Mercurial > repos > abims-sbr > blastalign
changeset 7:9c0044eff621 draft
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
| author | abims-sbr |
|---|---|
| date | Tue, 27 Feb 2018 08:47:11 -0500 |
| parents | e0bea88bb09f |
| children | f19cca5b8632 |
| files | BlastAlign.xml |
| diffstat | 1 files changed, 42 insertions(+), 24 deletions(-) [+] |
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--- a/BlastAlign.xml Thu Jan 18 09:02:24 2018 -0500 +++ b/BlastAlign.xml Tue Feb 27 08:47:11 2018 -0500 @@ -1,4 +1,4 @@ -<tool name="BlastAlign" id="blastalign" version="2.0"> +<tool name="BlastAlign" id="blastalign" version="2.1"> <description> Align the nucleic acid sequences using BLASTN @@ -35,7 +35,7 @@ && ln -s '$input.element_identifier'".fasta.phy" out.phy && ln -s '$input.element_identifier'".fasta.nxs" out.nxs - #if $fasta_out.value == True + #if $output_format.value == "fasta" && python $__tool_directory__/scripts/S01_phylip2fasta.py out.phy out.fasta #end if @@ -50,15 +50,23 @@ <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 ? " /> + + <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="Alignment of ${input.name} in phylip" hidden="True"/> - <data format="nexus" name="nxs" from_work_dir="out.nxs" label="Alignment of ${input.name} in nexus" hidden="True"/> - <data format="fasta" name="fasta" from_work_dir="out.fasta" label="Alignment of ${input.name} in fasta" hidden="True"> - <filter>fasta_out == True</filter> + <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> @@ -72,9 +80,7 @@ <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" /> + <param name="output_format" value="fasta" /> <output name="fasta" value="outputs/locus1_sp2.fasta" /> </test> <test> @@ -86,10 +92,8 @@ <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" /> + <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" /> @@ -100,8 +104,7 @@ <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" /> + <param name="output_format" value="nexus" /> <output name="nxs" value="outputs/locus3_sp2.nxs" /> </test> <test> @@ -113,10 +116,20 @@ <param name="n" value="False" /> <param name="s" value="0" /> </section> - <param name="fasta_out" value="True" /> - <output name="phy" value="outputs/locus8_sp2.phy" /> - <output name="nxs" value="outputs/locus8_sp2.nxs" /> - <output name="fasta" value="outputs/locus8_sp2.fasta" /> + <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--> @@ -171,17 +184,21 @@ 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 - - 'Alignment_{input.name}_phylip' : + - 'Blastalign_on_{input.name}_phylip' : the aligned sequences in Phylip format. - - 'Alignment_{input.name}_nexus' : + - 'Blastalign_on_{input.name}_nexus' : the aligned sequences in Nexus format. - - 'Alignment_{input_file}_fasta' : + - 'Blastalign_on_{input_file}_fasta' : the aligned sequences in Fasta format if the option "fasta format" is checked. --------- @@ -191,6 +208,7 @@ **Version 2.1 - 17/01/2018** + - New parameter "output format" - Applied some bugfixes and minor improvments **Version 2.0 - 21/04/2017**