| Previous changeset 5:8fc50fe60127 (2021-11-27) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 0daaffac75df549583b6d834113608c2dbacb1d3 |
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modified:
macros.xml test-data/gff_to_prot-in1.gff3 test-data/gff_to_prot-out1.txt test-data/resampling-sites1.txt transit_gumbel.xml |
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| diff -r 8fc50fe60127 -r a6c8b6e47c51 macros.xml --- a/macros.xml Sat Nov 27 09:48:57 2021 +0000 +++ b/macros.xml Tue May 27 19:59:34 2025 +0000 |
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| @@ -17,8 +17,9 @@ <yield /> </requirements> </xml> - <token name="@TOOL_VERSION@">3.0.2</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@TOOL_VERSION@">3.2.3</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">22.05</token> <xml name="outputs"> <yield /> <data name="sites" from_work_dir="transit_out.txt" format="tabular" label="${tool.name} on ${on_string} Sites" /> @@ -81,8 +82,7 @@ </token> <token name="@STANDARD_OPTIONS@"> -iN $nterm - -tC $cterm + -iC $cterm -n $normalization - -r $handle_replicates </token> </macros> |
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| diff -r 8fc50fe60127 -r a6c8b6e47c51 test-data/gff_to_prot-in1.gff3 --- a/test-data/gff_to_prot-in1.gff3 Sat Nov 27 09:48:57 2021 +0000 +++ b/test-data/gff_to_prot-in1.gff3 Tue May 27 19:59:34 2025 +0000 |
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| b'@@ -1,500 +1,5 @@\n-##sequence-region NC_007795.1 1 2821361\n-##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=93061\n-NC_007795.1\tRefSeq\tregion\t1\t2821361\t.\t+\t.\tID=NC_007795.1:1..2821361;Dbxref=taxon:93061;Is_circular=true;Name=ANONYMOUS;gbkey=Src;genome=chromosome;mol_type=genomic DNA;strain=NCTC 8325;sub-species=aureus\n-NC_007795.1\tRefSeq\tgene\t517\t1878\t.\t+\t.\tID=gene-SAOUHSC_00001;Dbxref=GeneID:3919798;Name=dnaA;gbkey=Gene;gene=dnaA;gene_biotype=protein_coding;locus_tag=SAOUHSC_00001\n-NC_007795.1\tRefSeq\tCDS\t517\t1878\t.\t+\t0\tID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=Genbank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11\n-NC_007795.1\tRefSeq\tgene\t2156\t3289\t.\t+\t.\tID=gene-SAOUHSC_00002;Dbxref=GeneID:3919799;Name=SAOUHSC_00002;gbkey=Gene;gene_biotype=protein_coding;locus_tag=SAOUHSC_00002\n-NC_007795.1\tRefSeq\tCDS\t2156\t3289\t.\t+\t0\tID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=Genbank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11\n-NC_007795.1\tRefSeq\tgene\t3670\t3915\t.\t+\t.\tID=gene-SAOUHSC_00003;Dbxref=GeneID:3919176;Name=SAOUHSC_00003;gbkey=Gene;gene_biotype=protein_coding;locus_tag=SAOUHSC_00003\n-NC_007795.1\tRefSeq\tCDS\t3670\t3915\t.\t+\t0\tID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=Genbank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserved hypothetical protein;gbkey=CDS;product=hypothetical protein;protein_id=YP_498611.1;transl_table=11\n-NC_007795.1\tRefSeq\tgene\t3912\t5024\t.\t+\t.\tID=gene-SAOUHSC_00004;Dbxref=GeneID:3919177;Name=recF;gbkey=Gene;gene=recF;gene_biotype=protein_coding;locus_tag=SAOUHSC_00004\n-NC_007795.1\tRefSeq\tCDS\t3912\t5024\t.\t+\t0\tID=cds-YP_498612.1;Parent=gene-SAOUHSC_00004;Dbxref=Genbank:YP_498612.1,GeneID:3919177;Name=YP_498612.1;Note=Required for DNA replication%3B binds preferentially to single-stranded%2C linear DNA;gbkey=CDS;gene=recF;product=recombination protein F;protein_id=YP_498612.1;transl_table=11\n-NC_007795.1\tRefSeq\tgene\t5034\t6968\t.\t+\t.