Mercurial > repos > eduardo > mergegffs
changeset 12:e188a09bf012 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mergegffs commit 96fe2c546e9e6a58707cfaf6e6435ed4289c55a2
| author | eduardo |
|---|---|
| date | Sat, 17 Jun 2017 07:52:11 -0400 |
| parents | 791fae70fa3c |
| children | 742d726397b3 |
| files | mergegffs.py tool_dependencies.xml |
| diffstat | 2 files changed, 5 insertions(+), 5 deletions(-) [+] |
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--- a/mergegffs.py Sun Apr 09 10:21:46 2017 -0400 +++ b/mergegffs.py Sat Jun 17 07:52:11 2017 -0400 @@ -25,16 +25,16 @@ db = gffutils.create_db(args.peptides, dbfn=args.database, force=True, keep_order=True,merge_strategy='merge', sort_attribute_values=True) if args.blastp is not None: os.system("convert2gff.py -i "+args.blastp+" -g "+args.peptides+" -p blastp -t protein_match -T -x > blastp.gff") - db.update("blastp.gff") + db=db.update("blastp.gff") if args.signalP is not None: os.system("convert2gff.py -i "+args.signalP+" -g "+args.peptides+" -T -p signalP -t signalpep > signalp.gff") - db.update("signalp.gff") + db=db.update("signalP.gff") if args.tmhmm is not None: os.system("convert2gff.py -i "+args.tmhmm+" -g "+args.peptides+" -T -p tmhmm -t trans_helix > tmhmm.gff") - db.update("tmhmm.gff") + db=db.update("tmhmm.gff") if args.pfam is not None: os.system("pfam2gff.py -i "+args.pfam+" -g "+args.peptides+" -T > PFAM.gff") - db.update("PFAM.gff") + db=db.update("PFAM.gff") with open(args.output, 'w') as fout: for f in db.all_features():
--- a/tool_dependencies.xml Sun Apr 09 10:21:46 2017 -0400 +++ b/tool_dependencies.xml Sat Jun 17 07:52:11 2017 -0400 @@ -4,7 +4,7 @@ <repository changeset_revision="72c3d12f78a7" name="package_python_2_7_gffutils_0_8" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> <package name="genomegtftools" version="1.0"> - <repository changeset_revision="4494aad6d1f3" name="package_genomegtftools_1_0" owner="eduardo" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="aa5434d2d309" name="package_genomegtftools_1_0" owner="eduardo" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> <package name="biopython" version="1.66"> <repository changeset_revision="d86f7eb34488" name="package_biopython_1_66" owner="biopython" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />