-d, --destination <ClcServerObjectUrl> |
Destination file or folder on server. If not specified the folder of the first input object will be used. |
--externalblastnparameters-db <String> |
Database (default: Test/gpipe/9606/allcontig_and_rna) |
--externalblastnparameters-entrez-query |
|
<[All_organisms, Viruses, Archaea, |
Limit by entrez query (default: All organisms) |
Bacteria, |
|
Fungi, Metazoa, Arthropoda, |
Eukaryota, Viridiplantae, |
Vertebrata, |
|
Primates, Aeropyrum_pernix, |
Mammalia, Rodentia, |
|
|
Arabidopsis_thaliana, |
|
Bacillus_subtilis, |
|
Caenorhabditis_elegans, |
Bos_taurus, |
Canis_familiaris, |
|
Dictyostelium_discoideum, |
Danio_rerio, |
|
|
Escherichia_coli, Gallus_gallus, |
|
|
|
Human_immunodeficiency_virus_type_1, |
|
|
|
Mus_musculus, Oryctolagus_cuniculus, |
|
Oryza_sativa, |
|
Plasmodium_falciparum, |
Ovis_aries, |
|
|
Saccharomyces_cerevisiae, |
|
|
|
Xenopus_tropicalis, |
|
|
|
Sus_scrofa, Synechocystis_PCC6803, |
|
Takifugu_rubripes, |
|
Zea_mays]> |
Xenopus_laevis, |
--externalblastnparameters-evalue |
|
Double: > 0.0 |
Expectation value (E) threshold for saving hits (default: 10.0) |
--externalblastnparameters-lcase- |
|
masking <Boolean> |
Mask lower case (default: false) |
--externalblastnparameters-lcomplex- |
|
mask <Boolean> |
Filter low complexity (default: true) |
--externalblastnparameters-mask-for- |
|
lookup <Boolean> |
Mask for lookup (default: false) |
--externalblastnparameters-mask-human- |
|
repeats <Boolean> |
Mask human repeats (default: false) |
--externalblastnparameters-match- |
|
mismatch-gapcosts < |
Match/Mismatch and GapCosts (default: Match_1_Mismatch_3_Existence_5_Extension_2) |
|
|
Match_1_Mismatch_4_Existence_1_Extension_2, |
|
|
|
Match_1_Mismatch_4_Existence_2_Extension_1, |
|
|
|
Match_1_Mismatch_3_Existence_5_Extension_2, |
|
|
|
Match_1_Mismatch_3_Existence_1_Extension_2, |
|
|
|
Match_1_Mismatch_3_Existence_2_Extension_1, |
|
|
|
Match_1_Mismatch_2_Existence_5_Extension_2, |
|
|
|
Match_1_Mismatch_2_Existence_1_Extension_2, |
|
|
|
Match_1_Mismatch_2_Existence_3_Extension_1, |
|
|
|
Match_1_Mismatch_2_Existence_1_Extension_1, |
|
|
|
Match_2_Mismatch_3_Existence_2_Extension_4, |
|
|
|
Match_2_Mismatch_3_Existence_3_Extension_3, |
|
|
|
Match_2_Mismatch_3_Existence_5_Extension_2, |
|
|
|
Match_2_Mismatch_3_Existence_2_Extension_2, |
|
|
|
Match_1_Mismatch_1_Existence_3_Extension_2, |
|
|
|
Match_1_Mismatch_1_Existence_1_Extension_2, |
|
|
|
Match_1_Mismatch_1_Existence_4_Extension_1, |
|
|
|
Match_1_Mismatch_1_Existence_2_Extension_1, |
|
|
|
Match_4_Mismatch_5_Existence_6_Extension_5, |
|
|
|
Match_4_Mismatch_5_Existence_4_Extension_5, |
|
|
|
> |
|
--externalblastnparameters-max-num-hits |
|
Integer: >= 1 |
Maximum number of hits (default: 100) |
--externalblastnparameters-word-size |
|
Integer: >= 2 |
Word size (default: 11) |
--externalblastpparameters-db <String> |
Database (default: nr) |
--externalblastpparameters-entrez-query |
|
<[All_organisms, Viruses, Archaea, |
Limit by entrez query (default: All organisms) |
Bacteria, |
|
Fungi, Metazoa, Arthropoda, |
Eukaryota, Viridiplantae, |
Vertebrata, |
|
Primates, Aeropyrum_pernix, |
Mammalia, Rodentia, |
|
|
Arabidopsis_thaliana, |
|
Bacillus_subtilis, |
|
Caenorhabditis_elegans, |
Bos_taurus, |
Canis_familiaris, |
|