\tID=gene-SAOUHSC_00005;Dbxref=GeneID:3919178;Name=SAOUHSC_00005;gbkey=Gene;gene_biotype=protein_coding;locus_tag=SAOUHSC_00005\n-NC_007795.1\tRefSeq\tCDS\t5034\t6968\t.\t+\t0\tID=cds-YP_498613.1;Parent=gene-SAOUHSC_00005;Dbxref=Genbank:YP_498613.1,GeneID:3919178;Name=YP_498613.1;Note=DNA gyrase%2C B subunit;gbkey=CDS;product=DNA gyrase subunit B;protein_id=YP_498613.1;transl_table=11\n-NC_007795.1\tRefSeq\tgene\t7005\t9668\t.\t+\t.\tID=gene-SAOUHSC_00006;Dbxref=GeneID:3919179;Name=SAOUHSC_00006;gbkey=Gene;gene_biotype=protein_coding;locus_tag=SAOUHSC_00006\n-NC_007795.1\tRefSeq\tCDS\t7005\t9668\t.\t+\t0\tID=cds-YP_498614.1;Parent=gene-SAOUHSC_00006;Dbxref=Genbank:YP_498614.1,GeneID:3919179;Name=YP_498614.1;Note=DNA gyrase%2C A subunit;gbkey=CDS;product=DNA gyrase subunit A;protein_id=YP_498614.1;transl_table=11\n-NC_007795.1\tRefSeq\tgene\t9755\t10456\t.\t-\t.\tID=gene-SAOUHSC_00007;Dbxref=GeneID:3919180;Name=SAOUHSC_00007;gbkey=Gene;gene_biotype=protein_coding;locus_tag=SAOUHSC_00007\n-NC_007795.1\tRefSeq\tCDS\t9755\t10456\t.\t-\t0\tID=cds-YP_498615.1;Parent=gene-SAOUHSC_00007;Dbxref=Genbank:YP_498615.1,GeneID:3919180;Name=YP_498615.1;Note=conserved hypothetical protein;gbkey=CDS;product=hypothetical protein;protein_id=YP_498615.1;transl_table=11\n-NC_007795.1\tRefSeq\tgene\t10893\t12407\t.\t+\t.\tID=gene-SAOUHSC_00008;Dbxref=GeneID:3919181;Name=SAOUHSC_00008;gbkey=Gene;gene_biotype=protein_coding;locus_tag=SAOUHSC_00008\n-NC_007795.1\tRefSeq\tCDS\t10893\t12407\t.\t+\t0\tID=cds-YP_498616.1;Parent=gene-SAOUHSC_00008;Dbxref=Genbank:YP_498616.1,GeneID:3919181;Name=YP_498616.1;Note=catalyzes the degradation of histidine to urocanate and ammmonia;gbkey=CDS;pr'..b'_coding;locus_tag=SAOUHSC_00259\n-NC_007795.1\tRefSeq\tCDS\t279337\t279795\t.\t+\t0\tID=cds-YP_498853.1;Parent=gene-SAOUHSC_00259;Dbxref=Genbank:YP_498853.1,GeneID:3919201;Name=YP_498853.1;Note=conserved hypothetical protein;gbkey=CDS;product=hypothetical protein;protein_id=YP_498853.1;transl_table=11\n-NC_007795.1\tRefSeq\tgene\t279728\t280009\t.\t+\t.\tID=gene-SAOUHSC_00260;Dbxref=GeneID:3919202;Name=SAOUHSC_00260;gbkey=Gene;gene_biotype=protein_coding;locus_tag=SAOUHSC_00260\n-NC_007795.1\tRefSeq\tCDS\t279728\t280009\t.\t+\t0\tID=cds-YP_498854.1;Parent=gene-SAOUHSC_00260;Dbxref=Genbank:YP_498854.1,GeneID:3919202;Name=YP_498854.1;Note=conserved hypothetical protein;gbkey=CDS;product=hypothetical protein;protein_id=YP_498854.1;transl_table=11\n-NC_007795.1\tRefSeq\tgene\t280022\t281356\t.\t+\t.\tID=gene-SAOUHSC_00261;Dbxref=GeneID:3919203;Name=SAOUHSC_00261;gbkey=Gene;gene_biotype=protein_coding;locus_tag=SAOUHSC_00261\n-NC_007795.1\tRefSeq\tCDS\t280022\t281356\t.\t+\t0\tID=cds-YP_498855.1;Parent=gene-SAOUHSC_00261;Dbxref=Genbank:YP_498855.1,GeneID:3919203;Name=YP_498855.1;Note=conserved hypothetical protein;gbkey=CDS;product=hypothetical protein;protein_id=YP_498855.1;transl_table=11\n-NC_007795.1\tRefSeq\tgene\t281378\t285817\t.\t+\t.\tID=gene-SAOUHSC_00262;Dbxref=GeneID:3919204;Name=SAOUHSC_00262;gbkey=Gene;gene_biotype=protein_coding;locus_tag=SAOUHSC_00262\n-NC_007795.1\tRefSeq\tCDS\t281378\t285817\t.\t+\t0\tID=cds-YP_498856.1;Parent=gene-SAOUHSC_00262;Dbxref=Genbank:YP_498856.1,GeneID:3919204;Name=YP_498856.1;Note=conserved hypothetical protein;gbkey=CDS;product=hypothetical protein;protein_id=YP_498856.1;transl_table=11\n-NC_007795.1\tRefSeq\tgene\t285847\t286239\t.\t+\t.\tID=gene-SAOUHSC_00264;Dbxref=GeneID:3919205;Name=SAOUHSC_00264;gbkey=Gene;gene_biotype=protein_coding;locus_tag=SAOUHSC_00264\n-NC_007795.1\tRefSeq\tCDS\t285847\t286239\t.\t+\t0\tID=cds-YP_498857.1;Parent=gene-SAOUHSC_00264;Dbxref=Genbank:YP_498857.1,GeneID:3919205;Name=YP_498857.1;Note=conserved hypothetical protein;gbkey=CDS;product=hypothetical protein;protein_id=YP_498857.1;transl_table=11\n-NC_007795.1\tRefSeq\tgene\t286255\t286569\t.\t+\t.\tID=gene-SAOUHSC_00265;Dbxref=GeneID:3919206;Name=SAOUHSC_00265;gbkey=Gene;gene_biotype=protein_coding;locus_tag=SAOUHSC_00265\n-NC_007795.1\tRefSeq\tCDS\t286255\t286569\t.\t+\t0\tID=cds-YP_498858.1;Parent=gene-SAOUHSC_00265;Dbxref=Genbank:YP_498858.1,GeneID:3919206;Name=YP_498858.1;Note=conserved hypothetical protein;gbkey=CDS;product=hypothetical protein;protein_id=YP_498858.1;transl_table=11\n-NC_007795.1\tRefSeq\tgene\t286569\t287243\t.\t+\t.\tID=gene-SAOUHSC_00266;Dbxref=GeneID:3919207;Name=SAOUHSC_00266;gbkey=Gene;gene_biotype=protein_coding;locus_tag=SAOUHSC_00266\n-NC_007795.1\tRefSeq\tCDS\t286569\t287243\t.\t+\t0\tID=cds-YP_498859.1;Parent=gene-SAOUHSC_00266;Dbxref=Genbank:YP_498859.1,GeneID:3919207;Name=YP_498859.1;Note=conserved hypothetical protein;gbkey=CDS;product=hypothetical protein;protein_id=YP_498859.1;transl_table=11\n-NC_007795.1\tRefSeq\tgene\t287243\t287560\t.\t+\t.\tID=gene-SAOUHSC_00267;Dbxref=GeneID:3919208;Name=SAOUHSC_00267;gbkey=Gene;gene_biotype=protein_coding;locus_tag=SAOUHSC_00267\n-NC_007795.1\tRefSeq\tCDS\t287243\t287560\t.\t+\t0\tID=cds-YP_498860.1;Parent=gene-SAOUHSC_00267;Dbxref=Genbank:YP_498860.1,GeneID:3919208;Name=YP_498860.1;Note=conserved hypothetical protein;gbkey=CDS;product=hypothetical protein;protein_id=YP_498860.1;transl_table=11\n-NC_007795.1\tRefSeq\tgene\t287570\t289414\t.\t+\t.\tID=gene-SAOUHSC_00268;Dbxref=GeneID:3919209;Name=SAOUHSC_00268;gbkey=Gene;gene_biotype=protein_coding;locus_tag=SAOUHSC_00268\n+##gff-version 3\n+chr1\tRefSeq\tgene\t100\t900\t.\t+\t.\tID=gene1;Name=example_gene;gene=example;gene_biotype=protein_coding;locus_tag=EX0001\n+chr1\tRefSeq\tCDS\t100\t900\t.\t+\t0\tID=cds1;Parent=gene1;product=hypothetical protein;protein_id=XP_000001;transl_table=11;locus_tag=EX0001\n+chr1\tRefSeq\tgene\t1000\t1500\t.\t-\t.\tID=gene2;Name=example2;gene_biotype=protein_coding;locus_tag=EX0002\n+chr1\tRefSeq\tCDS\t1000\t1500\t.\t-\t0\tID=cds2;Parent=gene2;product=another protein;protein_id=XP_000002;transl_table=11;locus_tag=EX0002\n' |
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| diff -r 8fc50fe60127 -r a6c8b6e47c51 test-data/gff_to_prot-out1.txt --- a/test-data/gff_to_prot-out1.txt Sat Nov 27 09:48:57 2021 +0000 +++ b/test-data/gff_to_prot-out1.txt Tue May 27 19:59:34 2025 +0000 |
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| b'@@ -1,247 +1,2 @@\n-binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.\t517\t1878\t+\t453\t-\t-\tdnaA\tSAOUHSC_00001\t-\r\n-binds the polymerase to DNA and acts as a sliding clamp\t2156\t3289\t+\t377\t-\t-\tSAOUHSC_00002\tSAOUHSC_00002\t-\r\n-conserved hypothetical protein\t3670\t3915\t+\t81\t-\t-\tSAOUHSC_00003\tSAOUHSC_00003\t-\r\n-Required for DNA replication%3B binds preferentially to single-stranded%2C linear DNA\t3912\t5024\t+\t370\t-\t-\trecF\tSAOUHSC_00004\t-\r\n-DNA gyrase%2C B subunit\t5034\t6968\t+\t644\t-\t-\tSAOUHSC_00005\tSAOUHSC_00005\t-\r\n-DNA gyrase%2C A subunit\t7005\t9668\t+\t887\t-\t-\tSAOUHSC_00006\tSAOUHSC_00006\t-\r\n-conserved hypothetical protein\t9755\t10456\t-\t233\t-\t-\tSAOUHSC_00007\tSAOUHSC_00007\t-\r\n-catalyzes the degradation of histidine to urocanate and ammmonia\t10893\t12407\t+\t504\t-\t-\tSAOUHSC_00008\tSAOUHSC_00008\t-\r\n-catalyzes a two-step reaction%2C first charging a serine molecule by linking its