Mercurial > repos > abims-sbr > blastalign
diff BlastAlign.xml @ 0:d0ae18156aa2 draft default tip
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
| author | abims-sbr |
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| date | Fri, 01 Feb 2019 10:25:52 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BlastAlign.xml Fri Feb 01 10:25:52 2019 -0500 @@ -0,0 +1,236 @@ +<tool name="BlastAlign" id="blastalign" version="2.1"> + + <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 $output_format.value == "fasta" + && 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="output_format" type="select" label="Output format" help="phylip, nexus, or fasta." > + <option value="fasta">fasta</option> + <option value="phylip">phylip</option> + <option value="nexus">nexus</option> + </param> + </inputs> + + <outputs> + <data format="phylip" name="phy" from_work_dir="out.phy" label="Blastalign on ${input.name} in phylip"> + <filter>output_format == "phylip"</filter> + </data> + <data format="nexus" name="nxs" from_work_dir="out.nxs" label="Blastalign on ${input.name} in nexus"> + <filter>output_format == "nexus"</filter> + </data> + <data format="fasta" name="fasta" from_work_dir="out.fasta" label="Blastalign on ${input.name} in fasta"> + <filter>output_format == "fasta"</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="output_format" value="fasta" /> + <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="output_format" value="phylip" /> + <output name="phy" value="outputs/locus1_sp3.phy" /> + </test> + <test> + <param name="input" ftype="fasta" value="inputs/locus3_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="output_format" value="nexus" /> + <output name="nxs" value="outputs/locus3_sp2.nxs" /> + </test> + <!-- + <test> + <param name="input" ftype="fasta" value="inputs/locus8_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="output_format" value="phylip" /> + <output name="phy" value="outputs/locus8_sp2.phy" /> + </test> + --> + <test> + <param name="input" ftype="fasta" value="inputs/locus8_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="output_format" value="fasta" /> + <output name="phy" value="outputs/locus8_sp2.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> + <![CDATA[ + +.. class:: infomark + +**Authors** BlastAlign has been written by Robert Belshaw and Aris Katzourakis. + +.. class:: infomark + +**Galaxy integration** Julie Baffard and ABiMS TEAM, Roscoff Marine Station + + | Contact support.abims@sb-roscoff.fr for any questions or concerns about the Galaxy implementation of this tool. + | Credits : Gildas le Corguillé, Misharl Monsoor, Victor Mataigne + +-------- + +**Description** + +BlastAlign takes a set of nucleic sequences in a file in fasta format and returns a multiple alignment (in Nexus and Phylip formats) using BLAST+. This Galaxy implementation works with dataset collections, which allows multiple parallels runs of BlastAlign at once on many files. + +-------- + +**Parameters** + +The choice of several parameters for the blast is possible. + +**-m : 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 sequences to be excluded from the analysis** + text. + names must be comma-separated. + + **-n** + If checked : retain original names in output files. + If not checked : output the 15 character name abbreviations (stripped of potentially problematic characters) that is used in the tool. + Default : checked. + +**-s : Number of sequences to be used in initial search for reference sequence** + integer (between 0 and total number of sequences). + Default : 0 + 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. + +** Output format :** + The user have the choice between three format (only one is returned per run) : fasta, phylip, and nexus. + +-------- + +**Outputs** + +The output format is + + - 'Blastalign_on_{input.name}_phylip' : + the aligned sequences in Phylip format. + + - 'Blastalign_on_{input.name}_nexus' : + the aligned sequences in Nexus format. + + - 'Blastalign_on_{input_file}_fasta' : + the aligned sequences in Fasta format if the option "fasta format" is checked. + +--------- + +Changelog +--------- + +**Version 2.1 - 17/01/2018** + + - New parameter "output format" + - Applied some bugfixes and minor improvments + +**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> + + <citations> + <citation type="doi">10.1093/bioinformatics/bth459</citation> + </citations> + +</tool> +