #end if

    ]]></command>
    <inputs>
        <param name="input" type="data" format="fasta" label="Choose your file" help="A fasta file with nucleotides sequences" />

        <section name="advanced_option" title="Blast advanced options" expanded="True">
            <param argument="-m" type="integer" value="95" min="0" max="100" label="Proportion of gaps allowed in any one sequence in the final alignement" help="default = 95, i.e. only removing sequences with extremely short matches" />
            <param argument="-r" type="text" area="True" size="1x20" label="Choose a reference sequence" help="default is to search for best candidate (if entered, the sequence will be extracted, written to a separate file, and blasted against the original input file)"/>
            <param argument="-x" type="text" area="True" size="5x25" label="Choose the sequences to be excluded from this analysis" help="name of comma-separated sequences " />
            <param argument="-n" type="boolean" checked="true" truevalue="T" falsevalue="F" label="Retain original names in output files" help="option F is to output the 15 character name abbreviations (stripped of potentially problematic characters) that is used in the program" />
            <param argument="-s" type="integer" value="0" min="0" label="Number of sequences to be used in initial search for reference sequence" help="default (= 0) is to find the reference sequence by blasting all sequences against all sequences, only randomly subsampling when it thinks the blast output file might be too large" />
        </section>

        <param name="fasta_out" type="boolean" checked="true" label="Do you want to convert the output phylip in fasta format ? " />
    </inputs>

    <outputs>
        <data format="phy" name="phy" from_work_dir="out.phy" label="Alignment of ${input.name} in phylip" />
        <data format="nxs" name="nxs" from_work_dir="out.nxs" label="Alignment of ${input.name} in nexus" />
        <data format="fasta" name="fasta" from_work_dir="out.fasta" label="Alignment of ${input.name} in fasta">
            <filter>fasta_out == True</filter>
        </data>
    </outputs>

    <tests>
        <test>
            <param name="input" ftype="fasta" value="inputs/locus1_sp2.fasta" />
            <section name="advanced_option">
                <param name="m" value="95" />
                <param name="r" value="" />
                <param name="x" value="" />
                <param name="n" value="False" />
                <param name="s" value="0" />
            </section>
            <param name="fasta_out" value="True" />
            <output name="phy" value="outputs/locus1_sp2.phy" />
            <output name="nxs" value="outputs/locus1_sp2.nxs" />
            <output name="fasta" value="outputs/locus1_sp2.fasta" />
        </test>
        <test>
            <param name="input" ftype="fasta" value="inputs/locus1_sp3.fasta" />
            <section name="advanced_option">
                <param name="m" value="95" />
                <param name="r" value="" />
                <param name="x" value="" />
                <param name="n" value="False" />
                <param name="s" value="0" />
            </section>
            <param name="fasta_out" value="True" />
            <output name="phy" value="outputs/locus1_sp3.phy" />
            <output name="nxs" value="outputs/locus1_sp3.nxs" />
            <output name="fasta" value="outputs/locus1_sp3.fasta" />
        </test>

        <!--locus10_sp2.fasta    locus1_sp3.fasta  locus2_sp2.fasta  locus3_sp2.fasta  locus4_sp2.fasta  locus5_sp2.fasta  locus6_sp2.fasta  locus7_sp2.fasta  locus8_sp2.fasta  locus9_sp2.fasta-->
    </tests>

    <help>

.. class:: infomark

**Authors**  The script in perl was written by **Robert Belshaw** and **Aris Katzourakis**.

@HELP_AUTHORS@

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

| This tool takes **nucleic sequences in fasta format** or **'dataset collection list' containing fasta files** and returns a multiple alignement (in Nexus and Phylip formats) using BLAST+
|

--------

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

The choice of several parameters for the blast is possible.

**-m [maximum proportion of gaps allowed in any one sequence in the final alignement]**
    | integer (between 0 and 100)
    | By default : 95%, i.e. only removes sequences with extremely short matches.
    | We find 50 the most useful.
    |

**-r [name of reference sequence]**
    | text
    | Default is searching for best candidate.
    | If entered, the sequence will be extracted, written to a separate file, and blasted against the original input file.
    |

**-x [name of comma-separated sequences to be excluded from this analysis]**
    | text
    |

**-n**
    | If it's checked : retain original names in output files.
    | If isn't checked : to output the 15 character name abbreviations (stripped of potentially problematic characters) that is used in the tool.
    |

**-s [number of sequences to be used in initial search for reference sequence]**
    | integer (between 0 and total number of sequences)
    | Default is finding the reference sequence by blasting all sequences against all sequences, only randomly subsampling when it thinks the blast output file might be too large.

--------

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

This tool, produces the following files :

**Alignment**
    | is the output with important informations.
    | when the alignment failed with BlastAlign, the name of the file is writting down this output.
    |

**Alignement_file_failed**
    | is the output containing the files failed during the run of BlastAlign.
    |

**Alignment_{inputfile}_phylip**
    | is the output with the aligned sequences in Phylip format.
    |

**Alignment_{inputfile}_nexus**
    | is the output with the aligned sequences in Nexus format.
    |

**Alignment_{input_file}_fasta**
    | is the output with the aligned sequences in Fasta format.

--------

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

------------------------------
The input file and its options
------------------------------

**Input file**

| &gt;Pf210_1/1_1.000_920
| CCGGTGGCCATTTTCTGCACCTCGTGGGTTATTGAGCTGAAAGTGGTTCAGCTCACTGTCTGTTAACAGCCGTGTCGGTCTGAGGGTATCACAGTTAATATAATGAATCAAGAGAAGTTGAAGCAGCTCCAGGCCCAAGTCCGCATCGGAGGAAAGGG
| CACAGCAAGAAGAAAGAAGAAGGTGATTCACAGAACAGCAACAACAGATGACAAGAAACTGCAAAGTACACTGAAGAAATTGGCAGTAAATAATATTCCGGGTATAGAAGAGGTTAACATGATAAAGGATGACGGGCAAGTAATACATTTTACCAATCCGA
| AGGTGCAGGCTTCTCTTCAGTCAAACACATTTGCCATTAATGGCCAAGCCGAAACGAAACAAATCACTGACTTGCTACCCGGTATATTAAATCAGCTGGGGGCTGAAAGTTTAACAAACTTGAAGAAGCTGGCTAAATCTGTGACTGCTGGAGTTGATTC
| TGATAACAAGCAGGATGCAGCAGATATTGATGAAGATGATGATGATGTCCCAGAACTGGTTGAAAACTTTGACGAAGCATCGAAGAATGAGGGGACGTAATTCTTCTCCCACTTTATGCCATGGTAGCATCAATCGTTTTGCTGATGATGGCGTGTTTATAC
| CTACCACCCAGTGTAGATTTGTCCAGACCTGGCTTGTTTGACATTGCTTGTTGGATTTTGCAACAATATCATGATTAGACTGCCTGGCTTTGTGGCCTAAATACTGTATTAAAGTGTCTGTAAAAGGGAAGCAATTTTTCTATTAAGAAGTTATCCACTAGCAT
| ATTGACAGTTTTGCATGTTTGATTTTGTTCCTCGTGCAGGTCAGAACACTGATTGTACAGTGGCTGATTACAGAAAAATTGTATTCAGAGTTAAATAAACACATTATTATCCAAA
| &gt;Pp_17_1/1_1.000_930
| CCGGTGGCCATTTTCTGCACCTCGTGGGTATCTTGGGTTCGATTTGTATCAGCTCCCTATGTAAAATTAAACAAACTTATAACATAGATTGCAGCTGACAATACAATGAACCAAGAAAAATTAAAACAACTCCAAGCCCAGGTGCGCATTGGAGGCAAGGG
| TACAGCAAGAAGAAAGAAGAAGGTCATTCATAGAACAGCAACAACAGATGATAAAAAACTGCAGAGTACATTAAAAAAACTAGCAGTAAATAATATTCCAGGTATAGAAGAGGTTAATATGATAAAAGATGATGGACAGGTAATACATTTTACCAATCCAAAA
| GTACAGGCTTCTCTACAGTCAAACACATTTGCTATTAATGGGCAAGCTGAGACAAAACAAATCACCGAATTGTTGCCTGGTATATTAAATCAGCTGGGAGCAGAAAGTTTAACAAATCTGAAGAAACTGGCTACATCCGTGACTGGTGGAGTTGATTCTGAT
| AACAAGCCAGAAACAGCAGAAATTGATGAAGACGATGATGATGTTCCAGATTTGGTTGAAAACTTTGACGAGGCATCCAAGAATGAAGGAACGTAATTTGTCATTGGTAGATCCTCCCATAGCCTGATTCTTGTGGCTGGCGACAGCTTGTTTATATTTTAC