carboxyl group to the alpha-phosphate of ATP%2C followed by transfer of the aminoacyl-adenylate to its tRNA\t12786\t14072\t+\t428\t-\t-\tSAOUHSC_00009\tSAOUHSC_00009\t-\r\n-conserved hypothetical protein\t14722\t15417\t+\t231\t-\t-\tSAOUHSC_00010\tSAOUHSC_00010\t-\r\n-conserved hypothetical protein\t15414\t15743\t+\t109\t-\t-\tSAOUHSC_00012\tSAOUHSC_00012\t-\r\n-conserved hypothetical protein\t16106\t17074\t+\t322\t-\t-\tSAOUHSC_00013\tSAOUHSC_00013\t-\r\n-conserved hypothetical protein\t17365\t18303\t+\t312\t-\t-\tSAOUHSC_00014\tSAOUHSC_00014\t-\r\n-conserved hypothetical protein\t18318\t20285\t+\t655\t-\t-\tSAOUHSC_00015\tSAOUHSC_00015\t-\r\n-in Escherichia coli this protein is wrapped around the base of the L1 stalk\t20282\t20734\t+\t150\t-\t-\trplI\tSAOUHSC_00017\t-\r\n-replicative DNA helicase\t20766\t22166\t+\t466\t-\t-\tSAOUHSC_00018\tSAOUHSC_00018\t-\r\n-catalyzes the formation of N6-(1%2C2%2C-dicarboxyethyl)-AMP from L-aspartate%2C inosine monophosphate and GTP in AMP biosynthesis\t22444\t23727\t+\t427\t-\t-\tSAOUHSC_00019\tSAOUHSC_00019\t-\r\n--\t24157\t24231\t+\t24\t-\t-\tSAOUHSC_T00018\tSAOUHSC_T00018\t-\r\n--\t24239\t24311\t+\t24\t-\t-\tSAOUHSC_T00011\tSAOUHSC_T00011\t-\r\n-two-component response regulator%2C putative\t24931\t25632\t+\t233\t-\t-\tSAOUHSC_00020\tSAOUHSC_00020\t-\r\n-sensory box histidine kinase VicK%2C putative\t25645\t27471\t+\t608\t-\t-\tSAOUHSC_00021\tSAOUHSC_00021\t-\r\n-conserved hypothetical protein\t27515\t28798\t+\t427\t-\t-\tSAOUHSC_00022\tSAOUHSC_00022\t-\r\n-conserved hypothetical protein\t28799\t29587\t+\t262\t-\t-\tSAOUHSC_00023\tSAOUHSC_00023\t-\r\n-conserved hypothetical protein\t29977\t30777\t+\t266\t-\t-\tSAOUHSC_00024\tSAOUHSC_00024\t-\r\n-conserved hypothetical protein\t31005\t33323\t+\t772\t-\t-\tSAOUHSC_00025\tSAOUHSC_00025\t-\r\n-conserved hypothetical protein\t33555\t34034\t-\t159\t-\t-\tSAOUHSC_00026\tSAOUHSC_00026\t-\r\n-SPOUT methyltransferase family protein%3B crystal structure shows homodimer%3B in Escherichia coli this protein methylates pseudouridine at position 1915 of the 23S ribosomal RNA\t33691\t34170\t+\t159\t-\t-\tSAOUHSC_00027\tSAOUHSC_00027\t-\r\n--\t34375\t34509\t-\t44\t-\t-\tSAOUHSC_00028\tSAOUHSC_00028\t-\r\n-conserved hypothetical protein\t34473\t34565\t+\t30\t-\t-\tSAOUHSC_00029\tSAOUHSC_00029\t-\r\n-conserved hypothetical protein\t34712\t36457\t+\t581\t-\t-\tSAOUHSC_00030\tSAOUHSC_00030\t-\r\n-conserved hypothetical protein\t36551\t37003\t-\t150\t-\t-\tSAOUHSC_00031\tSAOUHSC_00031\t-\r\n-conserved hypothetical protein\t37019\t37120\t-\t33\t-\t-\tSAOUHSC_00032\tSAOUHSC_00032\t-\r\n-conserved hypothetical protein\t37218\t37973\t-\t251\t-\t-\tSAOUHSC_00033\tSAOUHSC_00033\t-\r\n-conserved hypothetical protein\t37973\t38233\t-\t86\t-\t-\tSAOUHSC_00034\tSAOUHSC_00034\t-\r\n-conserved hypothetical protein\t38370\t39437\t+\t355\t-\t-\tSAOUHSC_00035\tSAOUHSC_00035\t-\r\n-conserved hypothetical protein\t39468\t40802\t+\t444\t-\t-\tSAOUHSC_00036\tSAOUHSC_00036\t-\r\n-conserved hypothetical protein\t40821\t42014\t+\t397\t-\t-\tSAOUHSC_00037\tSAOUHSC_00037\t-\r\n-conserved hypothetical protein\t42281\t42382\t-\t33\t-\t-\tSAOUHSC_00038\tSAOUHSC_00038\t-\r\n-conserved hypothetical protein\t42681\t43613\t-\t310\t-\t-\tSAOUHSC_00039\tSAOUHSC_00039\t-\r\n-conserved hypothetical protein\t43976\t44179\t+\t67\t-\t-\tSAOUHSC_00'..b' in isoprenoid and isopentenyl-PP biosynthesis%3B forms homodimers\t245250\t245966\t+\t238\t-\t-\tispD\tSAOUHSC_00225\t-\r\n-conserved hypothetical protein\t245959\t246984\t+\t341\t-\t-\tSAOUHSC_00226\tSAOUHSC_00226\t-\r\n-conserved