| Next changeset 1:e2d4343d73ad (2016-01-29) |
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Commit message:
Uploaded |
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added:
interproscan5/create_index.py interproscan5/data/__base__.gff3 interproscan5/data/__base__.html.tar.gz interproscan5/data/__base__.svg.tar.gz interproscan5/data/__base__.tsv interproscan5/data/__base__.xml interproscan5/data/input.fasta interproscan5/fake_ips.py interproscan5/interproscan.xml interproscan5/ips5.xml interproscan5/ipsfaux.xml interproscan5/readme.rst interproscan5/static/images/P51587.svg.png interproscan5/static/images/example_xml_output.png interproscan5/tool_dependencies.xml |
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| diff -r 000000000000 -r fe8e43a26870 interproscan5/create_index.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/interproscan5/create_index.py Thu Jan 28 19:34:51 2016 -0500 |
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| @@ -0,0 +1,14 @@ +#!/usr/bin/env python + +import os +import sys + +o = open(sys.argv[1], 'w+') + +o.write('<html> <body> <h1> InterProScan result summary page </h1> <ul>') + +for filename in [f for f in os.listdir(sys.argv[2]) if os.path.isfile(os.path.join(sys.argv[2], f))]: + o.write('<li><a href="%s"> %s </a></li>' % (filename, os.path.splitext(filename)[0])) + +o.write('</ul></body></html>') +o.close() |
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| diff -r 000000000000 -r fe8e43a26870 interproscan5/data/__base__.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/interproscan5/data/__base__.gff3 Thu Jan 28 19:34:51 2016 -0500 |
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| b'@@ -0,0 +1,377 @@\n+##gff-version 3\n+##feature-ontology http://song.cvs.sourceforge.net/viewvc/song/ontology/sofa.obo?revision=1.269\n+##sequence-region P00363 1 602\n+P00363\t.\tpolypeptide\t1\t602\t.\t+\t.\tmd5=0d2c0f1acdd08ab0157f2308531a58e4;ID=P00363\n+P00363\tSUPERFAMILY\tprotein_match\t361\t415\t2.27E-71\t+\t.\tName=SSF51905;Target=P00363 361 415;status=T;ID=match$1_361_415;Ontology_term="GO:0016491","GO:0055114";date=24-01-2016;Dbxref="InterPro:IPR023753"\n+P00363\tSUPERFAMILY\tprotein_match\t2\t250\t2.27E-71\t+\t.\tName=SSF51905;Target=P00363 2 250;status=T;ID=match$1_2_250;Ontology_term="GO:0016491","GO:0055114";date=24-01-2016;Dbxref="InterPro:IPR023753"\n+P00363\tTIGRFAM\tprotein_match\t7\t581\t4.7E-250\t+\t.\tName=TIGR01812;signature_desc=sdhA_frdA_Gneg: succinate dehydrogenase or fumarate reductase, flavoprotein subunit;Target=P00363 7 581;status=T;ID=match$2_7_581;Ontology_term="GO:0016627","GO:0022900","GO:0050660","GO:0055114";date=24-01-2016;Dbxref="InterPro:IPR014006"\n+P00363\tGene3D\tprotein_match\t234\t352\t3.6E-37\t+\t.\tName=G3DSA:3.90.700.10;Target=P00363 234 352;status=T;ID=match$3_234_352;date=24-01-2016;Dbxref="InterPro:IPR027477"\n+P00363\tPRINTS\tprotein_match\t375\t382\t2.5E-5\t+\t.\tName=PR00411;signature_desc=Pyridine nucleotide disulphide reductase class-I signature;Target=P00363 375 382;status=T;ID=match$4_375_382;date=24-01-2016\n+P00363\tPRINTS\tprotein_match\t7\t29\t2.5E-5\t+\t.\tName=PR00411;signature_desc=Pyridine nucleotide disulphide reductase class-I signature;Target=P00363 7 29;status=T;ID=match$4_7_29;date=24-01-2016\n+P00363\tGene3D\tprotein_match\t426\t537\t1.5E-38\t+\t.\tName=G3DSA:1.20.58.100;Target=P00363 426 537;status=T;ID=match$5_426_537;Ontology_term="GO:0016491","GO:0055114";date=24-01-2016;Dbxref="InterPro:IPR015939"\n+P00363\tCoils\tprotein_match\t423\t443\t.\t+\t.\tName=Coil;Target=P00363 423 443;status=T;ID=match$6_423_443;date=24-01-2016\n+P00363\tGene3D\tprotein_match\t353\t416\t5.9E-106\t+\t.\tName=G3DSA:3.50.50.60;Target=P00363 353 416;status=T;ID=match$7_353_416;Ontology_term="GO:0016491","GO:0055114";date=24-01-2016;Dbxref="InterPro:IPR023753"\n+P00363\tGene3D\tprotein_match\t2\t233\t5.9E-106\t+\t.\tName=G3DSA:3.50.50.60;Target=P00363 2 233;status=T;ID=match$7_2_233;Ontology_term="GO:0016491","GO:0055114";date=24-01-2016;Dbxref="InterPro:IPR023753"\n+P00363\tPANTHER\tprotein_match\t1\t584\t0.0\t+\t.\tName=PTHR11632;Target=P00363 1 584;status=T;ID=match$8_1_584;date=24-01-2016\n+P00363\tSUPERFAMILY\tprotein_match\t444\t590\t3.01E-46\t+\t.\tName=SSF46977;Target=P00363 444 590;status=T;ID=match$9_444_590;Ontology_term="GO:0016491","GO:0055114";date=24-01-2016;Dbxref="InterPro:IPR015939"\n+P00363\tPANTHER\tprotein_match\t1\t584\t0.0\t+\t.\tName=PTHR11632:SF50;Target=P00363 1 584;status=T;ID=match$10_1_584;date=24-01-2016\n+P00363\tPIRSF\tprotein_match\t1\t575\t2.0E-42\t+\t.\tName=PIRSF000171;Target=P00363 1 575;status=T;ID=match$11_1_575;date=24-01-2016;Dbxref="InterPro:IPR030664"\n+P00363\tTIGRFAM\tprotein_match\t3\t582\t0.0\t+\t.\tName=TIGR01176;signature_desc=fum_red_Fp: fumarate reductase (quinol), flavoprotein subunit;Target=P00363 3 582;status=T;ID=match$12_3_582;Ontology_term="GO:0009061","GO:0016491","GO:0055114";date=24-01-2016;Dbxref="InterPro:IPR005884"\n+P00363\tPfam\tprotein_match\t453\t581\t7.0E-39\t+\t.\tName=PF02910;signature_desc=Fumarate reductase flavoprotein C-term;Target=P00363 453 581;status=T;ID=match$13_453_581;Ontology_term="GO:0016491","GO:0055114";date=24-01-2016;Dbxref="InterPro:IPR015939"\n+P00363\tCoils\tprotein_match\t473\t493\t.\t+\t.\tName=Coil;Target=P00363 473 493;status=T;ID=match$14_473_493;date=24-01-2016\n+P00363\tProSitePatterns\tprotein_match\t43\t52\t.\t+\t.\tName=PS00504;signature_desc=Fumarate reductase / succinate dehydrogenase FAD-binding site.;Target=P00363 43 52;status=T;ID=match$15_43_52;Ontology_term="GO:0016491","GO:0055114";date=24-01-2016;Dbxref="InterPro:IPR003952"\n+P00363\tGene3D\tprotein_match\t543\t577\t5.5E-18\t+\t.\tName=G3DSA:4.10.80.40;Target=P00363 543 577;status=T;ID=match$16_543_577;date=24-01-2016\n+P00363\tSUPERFAMILY\tprotein_match\t227\t358\t6.88E-43\t+\t.\tName=SSF56425;Target=P00363 '..b'+>match$31_179_466\n+GHYVKMVHNGIEYGDMQLIAEAYSLLKGGLNLTNEELAQTFTEWNNGELSSYLIDITKDI\n+FTKKDEDGNYLVDVILDEAANKGTGKWTSQSALDLGEPLSLITESVFARYISSLKDQRVA\n+ASKVLSGPQAQPAGDKAEFIEKVRRALYLGKIVSYAQGFSQLRAASEEYNWDLNYGEIAK\n+IFRAGCIIRAQFLQKITDAYAENPQIANLLLAPYFKQIADDYQQALRDVVAYAVQNGIPV\n+PTFSAAVAYYDSYRAAVLPANLIQAQRDYFGAHTYKRIDKEGVFHTEW\n+>match$32_177_467\n+GAGHYVKMVHNGIEYGDMQLIAEAYSLLKGGLNLTNEELAQTFTEWNNGELSSYLIDITK\n+DIFTKKDEDGNYLVDVILDEAANKGTGKWTSQSALDLGEPLSLITESVFARYISSLKDQR\n+VAASKVLSGPQAQPAGDKAEFIEKVRRALYLGKIVSYAQGFSQLRAASEEYNWDLNYGEI\n+AKIFRAGCIIRAQFLQKITDAYAENPQIANLLLAPYFKQIADDYQQALRDVVAYAVQNGI\n+PVPTFSAAVAYYDSYRAAVLPANLIQAQRDYFGAHTYKRIDKEGVFHTEWL\n+>match$33_114_128\n+TFKNALTTLPMGGGK\n+>match$33_193_215\n+VFTGKGLSFGGSLIRPEATGYGL\n+>match$33_235_255\n+VSVSGSGNVAQYAIEKAMEFG\n+>match$33_372_383\n+ANAGGVATSGLE\n+>match$34_6_196\n+SLESFLNHVQKRDPNQTEFAQAVREVMTTLWPFLEQNPKYRQMSLLERLVEPERVIQFRV\n+VWVDDRNQIQVNRAWRVQFSSAIGPYKGGMRFHPSVNLSILKFLGFEQTFKNALTTLPMG\n+GGKGGSDFDPKGKSEGEVMRFCQALMTELYRHLGADTDVPAGDIGVGGREVGFMAGMMKK\n+LSNNTACVFTG\n+>match$35_68_188\n+VDDRNQIQVNRAWRVQFSSAIGPYKGGMRFHPSVNLSILKFLGFEQTFKNALTTLPMGGG\n+KGGSDFDPKGKSEGEVMRFCQALMTELYRHLGADTDVPAGDIGVGGREVGFMAGMMKKLS\n+N\n+>match$36_202_445\n+GGSLIRPEATGYGLVYFTEAMLKRHGMGFEGMRVSVSGSGNVAQYAIEKAMEFGARVITA\n+SDSSGTVVDESGFTKEKLARLIEIKASRDGRVADYAKEFGLVYLEGQQPWSLPVDIALPC\n+ATQNELDVDAAHQLIANGVKAVAEGANMPTTIEATELFQQAGVLFAPGKAANAGGVATSG\n+LEMAQNAARLGWKAEKVDARLHHIMLDIHHACVEHGGEGEQTNYVQGANIAGFVKVADAM\n+LAQG\n+>match$37_22_447\n+TEFAQAVREVMTTLWPFLEQNPKYRQMSLLERLVEPERVIQFRVVWVDDRNQIQVNRAWR\n+VQFSSAIGPYKGGMRFHPSVNLSILKFLGFEQTFKNALTTLPMGGGKGGSDFDPKGKSEG\n+EVMRFCQALMTELYRHLGADTDVPAGDIGVGGREVGFMAGMMKKLSNNTACVFTGKGLSF\n+GGSLIRPEATGYGLVYFTEAMLKRHGMGFEGMRVSVSGSGNVAQYAIEKAMEFGARVITA\n+SDSSGTVVDESGFTKEKLARLIEIKASRDGRVADYAKEFGLVYLEGQQPWSLPVDIALPC\n+ATQNELDVDAAHQLIANGVKAVAEGANMPTTIEATELFQQAGVLFAPGKAANAGGVATSG\n+LEMAQNAARLGWKAEKVDARLHHIMLDIHHACVEHGGEGEQTNYVQGANIAGFVKVADAM\n+LAQGVI\n+>match$38_204_445\n+SLIRPEATGYGLVYFTEAMLKRHGMGFEGMRVSVSGSGNVAQYAIEKAMEFGARVITASD\n+SSGTVVDESGFTKEKLARLIEIKASRDGRVADYAKEFGLVYLEGQQPWSLPVDIALPCAT\n+QNELDVDAAHQLIANGVKAVAEGANMPTTIEATELFQQAGVLFAPGKAANAGGVATSGLE\n+MAQNAARLGWKAEKVDARLHHIMLDIHHACVEHGGEGEQTNYVQGANIAGFVKVADAMLA\n+QG\n+>match$39_209_372\n+EATGYGLVYFTEAMLKRHGMGFEGMRVSVSGSGNVAQYAIEKAMEFGARVITASDSSGTV\n+VDESGFTKEKLARLIEIKASRDGRVADYAKEFGLVYLEGQQPWSLPVDIALPCATQNELD\n+VDAAHQLIANGVKAVAEGANMPTTIEATELFQQAGVLFAPGKAA\n+>match$40_202_446\n+GGSLIRPEATGYGLVYFTEAMLKRHGMGFEGMRVSVSGSGNVAQYAIEKAMEFGARVITA\n+SDSSGTVVDESGFTKEKLARLIEIKASRDGRVADYAKEFGLVYLEGQQPWSLPVDIALPC\n+ATQNELDVDAAHQLIANGVKAVAEGANMPTTIEATELFQQAGVLFAPGKAANAGGVATSG\n+LEMAQNAARLGWKAEKVDARLHHIMLDIHHACVEHGGEGEQTNYVQGANIAGFVKVADAM\n+LAQGV\n+>match$41_7_67\n+LESFLNHVQKRDPNQTEFAQAVREVMTTLWPFLEQNPKYRQMSLLERLVEPERVIQFRVV\n+W\n+>match$41_373_446\n+NAGGVATSGLEMAQNAARLGWKAEKVDARLHHIMLDIHHACVEHGGEGEQTNYVQGANIA\n+GFVKVADAMLAQGV\n+>match$42_122_135\n+LPMGGGKGGSDFDP\n+>match$43_57_184\n+PERVIQFRVVWVDDRNQIQVNRAWRVQFSSAIGPYKGGMRFHPSVNLSILKFLGFEQTFK\n+NALTTLPMGGGKGGSDFDPKGKSEGEVMRFCQALMTELYRHLGADTDVPAGDIGVGGREV\n+GFMAGMMK\n+>match$44_1_447\n+MDQTYSLESFLNHVQKRDPNQTEFAQAVREVMTTLWPFLEQNPKYRQMSLLERLVEPERV\n+IQFRVVWVDDRNQIQVNRAWRVQFSSAIGPYKGGMRFHPSVNLSILKFLGFEQTFKNALT\n+TLPMGGGKGGSDFDPKGKSEGEVMRFCQALMTELYRHLGADTDVPAGDIGVGGREVGFMA\n+GMMKKLSNNTACVFTGKGLSFGGSLIRPEATGYGLVYFTEAMLKRHGMGFEGMRVSVSGS\n+GNVAQYAIEKAMEFGARVITASDSSGTVVDESGFTKEKLARLIEIKASRDGRVADYAKEF\n+GLVYLEGQQPWSLPVDIALPCATQNELDVDAAHQLIANGVKAVAEGANMPTTIEATELFQ\n+QAGVLFAPGKAANAGGVATSGLEMAQNAARLGWKAEKVDARLHHIMLDIHHACVEHGGEG\n+EQTNYVQGANIAGFVKVADAMLAQGVI\n+>match$45_1_447\n+MDQTYSLESFLNHVQKRDPNQTEFAQAVREVMTTLWPFLEQNPKYRQMSLLERLVEPERV\n+IQFRVVWVDDRNQIQVNRAWRVQFSSAIGPYKGGMRFHPSVNLSILKFLGFEQTFKNALT\n+TLPMGGGKGGSDFDPKGKSEGEVMRFCQALMTELYRHLGADTDVPAGDIGVGGREVGFMA\n+GMMKKLSNNTACVFTGKGLSFGGSLIRPEATGYGLVYFTEAMLKRHGMGFEGMRVSVSGS\n+GNVAQYAIEKAMEFGARVITASDSSGTVVDESGFTKEKLARLIEIKASRDGRVADYAKEF\n+GLVYLEGQQPWSLPVDIALPCATQNELDVDAAHQLIANGVKAVAEGANMPTTIEATELFQ\n+QAGVLFAPGKAANAGGVATSGLEMAQNAARLGWKAEKVDARLHHIMLDIHHACVEHGGEG\n+EQTNYVQGANIAGFVKVADAMLAQGVI\n+>match$46_2_37\n+RQFYQHYFTATAKLCWLRWLSVPQRLTMLEGLMQWD\n' 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| diff -r 000000000000 -r fe8e43a26870 interproscan5/data/__base__.html.tar.gz |
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| Binary file interproscan5/data/__base__.html.tar.gz has changed |
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| diff -r 000000000000 -r fe8e43a26870 interproscan5/data/__base__.svg.tar.gz |
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| Binary file interproscan5/data/__base__.svg.tar.gz has changed |
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| diff -r 000000000000 -r fe8e43a26870 interproscan5/data/__base__.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/interproscan5/data/__base__.tsv Thu Jan 28 19:34:51 2016 -0500 |
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| b'@@ -0,0 +1,59 @@\n+P00363\t0d2c0f1acdd08ab0157f2308531a58e4\t602\tSUPERFAMILY\tSSF51905\t\t361\t415\t2.27E-71\tT\t24-01-2016\tIPR023753\tFAD/NAD(P)-binding domain\tGO:0016491|GO:0055114\n+P00363\t0d2c0f1acdd08ab0157f2308531a58e4\t602\tSUPERFAMILY\tSSF51905\t\t2\t250\t2.27E-71\tT\t24-01-2016\tIPR023753\tFAD/NAD(P)-binding domain\tGO:0016491|GO:0055114\n+P00363\t0d2c0f1acdd08ab0157f2308531a58e4\t602\tTIGRFAM\tTIGR01812\tsdhA_frdA_Gneg: succinate dehydrogenase or fumarate reductase, flavoprotein subunit\t7\t581\t4.7E-250\tT\t24-01-2016\tIPR014006\tSuccinate dehydrogenase/fumarate reductase, flavoprotein subunit\tGO:0016627|GO:0022900|GO:0050660|GO:0055114\n+P00363\t0d2c0f1acdd08ab0157f2308531a58e4\t602\tGene3D\tG3DSA:3.90.700.10\t\t234\t352\t3.6E-37\tT\t24-01-2016\tIPR027477\tSuccinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain\t\n+P00363\t0d2c0f1acdd08ab0157f2308531a58e4\t602\tPRINTS\tPR00411\tPyridine nucleotide disulphide reductase class-I signature\t375\t382\t2.5E-5\tT\t24-01-2016\n+P00363\t0d2c0f1acdd08ab0157f2308531a58e4\t602\tPRINTS\tPR00411\tPyridine nucleotide disulphide reductase class-I signature\t7\t29\t2.5E-5\tT\t24-01-2016\n+P00363\t0d2c0f1acdd08ab0157f2308531a58e4\t602\tGene3D\tG3DSA:1.20.58.100\t\t426\t537\t1.5E-38\tT\t24-01-2016\tIPR015939\tFumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal\tGO:0016491|GO:0055114\n+P00363\t0d2c0f1acdd08ab0157f2308531a58e4\t602\tCoils\tCoil\t\t423\t443\t-\tT\t24-01-2016\n+P00363\t0d2c0f1acdd08ab0157f2308531a58e4\t602\tGene3D\tG3DSA:3.50.50.60\t\t353\t416\t5.9E-106\tT\t24-01-2016\tIPR023753\tFAD/NAD(P)-binding domain\tGO:0016491|GO:0055114\n+P00363\t0d2c0f1acdd08ab0157f2308531a58e4\t602\tGene3D\tG3DSA:3.50.50.60\t\t2\t233\t5.9E-106\tT\t24-01-2016\tIPR023753\tFAD/NAD(P)-binding domain\tGO:0016491|GO:0055114\n+P00363\t0d2c0f1acdd08ab0157f2308531a58e4\t602\tPANTHER\tPTHR11632\t\t1\t584\t0.0\tT\t24-01-2016\n+P00363\t0d2c0f1acdd08ab0157f2308531a58e4\t602\tSUPERFAMILY\tSSF46977\t\t444\t590\t3.01E-46\tT\t24-01-2016\tIPR015939\tFumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal\tGO:0016491|GO:0055114\n+P00363\t0d2c0f1acdd08ab0157f2308531a58e4\t602\tPANTHER\tPTHR11632:SF50\t\t1\t584\t0.0\tT\t24-01-2016\n+P00363\t0d2c0f1acdd08ab0157f2308531a58e4\t602\tPIRSF\tPIRSF000171\t\t1\t575\t2.0E-42\tT\t24-01-2016\tIPR030664\tSuccinate dehydrogenase/fumarate reductase, alpha/adenylylsulphate reductase subunit\t\n+P00363\t0d2c0f1acdd08ab0157f2308531a58e4\t602\tTIGRFAM\tTIGR01176\tfum_red_Fp: fumarate reductase (quinol), flavoprotein subunit\t3\t582\t0.0\tT\t24-01-2016\tIPR005884\tFumarate reductase, flavoprotein subunit\tGO:0009061|GO:0016491|GO:0055114\n+P00363\t0d2c0f1acdd08ab0157f2308531a58e4\t602\tPfam\tPF02910\tFumarate reductase flavoprotein C-term\t453\t581\t7.0E-39\tT\t24-01-2016\tIPR015939\tFumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal\tGO:0016491|GO:0055114\n+P00363\t0d2c0f1acdd08ab0157f2308531a58e4\t602\tCoils\tCoil\t\t473\t493\t-\tT\t24-01-2016\n+P00363\t0d2c0f1acdd08ab0157f2308531a58e4\t602\tProSitePatterns\tPS00504\tFumarate reductase / succinate dehydrogenase FAD-binding site.\t43\t52\t-\tT\t24-01-2016\tIPR003952\tFumarate reductase/succinate dehydrogenase, FAD-binding site\tGO:0016491|GO:0055114\n+P00363\t0d2c0f1acdd08ab0157f2308531a58e4\t602\tGene3D\tG3DSA:4.10.80.40\t\t543\t577\t5.5E-18\tT\t24-01-2016\n+P00363\t0d2c0f1acdd08ab0157f2308531a58e4\t602\tSUPERFAMILY\tSSF56425\t\t227\t358\t6.88E-43\tT\t24-01-2016\tIPR027477\tSuccinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain\t\n+P00363\t0d2c0f1acdd08ab0157f2308531a58e4\t602\tPfam\tPF00890\tFAD binding domain\t7\t397\t1.1E-115\tT\t24-01-2016\tIPR003953\tFAD-dependent oxidoreductase 2, FAD binding domain\t\n+P00363\t0d2c0f1acdd08ab0157f2308531a58e4\t602\tPRINTS\tPR00368\tFAD-dependent pyridine nucleotide reductase signature\t8\t27\t3.0E-10\tT\t24-01-2016\n+P00363\t0d2c0f1acdd08ab0157f2308531a58e4\t602\tPRINTS\tPR00368\tFAD-dependent pyridine nucleotide reductase signature\t360\t382\t3.0E-10\tT\t24-01-2016\n+P00350\t1776f92beb74ff0ccd9ac47a65663644\t468\tSUPERFAMILY\tSSF51735\t\t4\t173\t4.86E-50\tT\t24-01-2016\tIPR016040\tNAD(P)-binding domain\t\n+P00350\t1776f92beb74ff0ccd9ac47a65663644\t468\tTIGRFAM\tTIGR00873\tgnd: 6-phosphogluconate de'..b'006183\t6-phosphogluconate dehydrogenase\tGO:0055114\n+P00350\t1776f92beb74ff0ccd9ac47a65663644\t468\tPRINTS\tPR00076\t6-phosphogluconate dehydrogenase signature\t356\t378\t1.521867E-89\tT\t24-01-2016\tIPR006183\t6-phosphogluconate dehydrogenase\tGO:0055114\n+P00350\t1776f92beb74ff0ccd9ac47a65663644\t468\tPANTHER\tPTHR11811:SF25\t\t1\t466\t7.6E-305\tT\t24-01-2016\n+P00350\t1776f92beb74ff0ccd9ac47a65663644\t468\tPANTHER\tPTHR11811\t\t1\t466\t7.6E-305\tT\t24-01-2016\n+P00350\t1776f92beb74ff0ccd9ac47a65663644\t468\tPfam\tPF00393\t6-phosphogluconate dehydrogenase, C-terminal domain\t179\t466\t2.0E-132\tT\t24-01-2016\tIPR006114\t6-phosphogluconate dehydrogenase, C-terminal\tGO:0004616|GO:0006098|GO:0055114\n+P00350\t1776f92beb74ff0ccd9ac47a65663644\t468\tSUPERFAMILY\tSSF48179\t\t177\t467\t6.8E-132\tT\t24-01-2016\tIPR008927\t6-phosphogluconate dehydrogenase C-terminal domain-like\tGO:0055114\n+P00370\t9ec8e26fcf5c160f533bf9a69dec0212\t447\tPRINTS\tPR00082\tGlutamate/leucine/phenylalanine/valine dehydrogenase signature\t372\t383\t2.5E-33\tT\t24-01-2016\tIPR006095\tGlutamate/phenylalanine/leucine/valine dehydrogenase\tGO:0006520|GO:0016491|GO:0055114\n+P00370\t9ec8e26fcf5c160f533bf9a69dec0212\t447\tPRINTS\tPR00082\tGlutamate/leucine/phenylalanine/valine dehydrogenase signature\t114\t128\t2.5E-33\tT\t24-01-2016\tIPR006095\tGlutamate/phenylalanine/leucine/valine dehydrogenase\tGO:0006520|GO:0016491|GO:0055114\n+P00370\t9ec8e26fcf5c160f533bf9a69dec0212\t447\tPRINTS\tPR00082\tGlutamate/leucine/phenylalanine/valine dehydrogenase signature\t235\t255\t2.5E-33\tT\t24-01-2016\tIPR006095\tGlutamate/phenylalanine/leucine/valine dehydrogenase\tGO:0006520|GO:0016491|GO:0055114\n+P00370\t9ec8e26fcf5c160f533bf9a69dec0212\t447\tPRINTS\tPR00082\tGlutamate/leucine/phenylalanine/valine dehydrogenase signature\t193\t215\t2.5E-33\tT\t24-01-2016\tIPR006095\tGlutamate/phenylalanine/leucine/valine dehydrogenase\tGO:0006520|GO:0016491|GO:0055114\n+P00370\t9ec8e26fcf5c160f533bf9a69dec0212\t447\tSUPERFAMILY\tSSF53223\t\t6\t196\t6.72E-74\tT\t24-01-2016\n+P00370\t9ec8e26fcf5c160f533bf9a69dec0212\t447\tGene3D\tG3DSA:3.40.192.10\t\t68\t188\t1.0E-60\tT\t24-01-2016\n+P00370\t9ec8e26fcf5c160f533bf9a69dec0212\t447\tPfam\tPF00208\tGlutamate/Leucine/Phenylalanine/Valine dehydrogenase\t202\t445\t1.3E-87\tT\t24-01-2016\tIPR006096\tGlutamate/phenylalanine/leucine/valine dehydrogenase, C-terminal\tGO:0006520|GO:0016491|GO:0055114\n+P00370\t9ec8e26fcf5c160f533bf9a69dec0212\t447\tPIRSF\tPIRSF000185\t\t22\t447\t1.8E-114\tT\t24-01-2016\tIPR014362\tGlutamate dehydrogenase\tGO:0016639|GO:0055114\n+P00370\t9ec8e26fcf5c160f533bf9a69dec0212\t447\tSMART\tSM00839\tGlutamate/Leucine/Phenylalanine/Valine dehydrogenase\t204\t445\t2.0E-93\tT\t24-01-2016\tIPR006096\tGlutamate/phenylalanine/leucine/valine dehydrogenase, C-terminal\tGO:0006520|GO:0016491|GO:0055114\n+P00370\t9ec8e26fcf5c160f533bf9a69dec0212\t447\tGene3D\tG3DSA:3.40.50.720\t\t209\t372\t1.6E-63\tT\t24-01-2016\tIPR016040\tNAD(P)-binding domain\t\n+P00370\t9ec8e26fcf5c160f533bf9a69dec0212\t447\tSUPERFAMILY\tSSF51735\t\t202\t446\t4.96E-77\tT\t24-01-2016\tIPR016040\tNAD(P)-binding domain\t\n+P00370\t9ec8e26fcf5c160f533bf9a69dec0212\t447\tGene3D\tG3DSA:1.10.285.10\t\t7\t67\t8.2E-28\tT\t24-01-2016\n+P00370\t9ec8e26fcf5c160f533bf9a69dec0212\t447\tGene3D\tG3DSA:1.10.285.10\t\t373\t446\t2.0E-26\tT\t24-01-2016\n+P00370\t9ec8e26fcf5c160f533bf9a69dec0212\t447\tProSitePatterns\tPS00074\tGlu / Leu / Phe / Val dehydrogenases active site.\t122\t135\t-\tT\t24-01-2016\tIPR006095\tGlutamate/phenylalanine/leucine/valine dehydrogenase\tGO:0006520|GO:0016491|GO:0055114\n+P00370\t9ec8e26fcf5c160f533bf9a69dec0212\t447\tPfam\tPF02812\tGlu/Leu/Phe/Val dehydrogenase, dimerisation domain\t57\t184\t6.3E-49\tT\t24-01-2016\tIPR006097\tGlutamate/phenylalanine/leucine/valine dehydrogenase, dimerisation domain\tGO:0006520|GO:0016491|GO:0055114\n+P00370\t9ec8e26fcf5c160f533bf9a69dec0212\t447\tPANTHER\tPTHR11606\t\t1\t447\t3.2E-250\tT\t24-01-2016\n+P00370\t9ec8e26fcf5c160f533bf9a69dec0212\t447\tPANTHER\tPTHR11606:SF4\t\t1\t447\t3.2E-250\tT\t24-01-2016\n+C1P5Z7\tabfa044baa298f169ea62ac6b48e1185\t43\tPfam\tPF15894\tInhibitor of glucose uptake transporter SgrT\t2\t37\t1.0E-11\tT\t24-01-2016\tIPR031767\tInhibitor of glucose uptake transporter SgrT\tGO:0046325\n' |
| b |
| diff -r 000000000000 -r fe8e43a26870 interproscan5/data/__base__.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/interproscan5/data/__base__.xml Thu Jan 28 19:34:51 2016 -0500 |
| b |