CCAGTGTAGATTTGTTCAAGAAGGTGTGCTGGCGTTGTTTGAATTTTGTAATAGTACCATGATTTAAATACCCGGTTAACGGCCTACCTGTTATGTAGAAATTGTAGAGAAAAAATTAAATCAATTTTGTATGAACTATAAGCAGCAGCTAATATATTTGCAGTTT
TACATGTTTATCTGTTCATCAGCATGGGTCAGAGAATGACCGTACTTTGCTGGTGATAGAATGCTTGTATTCAAAGTTTAATAAATGGTTGTAAGCCATTTAAAAAAAAAAAAAAA

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

**BlastAlign**

************************  BlastAlign  ************************

|
| This program takes nucleotide sequences in fasta format and returns a multiple alignment (in Nexus and Phylip formats) using BLASTN
|
| Input file locus_2_sp_8.fasta has 2 sequences and is 1894 bytes
| (maximum number of sequences that will be used to search for the reference sequence is 770)
|
|
| BlastAlign finished: it has produced a multiple alignment of 2 sequences and length 720 by aligning to sequence Pf2101/11000920 (proportion of gaps in each sequence is less than 0.95)
| 

**Alignment_{inputfile}_phylip**

| 2 720 S
| Pf2101/1100 ccggtggccattttctgcacctcgtgggttattgagctgaaagtggttcagctcactgtctgttaacagccgtgtcggtctgagggtatcacagttaatataatgaatcaagagaagttgaagcagctccaggcccaagtccgcatcggaggaaagggcacagcaagaagaaagaagaaggtgattcacagaacagcaacaacagat

gacaagaaactgcaaagtacactgaagaaattggcagtaaataatattccgggtatagaagaggttaacatgataaaggatgacgggcaagtaatacattttaccaatccgaaggtgcaggcttctcttcagtcaaacacatttgccattaatggccaagccgaaacgaaacaaatcactgacttgctacccggtatattaaatcagctgggggctgaaag
tttaacaaacttgaagaagctggctaaatctgtgactgctggagttgattctgataacaagcaggatgcagcagatattgatgaagatgatgatgatgtcccagaactggttgaaaactttgacgaagcatcgaagaatgaggggacgtaattcttctcccactttatgccatggtagcatcaatcgttttgctgatgatggcgtgtttatacctaccacccagtgtaga
tttgtccagacctggcttgtttgacattgcttgttggattttgcaacaatatcatgattaga

| Pp171/11000 ccggtggccattttctgcacctcgtgggt-------------------------------------------------------------------aatacaatgaaccaagaaaaattaaaacaactccaagcccaggtgcgcattggaggcaagggtacagcaagaagaaagaagaaggtcattcatagaacagcaacaacagatgataaaaaactgcagag
| tacattaaaaaaactagcagtaaataatattccaggtatagaagaggttaatatgataaaagatgatggacaggtaatacattttaccaatccaaaagtacaggcttctctacagtcaaacacatttgctattaatgggcaagctgagacaaaacaaatcaccgaattgttgcctggtatattaaatcagctgggagcagaaagtttaacaaatctgaagaaact
| ggctacatccgtgactggtggagttgattctgataacaagccagaaacagcagaaattgatgaagacgatgatgatgttccagatttggttgaaaactttgacgaggcatccaagaatgaaggaacgtaatt-----------------------------------------------------------------acccagtgtagatttgt----------------------------------------------
| -------------
|


**Alignment_{inputfile}_nexus**

| #NEXUS

[Aligned to seq Pf2101/1100  by BlastAlign. We have excluded sequences with more than 0.95 gaps]

