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view BlastAlign.xml @ 5:0d2da4c020dc draft
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit df6ba874c5e5f0cde12c9253b5c192e4a35f2280
author | abims-sbr |
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date | Thu, 18 Jan 2018 08:13:26 -0500 |
parents | 9eb5bb56bf41 |
children | e0bea88bb09f |
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<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 $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> <!-- visible="true" ? --> <data format="phylip" name="phy" from_work_dir="out.phy" label="Alignment of ${input.name} in phylip" /> <data format="nexus" 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> <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="fasta_out" value="False" /> <output name="phy" value="outputs/locus3_sp2.phy" /> <output name="nxs" value="outputs/locus3_sp2.nxs" /> </test> </tests> <help> <![CDATA[ . class:: infomark **Authors** BlastAlign has been written by Robert Belshaw and Aris Katzourakis. The scripts of this tool have been written by Eric Fontanillas. .. class:: infomark **Galaxy integration** Julie Baffard and ABiMS Team. Contact support.abims@sb-roscoff.fr for any questions or concerns about the Galaxy implementation of this tool. -------- **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. -------- **Outputs** - 'Alignment_{input.name}_phylip' : the aligned sequences in Phylip format. - 'Alignment_{input.name}_nexus' : the aligned sequences in Nexus format. - 'Alignment_{input_file}_fasta' : the aligned sequences in Fasta format if the option "fasta format" is checked. --------- Changelog --------- **Version 2.1 - 17/01/2018** - 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> <expand macro="citations" /> </tool>