| b'@@ -0,0 +1,2204 @@\n+<?xml version="1.0" encoding="UTF-8" standalone="yes"?>\n+<protein-matches xmlns="http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5">\n+ <protein>\n+ <sequence md5="0d2c0f1acdd08ab0157f2308531a58e4">MQTFQADLAIVGAGGAGLRAAIAAAQANPNAKIALISKVYPMRSHTVAAEGGSAAVAQDHDSFEYHFHDTVAGGDWLCEQDVVDYFVHHCPTEMTQLELWGCPWSRRPDGSVNVRRFGGMKIERTWFAADKTGFHMLHTLFQTSLQFPQIQRFDEHFVLDILVDDGHVRGLVAMNMMEGTLVQIRANAVVMATGGAGRVYRYNTNGGIVTGDGMGMALSHGVPLRDMEFVQYHPTGLPGSGILMTEGCRGEGGILVNKNGYRYLQDYGMGPETPLGEPKNKYMELGPRDKVSQAFWHEWRKGNTISTPRGDVVYLDLRHLGEKKLHERLPFICELAKAYVGVDPVKEPIPVRPTAHYTMGGIETDQNCETRIKGLFAVGECSSVGLHGANRLGSNSLAELVVFGRLAGEQATERAATAGNGNEAAIEAQAAGVEQRLKDLVNQDGGENWAKIRDEMGLAMEEGCGIYRTPELMQKTIDKLAELQERFKRVRITDTSSVFNTDLLYTIELGHGLNVAECMAHSAMARKESRGAHQRLDEGCTERDDVNFLKHTLAFRDADGTTRLEYSDVKITTLPPAKRVYGGEADAADKAEAANKKEKANG</sequence>\n+ <xref desc="FRDA_ECOLI Fumarate reductase flavoprotein subunit OS=Escherichia coli (strain K12) GN=frdA PE=1 SV=3"\n+ db="sp" id="P00363" name="Fumarate reductase flavoprotein subunit"/>\n+ <matches>\n+ <coils-match>\n+ <signature ac="Coil" name="Coil">\n+ <signature-library-release library="COILS" version="2.2.1"/>\n+ </signature>\n+ <locations>\n+ <coils-location start="423" end="443"/>\n+ </locations>\n+ </coils-match>\n+ <coils-match>\n+ <signature ac="Coil" name="Coil">\n+ <signature-library-release library="COILS" version="2.2.1"/>\n+ </signature>\n+ <locations>\n+ <coils-location start="473" end="493"/>\n+ </locations>\n+ </coils-match>\n+ <fingerprints-match evalue="2.5E-5" graphscan="I....I...">\n+ <signature ac="PR00411" desc="Pyridine nucleotide disulphide reductase class-I signature"\n+ name="PNDRDTASEI">\n+ <models>\n+ <model ac="PR00411" desc="Pyridine nucleotide disulphide reductase class-I signature"\n+ name="PNDRDTASEI"/>\n+ </models>\n+ <signature-library-release library="PRINTS" version="42.0"/>\n+ </signature>\n+ <locations>\n+ <fingerprints-location motifNumber="6" pvalue="0.0222" score="30.15" start="375" end="382"/>\n+ <fingerprints-location motifNumber="1" pvalue="4.15E-10" score="41.52" start="7" end="29"/>\n+ </locations>\n+ </fingerprints-match>\n+ <fingerprints-match evalue="3.0E-10" graphscan="I...I">\n+ <signature ac="PR00368" desc="FAD-dependent pyridine nucleotide reductase signature" name="FADPNR">\n+ <models>\n+ <model ac="PR00368" desc="FAD-dependent pyridine nucleotide reductase signature" name="FADPNR"/>\n+ </models>\n+ <signature-library-release library="PRINTS" version="42.0"/>\n+ </signature>\n+ <locations>\n+ <fingerprints-location motifNumber="1" pvalue="4.72E-9" score="47.18" start="8" end="27"/>\n+ <fingerprints-location motifNumber="5" pvalue="3.2E-8" score="30.52" start="360" end="382"/>\n+ </locations>\n+ </fingerprints-match>\n+ <hmmer3-match evalue="4.2E-250" score="829.0">\n+ <signature ac="TIGR01812"\n+ desc="sdhA_frdA_Gneg: succinate dehydrogenase or fumarate reductase, flavoprotein subunit"\n+ name="TIGR01812">\n+ <entry ac="IPR014006" desc="Succinate dehydrogenase/fumarate reductase, flavoprotein subunit"\n+ name="Succ_Dhase_FrdA_Gneg" type="FAMILY">\n+ <go-xref category="MOLECULAR_FUNCTION" db="GO" id="GO:0016627"\n+ '..b'>\n+ </signature>\n+ <locations>\n+ <superfamilyhmmer3-location start="4" end="173"/>\n+ </locations>\n+ </superfamilyhmmer3-match>\n+ <superfamilyhmmer3-match evalue="6.8E-132">\n+ <signature ac="SSF48179" name="6-phosphogluconate dehydrogenase C-terminal domain-like">\n+ <entry ac="IPR008927" desc="6-phosphogluconate dehydrogenase C-terminal domain-like"\n+ name="6-PGluconate_DH_C-like" type="DOMAIN">\n+ <go-xref category="BIOLOGICAL_PROCESS" db="GO" id="GO:0055114"\n+ name="oxidation-reduction process"/>\n+ </entry>\n+ <models>\n+ <model ac="0040234" name="6-phosphogluconate dehydrogenase C-terminal domain-like"/>\n+ <model ac="0036487" name="6-phosphogluconate dehydrogenase C-terminal domain-like"/>\n+ <model ac="0052836" name="6-phosphogluconate dehydrogenase C-terminal domain-like"/>\n+ <model ac="0035534" name="6-phosphogluconate dehydrogenase C-terminal domain-like"/>\n+ <model ac="0042865" name="6-phosphogluconate dehydrogenase C-terminal domain-like"/>\n+ <model ac="0048408" name="6-phosphogluconate dehydrogenase C-terminal domain-like"/>\n+ <model ac="0044957" name="6-phosphogluconate dehydrogenase C-terminal domain-like"/>\n+ <model ac="0049729" name="6-phosphogluconate dehydrogenase C-terminal domain-like"/>\n+ <model ac="0051872" name="6-phosphogluconate dehydrogenase C-terminal domain-like"/>\n+ <model ac="0054551" name="6-phosphogluconate dehydrogenase C-terminal domain-like"/>\n+ <model ac="0041099" name="6-phosphogluconate dehydrogenase C-terminal domain-like"/>\n+ <model ac="0052328" name="6-phosphogluconate dehydrogenase C-terminal domain-like"/>\n+ <model ac="0042306" name="6-phosphogluconate dehydrogenase C-terminal domain-like"/>\n+ <model ac="0048756" name="6-phosphogluconate dehydrogenase C-terminal domain-like"/>\n+ <model ac="0045524" name="6-phosphogluconate dehydrogenase C-terminal domain-like"/>\n+ <model ac="0054910" name="6-phosphogluconate dehydrogenase C-terminal domain-like"/>\n+ <model ac="0052564" name="6-phosphogluconate dehydrogenase C-terminal domain-like"/>\n+ <model ac="0040515" name="6-phosphogluconate dehydrogenase C-terminal domain-like"/>\n+ <model ac="0054098" name="6-phosphogluconate dehydrogenase C-terminal domain-like"/>\n+ <model ac="0053659" name="6-phosphogluconate dehydrogenase C-terminal domain-like"/>\n+ <model ac="0051796" name="6-phosphogluconate dehydrogenase C-terminal domain-like"/>\n+ <model ac="0050268" name="6-phosphogluconate dehydrogenase C-terminal domain-like"/>\n+ <model ac="0044958" name="6-phosphogluconate dehydrogenase C-terminal domain-like"/>\n+ <model ac="0037218" name="6-phosphogluconate dehydrogenase C-terminal domain-like"/>\n+ <model ac="0038855" name="6-phosphogluconate dehydrogenase C-terminal domain-like"/>\n+ <model ac="0037318" name="6-phosphogluconate dehydrogenase C-terminal domain-like"/>\n+ </models>\n+ <signature-library-release library="SUPERFAMILY" version="1.75"/>\n+ </signature>\n+ <locations>\n+ <superfamilyhmmer3-location start="177" end="467"/>\n+ </locations>\n+ </superfamilyhmmer3-match>\n+ </matches>\n+ </protein>\n+</protein-matches>\n' |
| b |
| diff -r 000000000000 -r fe8e43a26870 interproscan5/data/input.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/interproscan5/data/input.fasta Thu Jan 28 19:34:51 2016 -0500 |
| b |
| @@ -0,0 +1,32 @@ +>sp|C1P5Z7|SGRT_ECOLI Putative inhibitor of glucose uptake transporter SgrT OS=Escherichia coli (strain K12) GN=sgrT PE=1 SV=1 +MRQFYQHYFTATAKLCWLRWLSVPQRLTMLEGLMQWDDRNSES +>sp|P00350|6PGD_ECOLI 6-phosphogluconate dehydrogenase, decarboxylating OS=Escherichia coli (strain K12) GN=gnd PE=1 SV=2 +MSKQQIGVVGMAVMGRNLALNIESRGYTVSIFNRSREKTEEVIAENPGKKLVPYYTVKEF +VESLETPRRILLMVKAGAGTDAAIDSLKPYLDKGDIIIDGGNTFFQDTIRRNRELSAEGF +NFIGTGVSGGEEGALKGPSIMPGGQKEAYELVAPILTKIAAVAEDGEPCVTYIGADGAGH +YVKMVHNGIEYGDMQLIAEAYSLLKGGLNLTNEELAQTFTEWNNGELSSYLIDITKDIFT +KKDEDGNYLVDVILDEAANKGTGKWTSQSALDLGEPLSLITESVFARYISSLKDQRVAAS +KVLSGPQAQPAGDKAEFIEKVRRALYLGKIVSYAQGFSQLRAASEEYNWDLNYGEIAKIF +RAGCIIRAQFLQKITDAYAENPQIANLLLAPYFKQIADDYQQALRDVVAYAVQNGIPVPT +FSAAVAYYDSYRAAVLPANLIQAQRDYFGAHTYKRIDKEGVFHTEWLD +>sp|P00363|FRDA_ECOLI Fumarate reductase flavoprotein subunit OS=Escherichia coli (strain K12) GN=frdA PE=1 SV=3 +MQTFQADLAIVGAGGAGLRAAIAAAQANPNAKIALISKVYPMRSHTVAAEGGSAAVAQDH +DSFEYHFHDTVAGGDWLCEQDVVDYFVHHCPTEMTQLELWGCPWSRRPDGSVNVRRFGGM +KIERTWFAADKTGFHMLHTLFQTSLQFPQIQRFDEHFVLDILVDDGHVRGLVAMNMMEGT +LVQIRANAVVMATGGAGRVYRYNTNGGIVTGDGMGMALSHGVPLRDMEFVQYHPTGLPGS +GILMTEGCRGEGGILVNKNGYRYLQDYGMGPETPLGEPKNKYMELGPRDKVSQAFWHEWR +KGNTISTPRGDVVYLDLRHLGEKKLHERLPFICELAKAYVGVDPVKEPIPVRPTAHYTMG +GIETDQNCETRIKGLFAVGECSSVGLHGANRLGSNSLAELVVFGRLAGEQATERAATAGN +GNEAAIEAQAAGVEQRLKDLVNQDGGENWAKIRDEMGLAMEEGCGIYRTPELMQKTIDKL +AELQERFKRVRITDTSSVFNTDLLYTIELGHGLNVAECMAHSAMARKESRGAHQRLDEGC +TERDDVNFLKHTLAFRDADGTTRLEYSDVKITTLPPAKRVYGGEADAADKAEAANKKEKA +NG +>sp|P00370|DHE4_ECOLI NADP-specific glutamate dehydrogenase OS=Escherichia coli (strain K12) GN=gdhA PE=1 SV=1 +MDQTYSLESFLNHVQKRDPNQTEFAQAVREVMTTLWPFLEQNPKYRQMSLLERLVEPERV +IQFRVVWVDDRNQIQVNRAWRVQFSSAIGPYKGGMRFHPSVNLSILKFLGFEQTFKNALT +TLPMGGGKGGSDFDPKGKSEGEVMRFCQALMTELYRHLGADTDVPAGDIGVGGREVGFMA +GMMKKLSNNTACVFTGKGLSFGGSLIRPEATGYGLVYFTEAMLKRHGMGFEGMRVSVSGS +GNVAQYAIEKAMEFGARVITASDSSGTVVDESGFTKEKLARLIEIKASRDGRVADYAKEF +GLVYLEGQQPWSLPVDIALPCATQNELDVDAAHQLIANGVKAVAEGANMPTTIEATELFQ +QAGVLFAPGKAANAGGVATSGLEMAQNAARLGWKAEKVDARLHHIMLDIHHACVEHGGEG +EQTNYVQGANIAGFVKVADAMLAQGVI |
| b |
| diff -r 000000000000 -r fe8e43a26870 interproscan5/fake_ips.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/interproscan5/fake_ips.py Thu Jan 28 19:34:51 2016 -0500 |
| [ |
| @@ -0,0 +1,35 @@ +""" +""" + +__author__ = 'mkh' + +if __name__ == '__main__': + import argparse + import os + from shutil import copyfile + import sys + + parser = argparse.ArgumentParser(description='Fake IPS.') + + parser.add_argument('-dp', action='store_true') + parser.add_argument('--input') + parser.add_argument('--seqtype') + parser.add_argument('-f', dest='formats', default='tsv') + parser.add_argument('--applications') + parser.add_argument('--tempdir') + parser.add_argument('--pathways', action='store_true') + parser.add_argument('--goterms', action='store_true') + parser.add_argument('--iprlookup', action='store_true') + parser.add_argument('--mode') + parser.add_argument('--clusterrunid') + parser.add_argument('--output-file-base', dest='output_file_base') + parser.add_argument('-o', dest='output_file', default="/tmp/junk") + + args = parser.parse_args() + formats = args.formats.split(',') + src_data_dir = os.path.dirname(__file__) + '/data' + + for ext in formats: + if ext in ['html', 'svg']: + ext += '.tar.gz' + copyfile(src_data_dir + '/' + '__base__' + '.' + ext, args.output_file_base + '.' + ext) |
| b |
| diff -r 000000000000 -r fe8e43a26870 interproscan5/interproscan.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/interproscan5/interproscan.xml Thu Jan 28 19:34:51 2016 -0500 |
| [ |
| b'@@ -0,0 +1,285 @@\n+<tool id="interproscan" name="Interproscan functional predictions of ORFs" version="5.0.0a">\n+ <description>Interproscan functional predictions of ORFs</description>\n+ <requirements>\n+ <!--\n+ <requirement type="package">signalp</requirement>\n+ <requirement type="package">phobius</requirement>\n+ <requirement type="package">tmhmm</requirement>\n+ -->\n+ <requirement type="set_environment">INTERPROSCAN_SCRIPT_PATH</requirement>\n+ </requirements>\n+\n+ <command>\n+ #import os\n+ \\$IPS_HOME/interproscan.sh\n+ ## disables the precalculated lookup service, all calculation will be run locally\n+ -dp \n+ --input $infile \n+ --seqtype $seqtype \n+ -f $oformat \n+ --applications $appl \n+ --tempdir \\$TEMP\n+\n+ $pathways\n+ $goterms\n+ $iprlookup\n+ $mode\n+\n+ #if str($oformat) in [\'SVG\', \'HTML\']:\n+ --output-file-base $outfile\n+ 2>&1;\n+ mkdir -p $outfile.files_path;\n+ #set temp_archive_file = str($outfile) + \'.\' + str($oformat).lower() + \'.tar.gz\'\n+ tar -C $outfile.files_path -xvmzf $temp_archive_file;\n+ python \\$INTERPROSCAN_SCRIPT_PATH/create_index.py $outfile $outfile.files_path;\n+ rm $temp_archive_file\n+ #else:\n+ -o $outfile\n+ 2>&1\n+ #end if\n+ </command>\n+\n+ <inputs>\n+ <param name="infile" type="data" format="fasta" label="Protein Fasta File"/>\n+\n+ <param name="seqtype" type="select" label="Type of the input sequences" help="">\n+ <option value="p" selected="true">Protein</option>\n+ <option value="n">DNA / RNA</option>\n+ </param>\n+\n+ <param name="mode" type="boolean" label="Run on cluster?" help="Check to submit job to cluster."\n+ truevalue="--mode=cluster --clusterrunid=gtdi-ips-analysis"\n+ falsevalue=""/>\n+\n+ <param name="appl" type="select" multiple="True" display="checkboxes" label="Applications to run"\n+ help="Select your programm.">\n+ <option value="TIGRFAM"\n+ selected="true">TIGRFAM: protein families based on Hidden Markov Models or HMMs</option>\n+ <option value="PIRSF" selected="true">PIRSF: non-overlapping clustering of UniProtKB sequences into a hierarchical order (evolutionary relationships)</option>\n+ <option value="ProDom"\n+ selected="true">ProDom: set of protein domain families generated from the UniProtKB</option>\n+ <option value="Panther"\n+ selected="true">Panther: Protein ANalysis THrough Evolutionary Relationships</option>\n+ <option value="SMART" selected="true">SMART: identification and analysis of domain architectures based on Hidden Markov Models or HMMs</option>\n+ <option value="PrositeProfiles" selected="true">PROSITE Profiles: protein domains, families and functional sites as well as associated profiles to identify them</option>\n+ <option value="PrositePatterns" selected="true">PROSITE Pattern: protein domains, families and functional sites as well as associated patterns to identify them</option>\n+ <option value="HAMAP"\n+ selected="true">HAMAP: High-quality Automated Annotation of Microbial Proteomes</option>\n+ <option value="PfamA" selected="true">PfamA: protein families, each represented by multiple sequence alignments and hidden Markov models</option>\n+ <option value="PRINTS" selected="true">PRINTS: group of conserved motifs (fingerprints) used to characterise a protein family</option>\n+ <option value="SuperFamily"\n+ selected="true">SUPERFAMILY: database of structural and functional annotation</option>\n+ <option value="Coi'..b'of all the columns and attributes used on [http://www.sequenceontology.org/gff3.shtml].\n+\n+Example Output\n+--------------\n+\n+::\n+\n+ ##gff-version 3\n+ ##feature-ontology http://song.cvs.sourceforge.net/viewvc/song/ontology/sofa.obo?revision=1.269\n+ ##sequence-region AACH01000027 1 1347\n+ ##seqid|source|type|start|end|score|strand|phase|attributes\n+ AACH01000027 provided_by_user nucleic_acid 1 1347 . + . Name=AACH01000027;md5=b2a7416cb92565c004becb7510f46840;ID=AACH01000027\n+ AACH01000027 getorf ORF 1 1347 . + . Name=AACH01000027.2_21;Target=pep_AACH01000027_1_1347 1 449;md5=b2a7416cb92565c004becb7510f46840;ID=orf_AACH01000027_1_1347\n+ AACH01000027 getorf polypeptide 1 449 . + . md5=fd0743a673ac69fb6e5c67a48f264dd5;ID=pep_AACH01000027_1_1347\n+ AACH01000027 Pfam protein_match 84 314 1.2E-45 + . Name=PF00696;signature_desc=Amino acid kinase family;Target=null 84 314;status=T;ID=match$8_84_314;Ontology_term="GO:0008652";date=15-04-2013;Dbxref="InterPro:IPR001048","Reactome:REACT_13"\n+ ##sequence-region 2\n+ ...