Mercurial > repos > abims-sbr > blastalign
changeset 6:e0bea88bb09f draft
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 76e603ecd0118c8060d972b675a13db858956eb6
| author | abims-sbr |
|---|---|
| date | Thu, 18 Jan 2018 09:02:24 -0500 |
| parents | 0d2da4c020dc |
| children | 9c0044eff621 |
| files | BlastAlign.xml scripts/S01_phylip2fasta.py |
| diffstat | 2 files changed, 24 insertions(+), 8 deletions(-) [+] |
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--- a/BlastAlign.xml Thu Jan 18 08:13:26 2018 -0500 +++ b/BlastAlign.xml Thu Jan 18 09:02:24 2018 -0500 @@ -1,4 +1,4 @@ -<tool name="BlastAlign" id="blastalign" version="2.1"> +<tool name="BlastAlign" id="blastalign" version="2.0"> <description> Align the nucleic acid sequences using BLASTN @@ -55,10 +55,9 @@ </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" /> + <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> </outputs> @@ -105,6 +104,22 @@ <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 Thu Jan 18 08:13:26 2018 -0500 +++ b/scripts/S01_phylip2fasta.py Thu Jan 18 09:02:24 2018 -0500 @@ -13,14 +13,12 @@ """ ## 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 @@ -52,7 +50,10 @@ ################### F1.readline() ## jump the first line + fichier_txt, c = format(F1) ### DEF1 ### + F2.write(fichier_txt) + F1.close() F2.close()