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changeset 28:ed97258d0be4 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 85fc040346ec226df20082eede2665cdfe6e3091
author bgruening
date Sat, 10 Feb 2018 05:52:26 -0500
parents ab3eff2028f8
children 1bd412e72a7e
files antismash.xml test-data/ARBH01000003.1.cluster001 test-data/index.2.html test-data/index.html
diffstat 4 files changed, 132 insertions(+), 132 deletions(-) [+]
line wrap: on
line diff
--- a/antismash.xml	Wed Feb 07 06:21:45 2018 -0500
+++ b/antismash.xml	Sat Feb 10 05:52:26 2018 -0500
@@ -1,8 +1,8 @@
 <?xml version='1.0' encoding='utf-8'?>
-<tool id="antismash" name="Antismash" version="4.0.2" profile="17.01">
+<tool id="antismash" name="Antismash" version="4.1" profile="17.01">
     <description>allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters</description>
     <requirements>
-        <requirement type="package" version="4.0.2">antismash</requirement>
+        <requirement type="package" version="4.1">antismash</requirement>
     </requirements>
     <version_command>antismash --version</version_command>
     <command detect_errors="aggressive">
--- a/test-data/ARBH01000003.1.cluster001	Wed Feb 07 06:21:45 2018 -0500
+++ b/test-data/ARBH01000003.1.cluster001	Sat Feb 10 05:52:26 2018 -0500
@@ -10,12 +10,15 @@
             Amycolatopsis.
 FEATURES             Location/Qualifiers
      source          1..3500
-                     /organism="Amycolatopsis balhimycina FH 1894"
-                     /mol_type="genomic DNA"
-                     /strain="DSM 44591"
                      /culture_collection="DSM:44591"
                      /db_xref="taxon:1089545"
+                     /mol_type="genomic DNA"
+                     /organism="Amycolatopsis balhimycina FH 1894"
+                     /strain="DSM 44591"
      cluster         1..3500
+                     /contig_edge="True"
+                     /cutoff=20000
+                     /extension=20000
                      /note="Cluster number: 1"
                      /note="Detection rule(s) for this cluster type: t1pks:
                      ((PKS_KS & PKS_AT) or (ene_KS & PKS_AT) or (mod_KS &
@@ -23,16 +26,31 @@
                      (tra_KS & PKS_AT));"
                      /note="Monomers prediction: (mal)"
                      /note="Structure image: structures/genecluster1.png"
-                     /cutoff=20000
-                     /extension=20000
                      /product="t1pks"
-                     /contig_edge="True"
      CDS             3..3500
                      /aSProdPred="mal"
+                     /locus_tag="ctg1_1"
                      /note="smCOG:
                      SMCOG1001:short-chain_dehydrogenase/reductase_SDR (Score:
                      64.2; E-value: 2.2e-19);"
-                     /locus_tag="ctg1_1"
+                     /sec_met="Type: t1pks"
+                     /sec_met="Domains detected: PP-binding (E-value: 1.3e-15,
+                     bitscore: 44.0, seeds: 164); PKS_AT (E-value: 8.7e-82,
+                     bitscore: 260.9, seeds: 1682); mod_KS (E-value: 9.4e-224,
+                     bitscore: 729.0, seeds: 217); adh_short (E-value: 7.1e-52,
+                     bitscore: 162.1, seeds: 230)"
+                     /sec_met="Kind: biosynthetic"
+                     /sec_met="NRPS/PKS subtype: Type I Modular PKS"
+                     /sec_met="NRPS/PKS Domain: PKS_KR (60-237). E-value:
+                     1.4e-53. Score: 173.1; Predicted KR activity: active;
+                     Predicted KR stereochemistry: A2;"
+                     /sec_met="NRPS/PKS Domain: ACP (341-412). E-value: 7.8e-31.