BEGIN DATA;

| dimensions ntax=2 nchar=720;
| format gap=- datatype=DNA;
| matrix

Pf2101/1100 ccggtggccattttctgcacctcgtgggttattgagctgaaagtggttcagctcactgtctgttaacagccgtgtcggtctgagggtatcacagttaatataatgaatcaagagaagttgaagcagctccaggcccaagtccgcatcggaggaaagggcacagcaagaagaaagaagaaggtgattcacagaacagcaacaacagat
gacaagaaactgcaaagtacactgaagaaattggcagtaaataatattccgggtatagaagaggttaacatgataaaggatgacgggcaagtaatacattttaccaatccgaaggtgcaggcttctcttcagtcaaacacatttgccattaatggccaagccgaaacgaaacaaatcactgacttgctacccggtatattaaatcagctgggggctgaaag
tttaacaaacttgaagaagctggctaaatctgtgactgctggagttgattctgataacaagcaggatgcagcagatattgatgaagatgatgatgatgtcccagaactggttgaaaactttgacgaagcatcgaagaatgaggggacgtaattcttctcccactttatgccatggtagcatcaatcgttttgctgatgatggcgtgtttatacctaccacccagtgtaga
tttgtccagacctggcttgtttgacattgcttgttggattttgcaacaatatcatgattaga

| Pp171/11000 ccggtggccattttctgcacctcgtgggt-------------------------------------------------------------------aatacaatgaaccaagaaaaattaaaacaactccaagcccaggtgcgcattggaggcaagggtacagcaagaagaaagaagaaggtcattcatagaacagcaacaacagatgataaaaaactgcagag
| tacattaaaaaaactagcagtaaataatattccaggtatagaagaggttaatatgataaaagatgatggacaggtaatacattttaccaatccaaaagtacaggcttctctacagtcaaacacatttgctattaatgggcaagctgagacaaaacaaatcaccgaattgttgcctggtatattaaatcagctgggagcagaaagtttaacaaatctgaagaaac
| tggctacatccgtgactggtggagttgattctgataacaagccagaaacagcagaaattgatgaagacgatgatgatgttccagatttggttgaaaactttgacgaggcatccaagaatgaaggaacgtaatt-----------------------------------------------------------------acccagtgtagatttgt--------------------------------------------
| -------------
| ;
| end;
|


**Alignment_{inputfile}_fasta**

| &gt;Pf2101/11000920

ccggtggccattttctgcacctcgtgggttattgagctgaaagtggttcagctcactgtctgttaacagccgtgtcggtctgagggtatcacagttaatataatgaatcaagagaagttgaagcagctccaggcccaagtccgcatcggaggaaagggcacagcaagaagaaagaagaaggtgattcacagaacagcaacaacagatgacaagaaactg
caaagtacactgaagaaattggcagtaaataatattccgggtatagaagaggttaacatgataaaggatgacgggcaagtaatacattttaccaatccgaaggtgcaggcttctcttcagtcaaacacatttgccattaatggccaagccgaaacgaaacaaatcactgacttgctacccggtatattaaatcagctgggggctgaaagtttaacaaacttgaa
gaagctggctaaatctgtgactgctggagttgattctgataacaagcaggatgcagcagatattgatgaagatgatgatgatgtcccagaactggttgaaaactttgacgaagcatcgaagaatgaggggacgtaattcttctcccactttatgccatggtagcatcaatcgttttgctgatgatggcgtgtttatacctaccacccagtgtagatttgtccagacctggc
ttgtttgacattgcttgttggattttgcaacaatatcatgattaga

| &gt;Pp171/11000930

ccggtggccattttctgcacctcgtgggt-------------------------------------------------------------------aatacaatgaaccaagaaaaattaaaacaactccaagcccaggtgcgcattggaggcaagggtacagcaagaagaaagaagaaggtcattcatagaacagcaacaacagatgataaaaaactgcagagtacattaaaaaa
actagcagtaaataatattccaggtatagaagaggttaatatgataaaagatgatggacaggtaatacattttaccaatccaaaagtacaggcttctctacagtcaaacacatttgctattaatgggcaagctgagacaaaacaaatcaccgaattgttgcctggtatattaaatcagctgggagcagaaagtttaacaaatctgaagaaactggctacatccg
tgactggtggagttgattctgataacaagccagaaacagcagaaattgatgaagacgatgatgatgttccagatttggttgaaaactttgacgaggcatccaagaatgaaggaacgtaatt-----------------------------------------------------------------acccagtgtagatttgt---------------------------------------------------------


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

Changelog
---------

**Version 2.0 - 21/04/2017**

 - NEW: BlastAlign will now be launched on one file at once. Although, it will manage a Dataset Collection to deal with numerous files.


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

 - TEST: Add funtional test with planemo

 - IMPROVEMENT: Use conda dependencies for blastalign, blast-legacy, perl, python


    </help>

    <expand macro="citations" />

</tool>