Dictyostelium_discoideum, |
Danio_rerio, |
|
|
Escherichia_coli, Gallus_gallus, |
|
|
|
Human_immunodeficiency_virus_type_1, |
|
|
|
Mus_musculus, Oryctolagus_cuniculus, |
|
Oryza_sativa, |
|
Plasmodium_falciparum, |
Ovis_aries, |
|
|
Saccharomyces_cerevisiae, |
|
|
|
Xenopus_tropicalis, |
|
|
|
Sus_scrofa, Synechocystis_PCC6803, |
|
Takifugu_rubripes, |
|
Zea_mays]> |
Xenopus_laevis, |
--externalblastpparameters-evalue |
|
Double: > 0.0 |
Expectation value (E) threshold for saving hits (default: 10.0) |
--externalblastpparameters-lcase- |
|
masking <Boolean> |
Mask lower case (default: false) |
--externalblastpparameters-lcomplex- |
|
mask <Boolean> |
Filter low complexity (default: true) |
--externalblastpparameters-mask-for- |
|
lookup <Boolean> |
Mask for lookup (default: false) |
--externalblastpparameters-mask-human- |
|
repeats <Boolean> |
Mask human repeats (default: false) |
--externalblastpparameters-matrix- |
|
gapcosts < |
Protein Matrix And Gap Costs (default: BLOSUM62_Existence_11_Extension_1) |
|
|
PAM30_Existence_6_Extension_2, |
|
|
|
PAM30_Existence_10_Extension_1, |
|
|
|
PAM30_Existence_8_Extension_1, |
|
|
|
PAM70_Existence_7_Extension_2, |
|
|
|
PAM70_Existence_11_Extension_1, |
|
|
|
PAM70_Existence_9_Extension_1, |
|
|
|
BLOSUM80_Existence_7_Extension_2, |
|
|
|
BLOSUM80_Existence_11_Extension_1, |
|
|
|
BLOSUM80_Existence_9_Extension_1, |
|
|
|
BLOSUM62_Existence_8_Extension_2, |
|
|
|
BLOSUM62_Existence_12_Extension_1, |
|
|
|
BLOSUM62_Existence_10_Extension_1, |
|
|
|
BLOSUM45_Existence_12_Extension_3, |
|
|
|
BLOSUM45_Existence_10_Extension_3, |
|
|
|
BLOSUM45_Existence_14_Extension_2, |
|
|
|
BLOSUM45_Existence_12_Extension_2, |
|
|
|
BLOSUM45_Existence_18_Extension_1, |
|
|
|
BLOSUM45_Existence_16_Extension_1]> |
|
--externalblastpparameters-max-num-hits |
|
Integer: >= 1 |
Maximum number of hits (default: 100) |
--externalblastpparameters-word-size |
|
Integer: >= 2 |
Word size (default: 3) |
--externalblastxparameters-db <String> |
Database (default: nr) |
--externalblastxparameters-entrez-query |
|
<[All_organisms, Viruses, Archaea, |
Limit by entrez query (default: All organisms) |
Bacteria, |
|
Fungi, Metazoa, Arthropoda, |
Eukaryota, Viridiplantae, |
Vertebrata, |
|
Primates, Aeropyrum_pernix, |
Mammalia, Rodentia, |
|
|
Arabidopsis_thaliana, |
|
Bacillus_subtilis, |
|
Caenorhabditis_elegans, |
Bos_taurus, |
Canis_familiaris, |
|
Dictyostelium_discoideum, |
Danio_rerio, |
|
|
Escherichia_coli, Gallus_gallus, |
|
|
|
Human_immunodeficiency_virus_type_1, |
|
|
|
Mus_musculus, Oryctolagus_cuniculus, |
|
Oryza_sativa, |
|
Plasmodium_falciparum, |
Ovis_aries, |
|
|
Saccharomyces_cerevisiae, |
|
|
|
Xenopus_tropicalis, |
|
|
|
Sus_scrofa, Synechocystis_PCC6803, |
|
Takifugu_rubripes, |
|
Zea_mays]> |
Xenopus_laevis, |
--externalblastxparameters-evalue |
|
Double: > 0.0 |
Expectation value (E) threshold for saving hits (default: 10.0) |
--externalblastxparameters-lcase- |
|
masking <Boolean> |
Mask lower case (default: false) |
--externalblastxparameters-lcomplex- |
|
mask <Boolean> |
Filter low complexity (default: true) |
--externalblastxparameters-mask-for- |
|
lookup <Boolean> |
Mask for lookup (default: false) |
--externalblastxparameters-mask-human- |
|
repeats <Boolean> |
Mask human repeats (default: false) |