+                     Score: 97.8;"
+                     /sec_met="NRPS/PKS Domain: PKS_KS (434-858). E-value:
+                     3e-179. Score: 587.9;"
+                     /sec_met="NRPS/PKS Domain: PKS_AT (958-1166). E-value:
+                     4e-80. Score: 260.9; Substrate specificity predictions: mal
+                     (PKS signature), mal (Minowa), mal (consensus);"
                      /translation="GGVLALPAELDRRGGDRLAAVLSGATGEDQLAIRAAGVFGRRVVR
                      APAGDRAPARTWTPRGTTLITGGTGTLAPHLARWLAEQGAEHIVLTSRTGAEAPKARQL
                      LAELGETVEAVACDVTDKAALAALLARLRAEGRTVRNVVHTAAVIELHTLAETDLAAFS
@@ -54,81 +72,64 @@
                      IAAAHVAGVLSLADACALVAARGALMQALPSGGAMVSVRGSEADVAGHLGEDVAVAAVN
                      GPESVVLAGTEDAVLQAAGRLEAAGHKVRRLRVSHAFHSPLMDPVLAEFATVAQGLTYH
                      "
-                     /sec_met="Type: t1pks"
-                     /sec_met="Domains detected: PP-binding (E-value: 1.3e-15,
-                     bitscore: 44.0, seeds: 164); PKS_AT (E-value: 8.7e-82,
-                     bitscore: 260.9, seeds: 1682); mod_KS (E-value: 9.4e-224,
-                     bitscore: 729.0, seeds: 217); adh_short (E-value: 7.1e-52,
-                     bitscore: 162.1, seeds: 230)"
-                     /sec_met="Kind: biosynthetic"
-                     /sec_met="NRPS/PKS subtype: Type I Modular PKS"
-                     /sec_met="NRPS/PKS Domain: PKS_KR (60-237). E-value:
-                     1.4e-53. Score: 173.1; Predicted KR activity: active;
-                     Predicted KR stereochemistry: A2;"
-                     /sec_met="NRPS/PKS Domain: ACP (341-412). E-value: 7.8e-31.
-                     Score: 97.8;"
-                     /sec_met="NRPS/PKS Domain: PKS_KS (434-858). E-value:
-                     3e-179. Score: 587.9;"
-                     /sec_met="NRPS/PKS Domain: PKS_AT (958-1166). E-value:
-                     4e-80. Score: 260.9; Substrate specificity predictions: mal
-                     (PKS signature), mal (Minowa), mal (consensus);"
      aSDomain        183..713
-                     /domain="PKS_KR"
-                     /locus_tag="ctg1_1"
+                     /asDomain_id="nrpspksdomains_ctg1_1_KR1"
+                     /database="nrpspksdomains.hmm"
                      /detection="hmmscan"
-                     /database="nrpspksdomains.hmm"
+                     /domain="PKS_KR"
                      /evalue="1.40E-53"
+                     /label="ctg1_1_KR1"
+                     /locus_tag="ctg1_1"
                      /score="173.1"
+                     /specificity="KR activity: active"
+                     /specificity="KR stereochemistry: A2"
                      /translation="GTTLITGGTGTLAPHLARWLAEQGAEHIVLTSRTGAEAPKARQLL
                      AELGETVEAVACDVTDKAALAALLARLRAEGRTVRNVVHTAAVIELHTLAETDLAAFSR
                      TVHAKVVGARNLDELLDTDELDAFVLYSSTAGLWGTGAHAAYVAGNAYLHALAAHRRAR
                      GLRATALSWGIWAD"
-                     /label="ctg1_1_KR1"
-                     /asDomain_id="nrpspksdomains_ctg1_1_KR1"
-                     /specificity="KR activity: active"
-                     /specificity="KR stereochemistry: A2"
      CDS_motif       192..284
-                     /note="NRPS/PKS Motif: PKSI-KR_m1 (e-value: 3.8e-15,
-                     bit-score: 48.4)"
+                     /aSTool="pksnrpsmotif"
+                     /asDomain_id="nrpspksmotif_ctg1_1_0001"
+                     /database="abmotifs"
+                     /detection="hmmscan"
+                     /evalue="3.80E-15"
+                     /label="PKSI-KR_m1"
                      /locus_tag="ctg1_1"
                      /motif="PKSI-KR_m1"
-                     /database="abmotifs"
-                     /evalue="3.80E-15"
-                     /asDomain_id="nrpspksmotif_ctg1_1_0001"
-                     /detection="hmmscan"
+                     /note="NRPS/PKS Motif: PKSI-KR_m1 (e-value: 3.8e-15,
+                     bit-score: 48.4)"
                      /score="48.4"
+                     /translation="LITGGTGTLAPHLARWLAEQGAEHIVLTSRT"
+     CDS_motif       555..665
                      /aSTool="pksnrpsmotif"
-                     /translation="LITGGTGTLAPHLARWLAEQGAEHIVLTSRT"
-                     /label="PKSI-KR_m1"
-     CDS_motif       555..665
-                     /note="NRPS/PKS Motif: PKSI-KR_m4 (e-value: 1.6e-14,
-                     bit-score: 46.4)"
+                     /asDomain_id="nrpspksmotif_ctg1_1_0002"
+                     /database="abmotifs"
+                     /detection="hmmscan"
+                     /evalue="1.60E-14"
+                     /label="PKSI-KR_m4"
                      /locus_tag="ctg1_1"
                      /motif="PKSI-KR_m4"
-                     /database="abmotifs"
-                     /evalue="1.60E-14"
-                     /asDomain_id="nrpspksmotif_ctg1_1_0002"
-                     /detection="hmmscan"
+                     /note="NRPS/PKS Motif: PKSI-KR_m4 (e-value: 1.6e-14,
+                     bit-score: 46.4)"
                      /score="46.4"
-                     /aSTool="pksnrpsmotif"
                      /translation="LDAFVLYSSTAGLWGTGAHAAYVAGNAYLHALAAHRR"
-                     /label="PKSI-KR_m4"
      aSDomain        1026..1238
+                     /asDomain_id="nrpspksdomains_ctg1_1_Xdom01"
+                     /database="nrpspksdomains.hmm"
+                     /detection="hmmscan"
                      /domain="ACP"
+                     /evalue="7.80E-31"
                      /locus_tag="ctg1_1"
-                     /detection="hmmscan"
-                     /database="nrpspksdomains.hmm"
-                     /evalue="7.80E-31"
                      /score="97.8"
                      /translation="LELVRAEAAAVLGHASADALPEDRAFRDVGFDSVTAVDLRNRISA
                      GTGLTLPATMVFDHPTPRRLAGFLAA"
-                     /asDomain_id="nrpspksdomains_ctg1_1_Xdom01"
      aSDomain        1305..2576
+                     /asDomain_id="nrpspksdomains_ctg1_1_Xdom02"
+                     /database="nrpspksdomains.hmm"
+                     /detection="hmmscan"
                      /domain="PKS_KS"
+                     /evalue="3.00E-179"
                      /locus_tag="ctg1_1"
-                     /detection="hmmscan"
-                     /database="nrpspksdomains.hmm"
-                     /evalue="3.00E-179"
                      /score="587.9"
                      /translation="VAIIGMACRYPGGANTPERLWDLVVGGVDAISGFPADRNWPTDAL
                      YDPDPDAGGKTYSVQGGFLHEAAEFDPGFFGISPREALSMDPQQRLLLETAWEAFERAG
@@ -138,114 +139,113 @@
                      QQRVIRQALANARLSASEVDVIEGHGTGTALGDPIEAQALLATYGQDRERPLLLGSVKS
                      NIGHTQMASGVAGVIKVVQALRHGLVPKTLHVDEPSTHVDWSTGSIELPSGSVPWPESG
                      RPRRAGISSFGLSGTNVHTILEQAP"
-                     /asDomain_id="nrpspksdomains_ctg1_1_Xdom02"
      CDS_motif       1788..1835
-                     /note="NRPS/PKS Motif: PKSI-KS_m3 (e-value: 2e-06,
-                     bit-score: 19.7)"
+                     /aSTool="pksnrpsmotif"
+                     /asDomain_id="nrpspksmotif_ctg1_1_0003"
+                     /database="abmotifs"
+                     /detection="hmmscan"
+                     /evalue="2.00E-06"
+                     /label="PKSI-KS_m3"
                      /locus_tag="ctg1_1"
                      /motif="PKSI-KS_m3"
-                     /database="abmotifs"
-                     /evalue="2.00E-06"
