Mercurial > repos > abims-sbr > blastalign
changeset 5:0d2da4c020dc draft
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit df6ba874c5e5f0cde12c9253b5c192e4a35f2280
author | abims-sbr |
---|---|
date | Thu, 18 Jan 2018 08:13:26 -0500 |
parents | 9eb5bb56bf41 |
children | e0bea88bb09f |
files | BlastAlign.xml scripts/S01_phylip2fasta.py |
diffstat | 2 files changed, 8 insertions(+), 24 deletions(-) [+] |
line wrap: on
line diff
--- a/BlastAlign.xml Wed Jan 17 11:32:39 2018 -0500 +++ b/BlastAlign.xml Thu Jan 18 08:13:26 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 @@ -55,9 +55,10 @@ </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"> + <!-- 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> @@ -104,22 +105,6 @@ <output name="phy" value="outputs/locus3_sp2.phy" /> <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="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" /> - </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>
--- a/scripts/S01_phylip2fasta.py Wed Jan 17 11:32:39 2018 -0500 +++ b/scripts/S01_phylip2fasta.py Thu Jan 18 08:13:26 2018 -0500 @@ -13,12 +13,14 @@ """ ## INPUT +""" if os.path.isfile(sys.argv[1]) : f1 = sys.argv[1] else: print "No existing phylip file ; exiting ..." exit() - +""" +f1 = sys.argv[1] F1 = open("%s" %f1, 'r') ## OUTPUT @@ -50,10 +52,7 @@ ################### F1.readline() ## jump the first line - fichier_txt, c = format(F1) ### DEF1 ### - F2.write(fichier_txt) - F1.close() F2.close()