hypothetical protein\t247006\t248694\t+\t562\t-\t-\tSAOUHSC_00227\tSAOUHSC_00227\t-\r\n-conserved hypothetical protein\t248727\t250451\t+\t574\t-\t-\tSAOUHSC_00228\tSAOUHSC_00228\t-\r\n-involved in peptidoglycan cross-linking\t250591\t251265\t+\t224\t-\t-\tSAOUHSC_00229\tSAOUHSC_00229\t-\r\n-two-component sensor histidine kinase%2C putative\t251527\t253266\t+\t579\t-\t-\tSAOUHSC_00230\tSAOUHSC_00230\t-\r\n-two-component response regulator%2C putative\t253269\t254009\t+\t246\t-\t-\tSAOUHSC_00231\tSAOUHSC_00231\t-\r\n-negatively regulates murein hydrolase activity\t254122\t254565\t+\t147\t-\t-\tSAOUHSC_00232\tSAOUHSC_00232\t-\r\n-in conjunction with LrgA this protein inhibits the expression or activity of extracellular murein hydrolases\t254558\t255259\t+\t233\t-\t-\tSAOUHSC_00233\tSAOUHSC_00233\t-\r\n-conserved hypothetical protein\t255367\t256071\t-\t234\t-\t-\tSAOUHSC_00234\tSAOUHSC_00234\t-\r\n-conserved hypothetical protein\t256220\t257011\t+\t263\t-\t-\tSAOUHSC_00235\tSAOUHSC_00235\t-\r\n-6-phospho-beta-glucosidase%2C putative\t257027\t258463\t+\t478\t-\t-\tSAOUHSC_00236\tSAOUHSC_00236\t-\r\n-conserved hypothetical protein\t258896\t259657\t-\t253\t-\t-\tSAOUHSC_00237\tSAOUHSC_00237\t-\r\n--\t259676\t259810\t+\t44\t-\t-\tSAOUHSC_00238\tSAOUHSC_00238\t-\r\n-ribokinase%2C putative\t259908\t260822\t-\t304\t-\t-\tSAOUHSC_00239\tSAOUHSC_00239\t-\r\n-cytoplasmic mutarotase that catalyzes the conversion between beta-pyran and beta-furan forms of D-ribose%3B RbsD is required for efficient ribose utilization in E. coli%3B rbsD-mutant E. coli strains are unable to use ribose as a sole carbon source\t260850\t261254\t-\t134\t-\t-\tSAOUHSC_00240\tSAOUHSC_00240\t-\r\n-conserved hypothetical protein\t261269\t262150\t-\t293\t-\t-\tSAOUHSC_00241\tSAOUHSC_00241\t-\r\n-conserved hypothetical protein\t262382\t263380\t-\t332\t-\t-\tSAOUHSC_00242\tSAOUHSC_00242\t-\r\n-NADH dehydrogenase subunit%2C putative\t263531\t263710\t+\t59\t-\t-\tSAOUHSC_00243\tSAOUHSC_00243\t-\r\n-conserved hypothetical protein\t263760\t264152\t+\t130\t-\t-\tSAOUHSC_00244\tSAOUHSC_00244\t-\r\n-drug transporter%2C putative\t264825\t266201\t-\t458\t-\t-\tSAOUHSC_00246\tSAOUHSC_00246\t-\r\n-conserved hypothetical protein\t266435\t267427\t+\t330\t-\t-\tSAOUHSC_00247\tSAOUHSC_00247\t-\r\n-peptidoglycan hydrolase%2C putative\t267753\t268703\t+\t316\t-\t-\tSAOUHSC_00248\tSAOUHSC_00248\t-\r\n-conserved hypothetical protein\t268755\t269414\t-\t219\t-\t-\tSAOUHSC_00249\tSAOUHSC_00249\t-\r\n-conserved hypothetical protein\t269428\t270348\t-\t306\t-\t-\tSAOUHSC_00250\tSAOUHSC_00250\t-\r\n-conserved hypothetical protein\t270345\t271511\t-\t388\t-\t-\tSAOUHSC_00251\tSAOUHSC_00251\t-\r\n-conserved hypothetical protein\t271579\t273102\t-\t507\t-\t-\tSAOUHSC_00253\tSAOUHSC_00253\t-\r\n-conserved hypothetical protein\t273373\t274026\t+\t217\t-\t-\tSAOUHSC_00254\tSAOUHSC_00254\t-\r\n-conserved hypothetical protein\t274060\t274647\t+\t195\t-\t-\tSAOUHSC_00255\tSAOUHSC_00255\t-\r\n-conserved hypothetical protein\t274790\t275683\t-\t297\t-\t-\tSAOUHSC_00256\tSAOUHSC_00256\t-\r\n-conserved hypothetical protein\t275931\t276224\t+\t97\t-\t-\tSAOUHSC_00257\tSAOUHSC_00257\t-\r\n-conserved hypothetical protein\t276308\t279337\t+\t1009\t-\t-\tSAOUHSC_00258\tSAOUHSC_00258\t-\r\n-conserved hypothetical protein\t279337\t279795\t+\t152\t-\t-\tSAOUHSC_00259\tSAOUHSC_00259\t-\r\n-conserved hypothetical protein\t279728\t280009\t+\t93\t-\t-\tSAOUHSC_00260\tSAOUHSC_00260\t-\r\n-conserved hypothetical