-                     /asDomain_id="nrpspksmotif_ctg1_1_0003"
-                     /detection="hmmscan"
+                     /note="NRPS/PKS Motif: PKSI-KS_m3 (e-value: 2e-06,
+                     bit-score: 19.7)"
                      /score="19.7"
+                     /translation="GPAVTLDTACSSSLVA"
+     CDS_motif       2211..2255
                      /aSTool="pksnrpsmotif"
-                     /translation="GPAVTLDTACSSSLVA"
-                     /label="PKSI-KS_m3"
-     CDS_motif       2211..2255
+                     /asDomain_id="nrpspksmotif_ctg1_1_0004"
+                     /database="abmotifs"
+                     /detection="hmmscan"
+                     /evalue="1.90E-03"
+                     /label="PKSI-KS_m5"
+                     /locus_tag="ctg1_1"
+                     /motif="PKSI-KS_m5"
                      /note="NRPS/PKS Motif: PKSI-KS_m5 (e-value: 0.0019,
                      bit-score: 10.8)"
-                     /locus_tag="ctg1_1"
-                     /motif="PKSI-KS_m5"
+                     /score="10.8"
+                     /translation="IEGHGTGTALGDPIE"
+     CDS_motif       2310..2354
+                     /aSTool="pksnrpsmotif"
+                     /asDomain_id="nrpspksmotif_ctg1_1_0005"
                      /database="abmotifs"
-                     /evalue="1.90E-03"
-                     /asDomain_id="nrpspksmotif_ctg1_1_0004"
                      /detection="hmmscan"
-                     /score="10.8"
-                     /aSTool="pksnrpsmotif"
-                     /translation="IEGHGTGTALGDPIE"
-                     /label="PKSI-KS_m5"
-     CDS_motif       2310..2354
+                     /evalue="1.10E-03"
+                     /label="PKSI-KS_m6"
+                     /locus_tag="ctg1_1"
+                     /motif="PKSI-KS_m6"
                      /note="NRPS/PKS Motif: PKSI-KS_m6 (e-value: 0.0011,
                      bit-score: 11.5)"
-                     /locus_tag="ctg1_1"
-                     /motif="PKSI-KS_m6"
+                     /score="11.5"
+                     /translation="GSVKSNIGHTQMASG"
+     CDS_motif       2874..2927
+                     /aSTool="pksnrpsmotif"
+                     /asDomain_id="nrpspksmotif_ctg1_1_0006"
                      /database="abmotifs"
-                     /evalue="1.10E-03"
-                     /asDomain_id="nrpspksmotif_ctg1_1_0005"
                      /detection="hmmscan"
-                     /score="11.5"
-                     /aSTool="pksnrpsmotif"
-                     /translation="GSVKSNIGHTQMASG"
-                     /label="PKSI-KS_m6"
-     CDS_motif       2874..2927
-                     /note="NRPS/PKS Motif: PKSI-AT-mM_m1 (e-value: 2.3e-06,
-                     bit-score: 19.8)"
+                     /evalue="2.30E-06"
+                     /label="PKSI-AT-mM_m1"
                      /locus_tag="ctg1_1"
                      /motif="PKSI-AT-mM_m1"
-                     /database="abmotifs"
-                     /evalue="2.30E-06"
-                     /asDomain_id="nrpspksmotif_ctg1_1_0006"
-                     /detection="hmmscan"
+                     /note="NRPS/PKS Motif: PKSI-AT-mM_m1 (e-value: 2.3e-06,
+                     bit-score: 19.8)"
                      /score="19.8"
-                     /aSTool="pksnrpsmotif"
                      /translation="FLFAGQGSQRAGMGRELY"
-                     /label="PKSI-AT-mM_m1"
      aSDomain        2877..3500
+                     /asDomain_id="nrpspksdomains_ctg1_1_AT1"
+                     /database="nrpspksdomains.hmm"
+                     /detection="hmmscan"
                      /domain="PKS_AT"
+                     /evalue="4.00E-80"
+                     /label="ctg1_1_AT1"
                      /locus_tag="ctg1_1"