--externalblastxparameters-matrix- |
|
gapcosts < |
Protein Matrix And Gap Costs (default: BLOSUM62_Existence_11_Extension_1) |
|
|
PAM30_Existence_6_Extension_2, |
|
|
|
PAM30_Existence_10_Extension_1, |
|
|
|
PAM30_Existence_8_Extension_1, |
|
|
|
PAM70_Existence_7_Extension_2, |
|
|
|
PAM70_Existence_11_Extension_1, |
|
|
|
PAM70_Existence_9_Extension_1, |
|
|
|
BLOSUM80_Existence_7_Extension_2, |
|
|
|
BLOSUM80_Existence_11_Extension_1, |
|
|
|
BLOSUM80_Existence_9_Extension_1, |
|
|
|
BLOSUM62_Existence_8_Extension_2, |
|
|
|
BLOSUM62_Existence_12_Extension_1, |
|
|
|
BLOSUM62_Existence_10_Extension_1, |
|
|
|
BLOSUM45_Existence_12_Extension_3, |
|
|
|
BLOSUM45_Existence_10_Extension_3, |
|
|
|
BLOSUM45_Existence_14_Extension_2, |
|
|
|
BLOSUM45_Existence_12_Extension_2, |
|
|
|
BLOSUM45_Existence_18_Extension_1, |
|
|
|
BLOSUM45_Existence_16_Extension_1]> |
|
--externalblastxparameters-max-num-hits |
|
Integer: >= 1 |
Maximum number of hits (default: 100) |
--externalblastxparameters-query- |
|
gencode |
Query genetic code (default: 1) |
Integer: > |
= 1 |
--externalblastxparameters-word-size |
|
Integer: >= 2 |
Word size (default: 3) |
--externaltblastnparameters-db <String> |
Database (default: Test/gpipe/9606/allcontig_and_rna) |
--externaltblastnparameters-db-gencode |
|
Integer: 1 <= x <= 23 |
Genetic code to use to translate database/subjects (default: 1) |
--externaltblastnparameters-entrez- |
|
query <[All_organisms, Viruses, |
Limit by entrez query (default: All organisms) |
Archaea, |
|
Viridiplantae, Fungi, Metazoa, |
Bacteria, Eukaryota, |
Arthropoda, |
|
Rodentia, Primates, Aeropyrum_pernix, |
Vertebrata, Mammalia, |
|
|
Arabidopsis_thaliana, |
|
Bacillus_subtilis, |
|
Caenorhabditis_elegans, |
Bos_taurus, |
Canis_familiaris, |
|
Dictyostelium_discoideum, |
Danio_rerio, |
|
|
Escherichia_coli, Gallus_gallus, |
|
|
|
Human_immunodeficiency_virus_type_1, |
|
|
|
Mus_musculus, Oryctolagus_cuniculus, |
|
Oryza_sativa, |
|
Plasmodium_falciparum, |
Ovis_aries, |
|
|
Saccharomyces_cerevisiae, |
|
|
|
Xenopus_tropicalis, |
|
|
|
Sus_scrofa, Synechocystis_PCC6803, |
|
Takifugu_rubripes, |
|
Zea_mays]> |
Xenopus_laevis, |
--externaltblastnparameters-evalue |
|
Double: > 0.0 |
Expectation value (E) threshold for saving hits (default: 10.0) |
--externaltblastnparameters-lcase- |
|
masking <Boolean> |
Mask lower case (default: false) |
--externaltblastnparameters-lcomplex- |
|
mask <Boolean> |
Filter low complexity (default: true) |
--externaltblastnparameters-mask-for- |
|
lookup <Boolean> |
Mask for lookup (default: false) |
--externaltblastnparameters-mask-human- |
|
repeats <Boolean> |
Mask human repeats (default: false) |
--externaltblastnparameters-matrix- |
|
gapcosts < |
Protein Matrix And Gap Costs (default: BLOSUM62_Existence_11_Extension_1) |
|
|
PAM30_Existence_6_Extension_2, |
|
|
|
PAM30_Existence_10_Extension_1, |
|
|
|
PAM30_Existence_8_Extension_1, |
|
|
|
PAM70_Existence_7_Extension_2, |
|
|
|
PAM70_Existence_11_Extension_1, |
|
|
|
PAM70_Existence_9_Extension_1, |
|
|
|
BLOSUM80_Existence_7_Extension_2, |
|
|
|
BLOSUM80_Existence_11_Extension_1, |
|
|
|
BLOSUM80_Existence_9_Extension_1, |
|
|
|
BLOSUM62_Existence_8_Extension_2, |
|
|
|
BLOSUM62_Existence_12_Extension_1, |
|
|
|
BLOSUM62_Existence_10_Extension_1, |
|
|
|