protein\t280022\t281356\t+\t444\t-\t-\tSAOUHSC_00261\tSAOUHSC_00261\t-\r\n-conserved hypothetical protein\t281378\t285817\t+\t1479\t-\t-\tSAOUHSC_00262\tSAOUHSC_00262\t-\r\n-conserved hypothetical protein\t285847\t286239\t+\t130\t-\t-\tSAOUHSC_00264\tSAOUHSC_00264\t-\r\n-conserved hypothetical protein\t286255\t286569\t+\t104\t-\t-\tSAOUHSC_00265\tSAOUHSC_00265\t-\r\n-conserved hypothetical protein\t286569\t287243\t+\t224\t-\t-\tSAOUHSC_00266\tSAOUHSC_00266\t-\r\n-conserved hypothetical protein\t287243\t287560\t+\t105\t-\t-\tSAOUHSC_00267\tSAOUHSC_00267\t-\r\n--\t287570\t289414\t+\t614\t-\t-\tSAOUHSC_00268\tSAOUHSC_00268\t-\r\n+hypothetical protein\t100\t900\t+\t267\t-\t-\t-\tEX0001\t-\r\n+another protein\t1000\t1500\t-\t167\t-\t-\t-\tEX0002\t-\r\n' |
| b |
| diff -r 8fc50fe60127 -r a6c8b6e47c51 test-data/resampling-sites1.txt --- a/test-data/resampling-sites1.txt Sat Nov 27 09:48:57 2021 +0000 +++ b/test-data/resampling-sites1.txt Tue May 27 19:59:34 2025 +0000 |
| b |
| b"@@ -1,110 +1,111 @@\n #Resampling\n-#Console: python /Users/delphinel/miniconda3/envs/transit_test/bin/transit resampling transit-in1-rep2_smol.wig,transit-in1-rep1_smol.wig transit-co1-rep3_smol.wig,transit-co1-rep2_smol.wig,transit-co1-rep1_smol.wig transit-in1_smol.prot resampling-sites1_smol.txt\n-#Control Data: b'transit-in1-rep2_smol.wig,transit-in1-rep1_smol.wig'\n-#Experimental Data: b'transit-co1-rep3_smol.wig,transit-co1-rep2_smol.wig,transit-co1-rep1_smol.wig'\n-#Annotation path: b'transit-in1_smol.prot' \n-#Time: 64.01395511627197\n+#Console: python3 /usr/local/bin/transit resampling control_file_0.wig,control_file_1.wig,control_file_2.wig input_file_0.wig,input_file_1.wig annotation.dat transit_out.txt -iN 0.0 -iC 0.0 -n TTR -s 1000\n+#Parameters: samples=1000, norm=TTR, histograms=False, adaptive=False, excludeZeros=False, pseudocounts=1.0, LOESS=False, trim_Nterm=0.0, trim_Cterm=0.0\n+#Control Data: b'control_file_0.wig,control_file_1.wig,control_file_2.wig'\n+#Experimental Data: b'input_file_0.wig,input_file_1.wig'\n+#Annotation path: b'annotation.dat' \n+#Time: 9.306800127029419\n #Orf\tName\tDesc\tSites\tMean Ctrl\tMean Exp\tlog2FC\tSum Ctrl\tSum Exp\tDelta Mean\tp-value\tAdj. p-value\n Rv0001\tdnaA\tchromosomal replication initiation protein \t31\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n Rv0002\tdnaN\tDNA polymerase III subunit beta \t31\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n-Rv0003\trecF\trecombination protein F \t35\t22.6\t27.7\t0.30\t1579.1\t2907.67\t5.1\t0.66630\t1.00000\n-Rv0004\t-\thypothetical protein Rv0004 \t7\t2.9\t0.0\t-1.97\t40.8\t0.00\t-2.9\t0.40810\t1.00000\n-Rv0005\tgyrB\tDNA gyrase subunit B \t42\t11.3\t3.6\t-1.66\t951.9\t450.90\t-7.8\t0.40760\t1.00000\n-Rv0006\tgyrA\tDNA gyrase subunit A \t45\t5.7\t2.4\t-1.22\t511.8\t330.34\t-3.2\t0.50960\t1.00000\n-Rv0007\t-\tPOSSIBLE CONSERVED MEMBRANE PROTEIN \t10\t16.2\t53.7\t1.73\t323.1\t1610.25\t37.5\t0.47710\t1.00000\n-Rv0008c\t-\tPOSSIBLE MEMBRANE PROTEIN \t4\t235.5\t195.4\t-0.27\t1884.3\t2345.17\t-40.1\t0.74730\t1.00000\n-Rv0009\tppiA\tPROBABLE IRON-REGULATED PEPTIDYL-PROLYL CIS-TRANS ISOMERASE A PPIA (PPIase A) (ROTAMASE A) \t7\t175.3\t89.0\t-0.98\t2453.5\t1869.11\t-86.2\t0.24570\t1.00000\n-Rv0010c\t-\tPROBABLE CONSERVED MEMBRANE PROTEIN \t10\t179.3\t172.9\t-0.05\t3586.6\t5186.87\t-6.4\t0.94490\t1.00000\n+Rv0003\trecF\trecombination protein F \t35\t27.7\t22.6\t-0.28\t2907.7\t1579.07\t-5.1\t0.66000\t1.00000\n+Rv0004\t-\thypothetical protein Rv0004 \t7\t0.0\t2.9\t1.97\t0.0\t40.75\t2.9\t0.40100\t1.00000\n+Rv0005\tgyrB\tDNA gyrase subunit B \t42\t3.6\t11.3\t1.43\t450.9\t951.88\t7.8\t0.40100\t1.00000\n+Rv0006\tgyrA\tDNA gyrase subunit A \t45\t2.4\t5.7\t0.96\t330.3\t511.83\t3.2\t0.51200\t1.00000\n+Rv0007\t-\tPOSSIBLE CONSERVED MEMBRANE PROTEIN \t10\t53.7\t16.2\t-1.67\t1610.3\t323.06\t-37.5\t0.49200\t1.00000\n+Rv0008c\t-\tPOSSIBLE MEMBRANE PROTEIN \t4\t195.4\t235.5\t0.27\t2345.2\t1884.31\t40.1\t0.73800\t1.00000\n+Rv0009\tppiA\tPROBABLE IRON-REGULATED PEPTIDYL-PROLYL CIS-TRANS ISOMERASE A PPIA (PPIase A) (ROTAMASE A) \t7\t89.0\t175.3\t0.97\t1869.1\t2453.52\t86.2\t0.26100\t1.00000\n+Rv0010c\t-\tPROBABLE CONSERVED MEMBRANE PROTEIN \t10\t172.9\t179.3\t0.05\t5186.9\t3586.59\t6.4\t0.94600\t1.00000\n Rv0011c\t-\tputative septation inhibitor protein \t3\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n-Rv0012\t-\tPROBABLE CONSERVED MEMBRANE PROTEIN \t16\t247.6\t104.1\t-1.25\t7922.3\t4996.36\t-143.5\t0.02820\t1.00000\n-Rv0013\ttrpG\tpara-aminobenzoate synthase component II \t15\t0.7\t2.9\t2.03\t21.1\t129.04\t2.2\t0.90500\t1.00000\n+Rv0012\t-\tPROBABLE CONSERVED MEMBRANE PROTEIN \t16\t104.1\t247.6\t1.24\t4996.4\t7922.27\t143.5\t0.02800\t1.00000\n+Rv0013\ttrpG\tpara-aminobenzoate synthase component II \t15\t2.9\t0.7\t-1.18\t129.0\t21.13\t-2.2\t0.90400\t1.00000\n Rv0014c\tpknB\tTRANSMEMBRANE SERINE/THREONINE-PROTEIN KINASE B PKNB (PROTEIN KINASE B) (STPK B) \t24\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n-Rv0015c\tpknA\tTRANSMEMBRANE SERINE/THREONINE-PROTEIN KINASE A PKNA (PROTEIN KINASE A) (STPK A) \t16\t23.6\t12.4\t-0.92\t753.9\t596.59\t-11.1\t0.70820\t1.00000\n-Rv0016c\tpbpA\tPROBABLE PENICILLIN-BINDING PROTEIN PBPA \t37\t19.4\t12.9\t-0.58\t1436.0\t1436.86\t-6.5\t0.43400\t1.00000\n-Rv0017c\trodA\tPROBABLE CELL DIVISION PROTEIN RODA \t27\t50.3\t50.0\t-0.01\t2718.6\t4051"..b"TRANSCRIPTIONAL REGULATORY PROTEIN (POSSIBLY TETR-FAMILY) \t12\t48.4\t38.2\t-0.33\t1743.2\t917.12\t-10.2\t0.76100\t1.00000\n+Rv0068\t-\tshort chain dehydrogenase \t12\t277.6\t153.3\t-0.85\t9993.8\t3679.26\t-124.3\t0.43500\t1.00000\n+Rv0069c\tsdaA\tPROBABLE L-SERINE DEHYDRATASE SDAA (L-SERINE DEAMINASE) (SDH) (L-SD) \t12\t17205.5\t291.7\t-5.88\t619398.5\t7001.04\t-16913.8\t0.33400\t1.00000\n+Rv0070c\tglyA2\tPROBABLE SERINE HYDROXYMETHYLTRANSFERASE GLYA2 (SERINE METHYLASE 2) (SHMT 2) \t18\t130.7\t127.1\t-0.04\t7060.3\t4575.85\t-3.6\t0.94400\t1.00000\n+Rv0071\t-\tPOSSIBLE MATURASE \t8\t620.1\t489.0\t-0.34\t14883.4\t7824.71\t-131.1\t0.71900\t1.00000\n+Rv0072\t-\tPROBABLE GLUTAMINE-TRANSPORT TRANSMEMBRANE PROTEIN ABC TRANSPORTER \t16\t305.2\t266.0\t-0.20\t14648.0\t8510.71\t-39.2\t0.81300\t1.00000\n+Rv0073\t-\tPROBABLE GLUTAMINE-TRANSPORT ATP-BINDING PROTEIN ABC TRANSPORTER \t15\t283.3\t353.9\t0.32\t12750.6\t10617.86\t70.6\t0.48100\t1.00000\n+Rv0074\t-\thypothetical protein Rv0074 \t19\t100.2\t84.6\t-0.24\t5708.7\t3213.34\t-15.6\t0.65600\t1.00000\n+Rv0075\t-\tPROBABLE AMINOTRANSFERASE \t24\t269.9\t217.5\t-0.31\t19432.6\t10440.98\t-52.4\t0.42600\t1.00000\n+Rv0076c\t-\tPROBABLE MEMBRANE PROTEIN \t3\t289.0\t176.8\t-0.71\t2601.1\t1060.79\t-112.2\t0.65600\t1.00000\n+Rv0077c\t-\tPROBABLE OXIDOREDUCTASE \t14\t152.0\t185.8\t0.29\t6383.4\t5203.69\t33.9\t0.57100\t1.00000\n+Rv0078\t-\tPROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN \t8\t11.3\t19.7\t0.75\t271.6\t315.41\t8.4\t0.60800\t1.00000\n+Rv0078A\t-\thypothetical protein Rv0078A \t10\t117.9\t183.9\t0.64\t3537.6\t3677.34\t65.9\t0.30100\t1.00000\n+Rv0079\t-\thypothetical protein Rv0079 \t14\t408.8\t376.2\t-0.12\t17171.1\t10534.25\t-32.6\t0.85000\t1.00000\n+Rv0080\t-\thypothetical protein Rv0080 \t4\t600.3\t454.5\t-0.40\t7203.0\t3635.90\t-145.8\t0.77500\t1.00000\n+Rv0081\t-\tPROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN \t5\t346.7\t374.7\t0.11\t5200.2\t3747.15\t28.0\t0.83500\t1.00000\n+Rv0082\t-\tPROBABLE OXIDOREDUCTASE \t7\t159.4\t180.7\t0.18\t3347.3\t2530.16\t21.3\t0.81300\t1.00000\n+Rv0083\t-\tPROBABLE OXIDOREDUCTASE \t23\t144.4\t202.6\t0.49\t9966.2\t9320.28\t58.2\t0.20900\t1.00000\n+Rv0084\thycD\tPOSSIBLE FORMATE HYDROGENLYASE HYCD (FHL) \t9\t107.6\t183.6\t0.76\t2905.8\t3303.99\t75.9\t0.23000\t1.00000\n+Rv0085\thycP\tPOSSIBLE HYDROGENASE HYCP \t4\t73.2\t73.7\t0.01\t877.9\t589.71\t0.6\t0.99700\t1.00000\n+Rv0086\thycQ\tPOSSIBLE HYDROGENASE HYCQ \t15\t46.9\t33.6\t-0.47\t2112.5\t1007.69\t-13.4\t0.55000\t1.00000\n+Rv0087\thycE\tPOSSIBLE FORMATE HYDROGENASE HYCE (FHL) \t25\t25.0\t35.9\t0.51\t1871.8\t1796.31\t11.0\t0.65100\t1.00000\n+Rv0088\t-\thypothetical protein Rv0088 \t14\t54.7\t33.9\t-0.67\t2297.3\t949.04\t-20.8\t0.49500\t1.00000\n+Rv0089\t-\tPOSSIBLE METHYLTRANSFERASE/METHYLASE \t10\t134.6\t111.8\t-0.27\t4037.9\t2235.26\t-22.8\t0.74000\t1.00000\n+Rv0090\t-\tPOSSIBLE MEMBRANE PROTEIN \t12\t129.1\t141.2\t0.13\t4648.1\t3389.28\t12.1\t0.83800\t1.00000\n+Rv0091\tmtn\tPROBABLE BIFUNCTIONAL MTA/SAH NUCLEOSIDASE MTN: 5'-METHYLTHIOADENOSINE NUCLEOSIDASE (METHYLTHIOADENOSINE METHYLTHIORIBOHYDROLASE) + S-ADENOSYLHOMOCYSTEINE NUCLEOSIDASE (S-ADENOSYL-L-HOMOCYSTEINE HOMOCYSTEINYLRIBOHYDROLASE) \t11\t269.6\t372.5\t0.46\t8897.3\t8195.54\t102.9\t0.46400\t1.00000\n+Rv0092\tctpA\tPROBABLE CATION TRANSPORTER P-TYPE ATPASE A CTPA \t30\t97.1\t171.9\t0.82\t8736.7\t10315.46\t74.9\t0.02700\t1.00000\n+Rv0093c\t-\tPROBABLE CONSERVED MEMBRANE PROTEIN \t8\t76.1\t78.5\t0.05\t1825.5\t1256.71\t2.5\t0.96100\t1.00000\n+Rv0094c\t-\thypothetical protein Rv0094c \t14\t129.1\t120.7\t-0.10\t5422.5\t3379.17\t-8.4\t0.77900\t1.00000\n+Rv0095c\t-\thypothetical protein Rv0095c \t9\t78.1\t80.6\t0.05\t2107.9\t1450.54\t2.5\t0.97200\t1.00000\n+Rv0096\tPPE1\tPPE FAMILY PROTEIN \t34\t203.8\t185.2\t-0.14\t20782.9\t12590.44\t-18.6\t0.77400\t1.00000\n+Rv0097\t-\tPOSSIBLE OXIDOREDUCTASE \t26\t96.4\t162.2\t0.74\t7517.5\t8433.61\t65.8\t0.20600\t1.00000\n+Rv0098\t-\thypothetical protein Rv0098 \t11\t80.2\t40.3\t-0.98\t2646.9\t886.41\t-39.9\t0.31400\t1.00000\n+Rv0099\tfadD10\tacyl-CoA synthetase \t26\t44.7\t33.2\t-0.42\t3488.1\t1727.10\t-11.5\t0.58000\t1.00000\n Rv0100\t-\thypothetical protein Rv0100 \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n Rv0101\tnrp\tPROBABLE PEPTIDE SYNTHETASE NRP (PEPTIDE SYNTHASE) \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n Rv0102\t-\tPROBABLE CONSERVED INTEGRAL MEMBRANE PROTEIN \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n" |
| b |
| diff -r 8fc50fe60127 -r a6c8b6e47c51 transit_gumbel.xml --- a/transit_gumbel.xml Sat Nov 27 09:48:57 2021 +0000 +++ b/transit_gumbel.xml Tue May 27 19:59:34 2025 +0000 |
| b |
| @@ -10,7 +10,8 @@ @LINK_INPUTS@ transit gumbel $input_files annotation.dat transit_out.txt @STANDARD_OPTIONS@ - -s $samples -b $burnin -m $smallest -t $trim + -r $handle_replicates + -s $samples -b $burnin -m $smallest -t $trim ]]> </command> <inputs> @@ -123,8 +124,8 @@ See `TRANSIT documentation` -- TRANSIT: https://transit.readthedocs.io/en/latest/index.html -- `TRANSIT Gumbel`: https://transit.readthedocs.io/en/latest/transit_methods.html#gumbel +- TRANSIT: https://transit.readthedocs.io/en/v@TOOL_VERSION@/index.html +- `TRANSIT Gumbel`: https://transit.readthedocs.io/en/v@TOOL_VERSION@/transit_methods.html#gumbel ]]></help> <expand macro="citations" /> |