-                     /detection="hmmscan"
-                     /database="nrpspksdomains.hmm"
-                     /evalue="4.00E-80"
                      /score="260.9"
+                     /specificity="PKS signature: mal"
+                     /specificity="Minowa: mal"
+                     /specificity="consensus: mal"
                      /translation="LFAGQGSQRAGMGRELYERHPVFADALDAVLGHFDLPRALRDVMW
                      DDDSTALDETGYTQPALFAFEVALFRLLESWGVTPDYLAGHSIGEIAAAHVAGVLSLAD
                      ACALVAARGALMQALPSGGAMVSVRGSEADVAGHLGEDVAVAAVNGPESVVLAGTEDAV
                      LQAAGRLEAAGHKVRRLRVSHAFHSPLMDPVLAEFATVAQGLTYH"
-                     /label="ctg1_1_AT1"
-                     /asDomain_id="nrpspksdomains_ctg1_1_AT1"
-                     /specificity="PKS signature: mal"
-                     /specificity="Minowa: mal"
-                     /specificity="consensus: mal"
      CDS_motif       3033..3095
-                     /note="NRPS/PKS Motif: PKSI-AT-mM_m2 (e-value: 0.0032,
-                     bit-score: 10.9)"
+                     /aSTool="pksnrpsmotif"
+                     /asDomain_id="nrpspksmotif_ctg1_1_0007"
+                     /database="abmotifs"
+                     /detection="hmmscan"
+                     /evalue="3.20E-03"
+                     /label="PKSI-AT-mM_m2"
                      /locus_tag="ctg1_1"
                      /motif="PKSI-AT-mM_m2"
-                     /database="abmotifs"
-                     /evalue="3.20E-03"
-                     /asDomain_id="nrpspksmotif_ctg1_1_0007"
-                     /detection="hmmscan"
+                     /note="NRPS/PKS Motif: PKSI-AT-mM_m2 (e-value: 0.0032,
+                     bit-score: 10.9)"
                      /score="10.9"
+                     /translation="DETGYTQPALFAFEVALFRLL"
+     CDS_motif       3105..3227
                      /aSTool="pksnrpsmotif"
-                     /translation="DETGYTQPALFAFEVALFRLL"
-                     /label="PKSI-AT-mM_m2"
-     CDS_motif       3105..3227
+                     /asDomain_id="nrpspksmotif_ctg1_1_0008"
+                     /database="abmotifs"
+                     /detection="hmmscan"
+                     /evalue="2.30E-22"
+                     /label="PKSI-AT-M_m3"
+                     /locus_tag="ctg1_1"
+                     /motif="PKSI-AT-M_m3"
                      /note="NRPS/PKS Motif: PKSI-AT-M_m3 (e-value: 2.3e-22,
                      bit-score: 71.3)"
-                     /locus_tag="ctg1_1"
-                     /motif="PKSI-AT-M_m3"
+                     /score="71.3"
+                     /translation="GVTPDYLAGHSIGEIAAAHVAGVLSLADACALVAARGALMQ"
+     CDS_motif       3312..3350
+                     /aSTool="pksnrpsmotif"
+                     /asDomain_id="nrpspksmotif_ctg1_1_0009"
                      /database="abmotifs"
-                     /evalue="2.30E-22"
-                     /asDomain_id="nrpspksmotif_ctg1_1_0008"
                      /detection="hmmscan"
-                     /score="71.3"
-                     /aSTool="pksnrpsmotif"
-                     /translation="GVTPDYLAGHSIGEIAAAHVAGVLSLADACALVAARGALMQ"
-                     /label="PKSI-AT-M_m3"
-     CDS_motif       3312..3350
+                     /evalue="4.70E-04"
+                     /label="PKSI-AT-M_m5"
+                     /locus_tag="ctg1_1"
+                     /motif="PKSI-AT-M_m5"
                      /note="NRPS/PKS Motif: PKSI-AT-M_m5 (e-value: 0.00047,
                      bit-score: 13.4)"
-                     /locus_tag="ctg1_1"
-                     /motif="PKSI-AT-M_m5"
-                     /database="abmotifs"
-                     /evalue="4.70E-04"
-                     /asDomain_id="nrpspksmotif_ctg1_1_0009"