\n+ >pep_AACH01000027_1_1347\n+ LVLLAAFDCIDDTKLVKQIIISEIINSLPNIVNDKYGRKVLLYLLSPRDPAHTVREIIEV\n+ LQKGDGNAHSKKDTEIRRREMKYKRIVFKVGTSSLTNEDGSLSRSKVKDITQQLAMLHEA\n+ GHELILVSSGAIAAGFGALGFKKRPTKIADKQASAAVGQGLLLEEYTTNLLLRQIVSAQI\n+ LLTQDDFVDKRRYKNAHQALSVLLNRGAIPIINENDSVVIDELKVGDNDTLSAQVAAMVQ\n+ ADLLVFLTDVDGLYTGNPNSDPRAKRLERIETINREIIDMAGGAGSSNGTGGMLTKIKAA\n+ TIATESGVPVYICSSLKSDSMIEAAEETEDGSYFVAQEKGLRTQKQWLAFYAQSQGSIWV\n+ DKGAAEALSQYGKSLLLSGIVEAEGVFSYGDIVTVFDKESGKSLGKGRVQFGASALEDML\n+ RSQKAKGVLIYRDDWISITPEIQLLFTEF\n+ ...\n+ >match$8_84_314\n+ KRIVFKVGTSSLTNEDGSLSRSKVKDITQQLAMLHEAGHELILVSSGAIAAGFGALGFKK\n+ RPTKIADKQASAAVGQGLLLEEYTTNLLLRQIVSAQILLTQDDFVDKRRYKNAHQALSVL\n+ LNRGAIPIINENDSVVIDELKVGDNDTLSAQVAAMVQADLLVFLTDVDGLYTGNPNSDPR\n+ AKRLERIETINREIIDMAGGAGSSNGTGGMLTKIKAATIATESGVPVYICS\n+ \n+\n+Scalable Vector Graphics (SVG) and HyperText Markup Language (HTML)\n+====================================================================\n+\n+InterProScan_ 5 outputs a single HTML/SVG file for each protein sequence analysed. \n+\n+\n+Example Output\n+--------------\n+\n+.. image:: $PATH_TO_IMAGES/P51587.svg.png\n+\n+.. _InterProScan: http://www.ebi.ac.uk/interpro\n+\n+\n+----------\n+References\n+----------\n+\n+\n+If you use this Galaxy tool in work leading to a scientific publication please\n+cite the following papers:\n+\n+Peter J.A. Cock, Bj\xc3\xb6rn A. Gr\xc3\xbcning, Konrad Paszkiewicz and Leighton Pritchard (2013).\n+Galaxy tools and workflows for sequence analysis with applications\n+in molecular plant pathology. PeerJ 1:e167\n+http://dx.doi.org/10.7717/peerj.167\n+\n+Zdobnov EM, Apweiler R (2001)\n+InterProScan an integration platform for the signature-recognition methods in InterPro.\n+Bioinformatics 17, 847-848.\n+http://dx.doi.org/10.1093/bioinformatics/17.9.847\n+\n+Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, Lopez R (2005)\n+InterProScan: protein domains identifier.\n+Nucleic Acids Research 33 (Web Server issue), W116-W120.\n+http://dx.doi.org/10.1093/nar/gki442\n+\n+Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, Finn RD, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Laugraud A, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Mulder N, Natale D, Orengo C, Quinn AF, Selengut JD, Sigrist CJ, Thimma M, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C. (2009)\n+InterPro: the integrative protein signature database.\n+Nucleic Acids Research 37 (Database Issue), D224-228.\n+http://dx.doi.org/10.1093/nar/gkn785\n+\n+\n+This wrapper is available to install into other Galaxy Instances via the Galaxy Tool Shed at\n+http://toolshed.g2.bx.psu.edu/view/bgruening/interproscan5\n+\n+\n+**Galaxy Wrapper Author**::\n+\n+ * Bjoern Gruening, University of Freiburg\n+ * Konrad Paszkiewicz, University of Exeter\n+\n+ </help>\n+</tool>\n' |
| b |
| diff -r 000000000000 -r fe8e43a26870 interproscan5/ips5.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/interproscan5/ips5.xml Thu Jan 28 19:34:51 2016 -0500 |
| [ |
| b'@@ -0,0 +1,313 @@\n+<tool id="ips5" name="Interproscan functional predictions of ORFs" version="5.0.0mkh">\n+ <description>Interproscan functional predictions of ORFs.</description>\n+ <requirements>\n+ <!--\n+ <requirement type="package">signalp</requirement>\n+ <requirement type="package">phobius</requirement>\n+ <requirement type="package">tmhmm</requirement>\n+ -->\n+ <requirement type="set_environment">INTERPROSCAN_SCRIPT_PATH</requirement>\n+ </requirements>\n+\n+ <command>\n+ #import os\n+\n+ \\$IPS_HOME/interproscan.sh\n+ ## disables the precalculated lookup service, all calculation will be run locally\n+ -dp\n+ --input $infile\n+ --seqtype $seqtype\n+ -f $output_types\n+ --applications $appl\n+ --tempdir \\$TEMP\n+\n+ $pathways\n+ $goterms\n+ $iprlookup\n+ $mode\n+ --output-file-base __base__\n+ 2>&1;\n+\n+ #if \'tsv\' in str($output_types):\n+ mv __base__.tsv $tsv_file;\n+ #end if\n+\n+ #if \'gff3\' in str($output_types):\n+ mv __base__.gff3 $gff3_file;\n+ #end if\n+\n+ #if \'xml\' in str($output_types):\n+ mv __base__.xml $xml_file;\n+ #end if\n+\n+ #if \'html\' in str($output_types):\n+ mkdir -p $html_file.files_path;\n+ #set temp_archive_file = \'__base__.html.tar.gz\'\n+ tar -C $html_file.files_path -xvmzf $temp_archive_file;\n+ python \\$INTERPROSCAN_SCRIPT_PATH/interproscan5/create_index.py $html_file $html_file.files_path;\n+ rm $temp_archive_file;\n+ #end if\n+\n+ #if \'svg\' in str($output_types):\n+ mkdir -p $svg_file.files_path;\n+ #set temp_archive_file = \'__base__.svg.tar.gz\'\n+ tar -C $svg_file.files_path -xvmzf $temp_archive_file;\n+ python \\$INTERPROSCAN_SCRIPT_PATH/interproscan5/create_index.py $svg_file $svg_file.files_path;\n+ rm $temp_archive_file;\n+ #end if\n+\n+ echo "End of ipsfaux"\n+ </command>\n+\n+ <inputs>\n+ <param name="infile" type="data" format="fasta" label="Sequence Fasta File (ignored -- faux mode)"/>\n+\n+ <param name="seqtype" type="select" label="Type of the input sequences" help="">\n+ <option value="p" selected="true">Protein</option>\n+ <option value="n">DNA / RNA</option>\n+ </param>\n+\n+ <param name="mode" type="boolean" label="Run on cluster?" help="Check to submit job to cluster."\n+ truevalue="--mode=cluster --clusterrunid=gtdi-ips-analysis"\n+ falsevalue=""/>\n+\n+ <param name="appl" type="select" multiple="True" display="checkboxes" label="Applications to run"\n+ help="Select your programm.">\n+ <option value="TIGRFAM"\n+ selected="true">TIGRFAM: protein families based on Hidden Markov Models or HMMs</option>\n+ <option value="PIRSF" selected="true">PIRSF: non-overlapping clustering of UniProtKB sequences into a hierarchical order (evolutionary relationships)</option>\n+ <option value="ProDom"\n+ selected="true">ProDom: set of protein domain families generated from the UniProtKB</option>\n+ <option value="Panther"\n+ selected="true">Panther: Protein ANalysis THrough Evolutionary Relationships</option>\n+ <option value="SMART" selected="true">SMART: identification and analysis of domain architectures based on Hidden Markov Models or HMMs</option>\n+ <option value="PrositeProfiles" selected="true">PROSITE Profiles: protein domains, families and functional sites as well as associated profiles to identify them</option>\n+ <option value="PrositePatterns" selected="true">PROSITE Pattern: protein domains, families and functional sites as well as associated patterns to identify them</option>\n+ <opti'..b'on of all the columns and attributes used on [http://www.sequenceontology.org/gff3.shtml].