BLOSUM45_Existence_12_Extension_3, |
|
|
|
BLOSUM45_Existence_10_Extension_3, |
|
|
|
BLOSUM45_Existence_14_Extension_2, |
|
|
|
BLOSUM45_Existence_12_Extension_2, |
|
|
|
BLOSUM45_Existence_18_Extension_1, |
|
|
|
BLOSUM45_Existence_16_Extension_1]> |
|
--externaltblastnparameters-max-num- |
|
hits |
Maximum number of hits (default: 100) |
Integer: > |
= 1 |
--externaltblastnparameters-word-size |
|
Integer: >= 2 |
Word size (default: 3) |
--externaltblastxparameters-db <String> |
Database (default: Test/gpipe/9606/allcontig_and_rna) |
--externaltblastxparameters-db-gencode |
|
Integer: 1 <= x <= 23 |
Genetic code to use to translate database/subjects (default: 1) |
--externaltblastxparameters-entrez- |
|
query <[All_organisms, Viruses, |
Limit by entrez query (default: All organisms) |
Archaea, |
|
Viridiplantae, Fungi, Metazoa, |
Bacteria, Eukaryota, |
Arthropoda, |
|
Rodentia, Primates, Aeropyrum_pernix, |
Vertebrata, Mammalia, |
|
|
Arabidopsis_thaliana, |
|
Bacillus_subtilis, |
|
Caenorhabditis_elegans, |
Bos_taurus, |
Canis_familiaris, |
|
Dictyostelium_discoideum, |
Danio_rerio, |
|
|
Escherichia_coli, Gallus_gallus, |
|
|
|
Human_immunodeficiency_virus_type_1, |
|
|
|
Mus_musculus, Oryctolagus_cuniculus, |
|
Oryza_sativa, |
|
Plasmodium_falciparum, |
Ovis_aries, |
|
|
Saccharomyces_cerevisiae, |
|
|
|
Xenopus_tropicalis, |
|
|
|
Sus_scrofa, Synechocystis_PCC6803, |
|
Takifugu_rubripes, |
|
Zea_mays]> |
Xenopus_laevis, |
--externaltblastxparameters-evalue |
|
Double: > 0.0 |
Expectation value (E) threshold for saving hits (default: 10.0) |
--externaltblastxparameters-lcase- |
|
masking <Boolean> |
Mask lower case (default: false) |
--externaltblastxparameters-lcomplex- |
|
mask <Boolean> |
Filter low complexity (default: true) |
--externaltblastxparameters-mask-for- |
|
lookup <Boolean> |
Mask for lookup (default: false) |
--externaltblastxparameters-mask-human- |
|
repeats <Boolean> |
Mask human repeats (default: false) |
--externaltblastxparameters-max-num- |
|
hits |
Maximum number of hits (default: 100) |
Integer: > |
= 1 |
--externaltblastxparameters-query- |
|
gencode |
Query genetic code (default: 1) |
Integer: > |
= 1 |
--externaltblastxparameters-word-size |
|
Integer: >= 2 |
Word size (default: 3) |
-i, --input <ClcObjectUrl> |
Input data on server |
--log <Boolean> |
Enable creation of algo log file. (default: true) |
--matrix |
|
<[PAM30_Existence_7_Extension_2, |
|
PAM30_Existence_6_Extension_2, |
|
PAM30_Existence_5_Extension_2, |
|
PAM30_Existence_10_Extension_1, |
Matrix (default: BLOSUM62) |
|
|
PAM30_Existence_8_Extension_1, |
|
|
|
PAM70_Existence_7_Extension_2, |
|
|
|
PAM70_Existence_11_Extension_1, |
|
|
|
PAM70_Existence_9_Extension_1, |
|
|
|
BLOSUM80_Existence_7_Extension_2, |
|
|
|
BLOSUM80_Existence_11_Extension_1, |
|
|
|
BLOSUM80_Existence_9_Extension_1, |
|
|
|
BLOSUM62_Existence_8_Extension_2, |
|
|
|
BLOSUM62_Existence_12_Extension_1, |
|
|
|
BLOSUM62_Existence_10_Extension_1, |
|
|
|
BLOSUM45_Existence_12_Extension_3, |
|
|
|
BLOSUM45_Existence_10_Extension_3, |
|
|
|
BLOSUM45_Existence_14_Extension_2, |
|
|
|
BLOSUM45_Existence_12_Extension_2, |
|
|
|
BLOSUM45_Existence_18_Extension_1, |
|
|
|
BLOSUM45_Existence_16_Extension_1]> |
|
--program |
|
<[blastp, blastn, blastx,tblastn, tblastx]> |
Program (default: blastp) |