-                     /detection="hmmscan"
                      /score="13.4"
-                     /aSTool="pksnrpsmotif"
                      /translation="AAVNGPESVVLAG"
-                     /label="PKSI-AT-M_m5"
 ORIGIN
         1 ggggcggcgt gctcgccctg cccgccgagc tggaccgccg cggcggcgac cggctggcgg
        61 ctgtgctgtc cggcgccacc ggcgaagacc agctggccat ccgcgccgcc ggcgtgttcg
--- a/test-data/index.2.html	Wed Feb 07 06:21:45 2018 -0500
+++ b/test-data/index.2.html	Sat Feb 10 05:52:26 2018 -0500
@@ -10,7 +10,7 @@
       <div class="top-header">
         <img class="antismash-logo" src="images/bacteria_logo.png" alt="antiSMASH">
         <span class="antismash-title"><a class="main-link" href="http://antismash.secondarymetabolites.org/">antibiotics &amp; Secondary Metabolite Analysis SHell</a><br>
-            <span class="white">Version <span id="antismash-version">4.0.2</span></span>
+            <span class="white">Version <span id="antismash-version">4.1.0</span></span>
         </span>
         <div id="icons">
           <a class="main-link" href="http://antismash.secondarymetabolites.org/"><img src="images/bacteria_home.png" alt="home" title="Go to start page"></a>
@@ -48,7 +48,7 @@
           </tr>
         </thead>
         <tbody>
-        <tr class="separator-row"><td class="separator-text" colspan="2">The following clusters are from record ARBH01000003.1:</td></tr><tr><td class="clbutton t1pks"><a href="#cluster-1">Cluster 1</a></td><td><a href="http://antismash.secondarymetabolites.org/help#t1pks" target="_blank">T1pks</a></td><td class="digits">1</td><td class="digits">3500</td><td>-</td><td>-</td></tr></tbody>
+        <tr class="separator-row"><td class="separator-text" colspan="2">The following clusters are from record ARBH01000003.1:</td></tr><tr><td class="clbutton t1pks"><a href="#cluster-1">Cluster 1</a></td><td><a href="https://docs.antismash.secondarymetabolites.org/glossary/#t1pks" target="_blank">T1pks</a></td><td class="digits">1</td><td class="digits">3500</td><td>-</td><td>-</td></tr></tbody>
       </table>
     </div>
 
--- a/test-data/index.html	Wed Feb 07 06:21:45 2018 -0500
+++ b/test-data/index.html	Sat Feb 10 05:52:26 2018 -0500
@@ -10,7 +10,7 @@
       <div class="top-header">
         <img class="antismash-logo" src="images/bacteria_logo.png" alt="antiSMASH">
         <span class="antismash-title"><a class="main-link" href="http://antismash.secondarymetabolites.org/">antibiotics &amp; Secondary Metabolite Analysis SHell</a><br>
-            <span class="white">Version <span id="antismash-version">4.0.2</span></span>
+            <span class="white">Version <span id="antismash-version">4.1.0</span></span>
         </span>
         <div id="icons">
           <a class="main-link" href="http://antismash.secondarymetabolites.org/"><img src="images/bacteria_home.png" alt="home" title="Go to start page"></a>
@@ -48,7 +48,7 @@
           </tr>
         </thead>
         <tbody>
-        <tr class="separator-row"><td class="separator-text" colspan="2">The following clusters are from record ARBH01000003.1:</td></tr><tr><td class="clbutton t1pks"><a href="#cluster-1">Cluster 1</a></td><td><a href="http://antismash.secondarymetabolites.org/help#t1pks" target="_blank">T1pks</a></td><td class="digits">1</td><td class="digits">3500</td><td>-</td><td>-</td></tr></tbody>
+        <tr class="separator-row"><td class="separator-text" colspan="2">The following clusters are from record ARBH01000003.1:</td></tr><tr><td class="clbutton t1pks"><a href="#cluster-1">Cluster 1</a></td><td><a href="https://docs.antismash.secondarymetabolites.org/glossary/#t1pks" target="_blank">T1pks</a></td><td class="digits">1</td><td class="digits">3500</td><td>-</td><td>-</td></tr></tbody>
       </table>
     </div>