\n+\n+Example Output\n+--------------\n+\n+::\n+\n+ ##gff-version 3\n+ ##feature-ontology http://song.cvs.sourceforge.net/viewvc/song/ontology/sofa.obo?revision=1.269\n+ ##sequence-region AACH01000027 1 1347\n+ ##seqid|source|type|start|end|score|strand|phase|attributes\n+ AACH01000027 provided_by_user nucleic_acid 1 1347 . + . Name=AACH01000027;md5=b2a7416cb92565c004becb7510f46840;ID=AACH01000027\n+ AACH01000027 getorf ORF 1 1347 . + . Name=AACH01000027.2_21;Target=pep_AACH01000027_1_1347 1 449;md5=b2a7416cb92565c004becb7510f46840;ID=orf_AACH01000027_1_1347\n+ AACH01000027 getorf polypeptide 1 449 . + . md5=fd0743a673ac69fb6e5c67a48f264dd5;ID=pep_AACH01000027_1_1347\n+ AACH01000027 Pfam protein_match 84 314 1.2E-45 + . Name=PF00696;signature_desc=Amino acid kinase family;Target=null 84 314;status=T;ID=match$8_84_314;Ontology_term="GO:0008652";date=15-04-2013;Dbxref="InterPro:IPR001048","Reactome:REACT_13"\n+ ##sequence-region 2\n+ ...\n+ >pep_AACH01000027_1_1347\n+ LVLLAAFDCIDDTKLVKQIIISEIINSLPNIVNDKYGRKVLLYLLSPRDPAHTVREIIEV\n+ LQKGDGNAHSKKDTEIRRREMKYKRIVFKVGTSSLTNEDGSLSRSKVKDITQQLAMLHEA\n+ GHELILVSSGAIAAGFGALGFKKRPTKIADKQASAAVGQGLLLEEYTTNLLLRQIVSAQI\n+ LLTQDDFVDKRRYKNAHQALSVLLNRGAIPIINENDSVVIDELKVGDNDTLSAQVAAMVQ\n+ ADLLVFLTDVDGLYTGNPNSDPRAKRLERIETINREIIDMAGGAGSSNGTGGMLTKIKAA\n+ TIATESGVPVYICSSLKSDSMIEAAEETEDGSYFVAQEKGLRTQKQWLAFYAQSQGSIWV\n+ DKGAAEALSQYGKSLLLSGIVEAEGVFSYGDIVTVFDKESGKSLGKGRVQFGASALEDML\n+ RSQKAKGVLIYRDDWISITPEIQLLFTEF\n+ ...\n+ >match$8_84_314\n+ KRIVFKVGTSSLTNEDGSLSRSKVKDITQQLAMLHEAGHELILVSSGAIAAGFGALGFKK\n+ RPTKIADKQASAAVGQGLLLEEYTTNLLLRQIVSAQILLTQDDFVDKRRYKNAHQALSVL\n+ LNRGAIPIINENDSVVIDELKVGDNDTLSAQVAAMVQADLLVFLTDVDGLYTGNPNSDPR\n+ AKRLERIETINREIIDMAGGAGSSNGTGGMLTKIKAATIATESGVPVYICS\n+\n+\n+Scalable Vector Graphics (SVG) and HyperText Markup Language (HTML)\n+====================================================================\n+\n+InterProScan_ 5 outputs a single HTML/SVG file for each protein sequence analysed.\n+\n+\n+Example Output\n+--------------\n+\n+.. image:: $PATH_TO_IMAGES/P51587.svg.png\n+\n+.. _InterProScan: http://www.ebi.ac.uk/interpro\n+\n+\n+----------\n+References\n+----------\n+\n+\n+If you use this Galaxy tool in work leading to a scientific publication please\n+cite the following papers:\n+\n+Peter J.A. Cock, Bj\xc3\xb6rn A. Gr\xc3\xbcning, Konrad Paszkiewicz and Leighton Pritchard (2013).\n+Galaxy tools and workflows for sequence analysis with applications\n+in molecular plant pathology. PeerJ 1:e167\n+http://dx.doi.org/10.7717/peerj.167\n+\n+Zdobnov EM, Apweiler R (2001)\n+InterProScan an integration platform for the signature-recognition methods in InterPro.\n+Bioinformatics 17, 847-848.\n+http://dx.doi.org/10.1093/bioinformatics/17.9.847\n+\n+Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, Lopez R (2005)\n+InterProScan: protein domains identifier.\n+Nucleic Acids Research 33 (Web Server issue), W116-W120.\n+http://dx.doi.org/10.1093/nar/gki442\n+\n+Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, Finn RD, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Laugraud A, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Mulder N, Natale D, Orengo C, Quinn AF, Selengut JD, Sigrist CJ, Thimma M, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C. (2009)\n+InterPro: the integrative protein signature database.\n+Nucleic Acids Research 37 (Database Issue), D224-228.\n+http://dx.doi.org/10.1093/nar/gkn785\n+\n+\n+This wrapper is available to install into other Galaxy Instances via the Galaxy Tool Shed at\n+http://toolshed.g2.bx.psu.edu/view/bgruening/interproscan5\n+\n+\n+**Galaxy Wrapper Author**::\n+\n+ * Bjoern Gruening, University of Freiburg\n+ * Konrad Paszkiewicz, University of Exeter\n+\n+ </help>\n+</tool>\n' |
| b |
| diff -r 000000000000 -r fe8e43a26870 interproscan5/ipsfaux.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/interproscan5/ipsfaux.xml Thu Jan 28 19:34:51 2016 -0500 |
| [ |
| b'@@ -0,0 +1,315 @@\n+<tool id="ipsfaux" name="Interproscan functional predictions of ORFs (faux)" version="1.0.0a">\n+ <description>Interproscan functional predictions of ORFs (faux). Input file and computation options are\n+ ignored (other than the types of outputs). The same precomputed results are produced every time.</description>\n+ <requirements>\n+ <!--\n+ <requirement type="package">signalp</requirement>\n+ <requirement type="package">phobius</requirement>\n+ <requirement type="package">tmhmm</requirement>\n+ -->\n+ <requirement type="set_environment">INTERPROSCAN_SCRIPT_PATH</requirement>\n+ </requirements>\n+\n+ <command>\n+ #import os\n+ echo "output_types=$output_types";\n+\n+ python \\$INTERPROSCAN_SCRIPT_PATH/interproscan5/fake_ips.py\n+ ## disables the precalculated lookup service, all calculation will be run locally\n+ -dp\n+ --input $infile\n+ --seqtype $seqtype\n+ -f $output_types\n+ --applications $appl\n+ --tempdir \\$TEMP\n+\n+ $pathways\n+ $goterms\n+ $iprlookup\n+ $mode\n+ --output-file-base __base__\n+ 2>&1;\n+\n+ #if \'tsv\' in str($output_types):\n+ mv __base__.tsv $tsv_file;\n+ #end if\n+\n+ #if \'gff3\' in str($output_types):\n+ mv __base__.gff3 $gff3_file;\n+ #end if\n+\n+ #if \'xml\' in str($output_types):\n+ mv __base__.xml $xml_file;\n+ #end if\n+\n+ #if \'html\' in str($output_types):\n+ mkdir -p $html_file.files_path;\n+ #set temp_archive_file = \'__base__.html.tar.gz\'\n+ tar -C $html_file.files_path -xvmzf $temp_archive_file;\n+ python \\$INTERPROSCAN_SCRIPT_PATH/interproscan5/create_index.py $html_file $html_file.files_path;\n+ rm $temp_archive_file;\n+ #end if\n+\n+ #if \'svg\' in str($output_types):\n+ mkdir -p $svg_file.files_path;\n+ #set temp_archive_file = \'__base__.svg.tar.gz\'\n+ tar -C $svg_file.files_path -xvmzf $temp_archive_file;\n+ python \\$INTERPROSCAN_SCRIPT_PATH/interproscan5/create_index.py $svg_file $svg_file.files_path;\n+ rm $temp_archive_file;\n+ #end if\n+\n+ echo "End of ipsfaux"\n+ </command>\n+\n+ <inputs>\n+ <param name="infile" type="data" format="fasta" label="Sequence Fasta File (ignored -- faux mode)"/>\n+\n+ <param name="seqtype" type="select" label="Type of the input sequences" help="">\n+ <option value="p" selected="true">Protein</option>\n+ <option value="n">DNA / RNA</option>\n+ </param>\n+\n+ <param name="mode" type="boolean" label="Run on cluster?" help="Check to submit job to cluster."\n+ truevalue="--mode=cluster --clusterrunid=gtdi-ips-analysis"\n+ falsevalue=""/>\n+\n+ <param name="appl" type="select" multiple="True" display="checkboxes" label="Applications to run"\n+ help="Select your programm.">\n+ <option value="TIGRFAM"\n+ selected="true">TIGRFAM: protein families based on Hidden Markov Models or HMMs</option>\n+ <option value="PIRSF" selected="true">PIRSF: non-overlapping clustering of UniProtKB sequences into a hierarchical order (evolutionary relationships)</option>\n+ <option value="ProDom"\n+ selected="true">ProDom: set of protein domain families generated from the UniProtKB</option>\n+ <option value="Panther"\n+ selected="true">Panther: Protein ANalysis THrough Evolutionary Relationships</option>\n+ <option value="SMART" selected="true">SMART: identification and analysis of domain architectures based on Hidden Markov Models or HMMs</option>\n+ <option value="PrositeProfiles" selected="true">PROSITE Profiles: protein domains, families and functional sites as well as associated pr'..b'on of all the columns and attributes used on [http://www.sequenceontology.org/gff3.shtml].\n+\n+Example Output\n+--------------\n+\n+::\n+\n+ ##gff-version 3\n+ ##feature-ontology http://song.cvs.sourceforge.net/viewvc/song/ontology/sofa.obo?revision=1.269\n+ ##sequence-region AACH01000027 1 1347\n+ ##seqid|source|type|start|end|score|strand|phase|attributes\n+ AACH01000027 provided_by_user nucleic_acid 1 1347 . + . Name=AACH01000027;md5=b2a7416cb92565c004becb7510f46840;ID=AACH01000027\n+ AACH01000027 getorf ORF 1 1347 . + . Name=AACH01000027.2_21;Target=pep_AACH01000027_1_1347 1 449;md5=b2a7416cb92565c004becb7510f46840;ID=orf_AACH01000027_1_1347\n+ AACH01000027 getorf polypeptide 1 449 . + . md5=fd0743a673ac69fb6e5c67a48f264dd5;ID=pep_AACH01000027_1_1347\n+ AACH01000027 Pfam protein_match 84 314 1.2E-45 + . Name=PF00696;signature_desc=Amino acid kinase family;Target=null 84 314;status=T;ID=match$8_84_314;Ontology_term="GO:0008652";date=15-04-2013;Dbxref="InterPro:IPR001048","Reactome:REACT_13"\n+ ##sequence-region 2\n+ ...\n+ >pep_AACH01000027_1_1347\n+ LVLLAAFDCIDDTKLVKQIIISEIINSLPNIVNDKYGRKVLLYLLSPRDPAHTVREIIEV\n+ LQKGDGNAHSKKDTEIRRREMKYKRIVFKVGTSSLTNEDGSLSRSKVKDITQQLAMLHEA\n+ GHELILVSSGAIAAGFGALGFKKRPTKIADKQASAAVGQGLLLEEYTTNLLLRQIVSAQI\n+ LLTQDDFVDKRRYKNAHQALSVLLNRGAIPIINENDSVVIDELKVGDNDTLSAQVAAMVQ\n+ ADLLVFLTDVDGLYTGNPNSDPRAKRLERIETINREIIDMAGGAGSSNGTGGMLTKIKAA\n+ TIATESGVPVYICSSLKSDSMIEAAEETEDGSYFVAQEKGLRTQKQWLAFYAQSQGSIWV\n+ DKGAAEALSQYGKSLLLSGIVEAEGVFSYGDIVTVFDKESGKSLGKGRVQFGASALEDML\n+ RSQKAKGVLIYRDDWISITPEIQLLFTEF\n+ ...\n+ >match$8_84_314\n+ KRIVFKVGTSSLTNEDGSLSRSKVKDITQQLAMLHEAGHELILVSSGAIAAGFGALGFKK\n+ RPTKIADKQASAAVGQGLLLEEYTTNLLLRQIVSAQILLTQDDFVDKRRYKNAHQALSVL\n+ LNRGAIPIINENDSVVIDELKVGDNDTLSAQVAAMVQADLLVFLTDVDGLYTGNPNSDPR\n+ AKRLERIETINREIIDMAGGAGSSNGTGGMLTKIKAATIATESGVPVYICS\n+\n+\n+Scalable Vector Graphics (SVG) and HyperText Markup Language (HTML)\n+====================================================================\n+\n+InterProScan_ 5 outputs a single HTML/SVG file for each protein sequence analysed.\n+\n+\n+Example Output\n+--------------\n+\n+.. image:: $PATH_TO_IMAGES/P51587.svg.png\n+\n+.. _InterProScan: http://www.ebi.ac.uk/interpro\n+\n+\n+----------\n+References\n+----------\n+\n+\n+If you use this Galaxy tool in work leading to a scientific publication please\n+cite the following papers:\n+\n+Peter J.A. Cock, Bj\xc3\xb6rn A. Gr\xc3\xbcning, Konrad Paszkiewicz and Leighton Pritchard (2013).\n+Galaxy tools and workflows for sequence analysis with applications\n+in molecular plant pathology. PeerJ 1:e167\n+http://dx.doi.org/10.7717/peerj.167\n+\n+Zdobnov EM, Apweiler R (2001)\n+InterProScan an integration platform for the signature-recognition methods in InterPro.\n+Bioinformatics 17, 847-848.\n+http://dx.doi.org/10.1093/bioinformatics/17.9.847\n+\n+Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, Lopez R (2005)\n+InterProScan: protein domains identifier.\n+Nucleic Acids Research 33 (Web Server issue), W116-W120.\n+http://dx.doi.org/10.1093/nar/gki442\n+\n+Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, Finn RD, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Laugraud A, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Mulder N, Natale D, Orengo C, Quinn AF, Selengut JD, Sigrist CJ, Thimma M, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C. (2009)\n+InterPro: the integrative protein signature database.\n+Nucleic Acids Research 37 (Database Issue), D224-228.\n+http://dx.doi.org/10.1093/nar/gkn785\n+\n+\n+This wrapper is available to install into other Galaxy Instances via the Galaxy Tool Shed at\n+http://toolshed.g2.bx.psu.edu/view/bgruening/interproscan5\n+\n+\n+**Galaxy Wrapper Author**::\n+\n+ * Bjoern Gruening, University of Freiburg\n+ * Konrad Paszkiewicz, University of Exeter\n+\n+ </help>\n+</tool>\n' |
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| diff -r 000000000000 -r fe8e43a26870 interproscan5/readme.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/interproscan5/readme.rst Thu Jan 28 19:34:51 2016 -0500 |
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| @@ -0,0 +1,83 @@ +================================================== +Galaxy wrapper for InterProScan 5 prediction tools +================================================== + +InterProScan is a tool that combines different protein signature recognition methods native to the InterPro +member databases into one resource with look up of corresponding InterPro and GO annotation. + +This wrapper is copyright 2013 by: + * Bjoern Gruening + * Konrad Paszkiewicz + + +This prepository contains a wrapper for the InterProScan_ command line tool. + +.. _InterProScan: http://www.ebi.ac.uk/interpro/interproscan.html + + +Quevillon E., Silventoinen V., Pillai S., Harte N., Mulder N., Apweiler R., Lopez R. (2005). InterProScan: protein domains identifier. Nucleic Acids Res. 33 (Web Server issue): W116-W120 + + +============ +Installation +============ + +Please download install InterProScan according to: + +https://code.google.com/p/interproscan/wiki/HowToDownload + + +======== +Citation +======== + +If you use this Galaxy tool in work leading to a scientific +publication, in addition to citing the invididual underlying tools, please cite: + +Peter Cock, Bjoern Gruening, Konrad Paszkiewicz and Leighton Pritchard (2013). +Galaxy tools and workflows for sequence analysis with applications +in molecular plant pathology. PeerJ 1:e167 +http://dx.doi.org/10.7717/peerj.167 + +Full reference information is included in the help text. + + +============= +Input formats +============= + +The standard interproscan input is either genomic or protein sequences. +In the case of genomic sequences Interproscan will run an ORF prediction tool. + + +======= +History +======= + +interproscan: + + - v5.0: Initial public release of version 5.0 + + +============= +Licence (MIT) +============= + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in +all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +THE SOFTWARE. + |
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| @@ -0,0 +1,7 @@ +<?xml version="1.0"?> +<tool_dependency> + <set_environment version="1.0"> + <environment_variable name="INTERPROSCAN_SCRIPT_PATH" + action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> + </set_environment> +</tool_dependency> |
