Mercurial > repos > bgruening > antismash

changeset 9:b11e1dfbc7c9 draft

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Uploaded
author bgruening
date Wed, 09 Oct 2013 10:05:11 -0400
parents 5d4078513d71
children d2c785cdf23e
files antismash.xml tool_data_table_conf.xml.sample tool_dependencies.xml
diffstat 3 files changed, 39 insertions(+), 55 deletions(-) [+]
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line diff
--- a/antismash.xml	Wed Oct 09 04:14:07 2013 -0400
+++ b/antismash.xml	Wed Oct 09 10:05:11 2013 -0400
@@ -26,8 +26,9 @@
 
             --pfamdir  $pfam_database.fields.path
 
-              ##--from START          Start analysis at nucleotide specified
-              ##--to END  
+            ## leave out the start and end features, it can be easily replaced with Galaxy tools
+            ##--from START          Start analysis at nucleotide specified
+            ##--to END  
 
     </command>
     <inputs>
@@ -41,7 +42,7 @@
         <param name="full_hmmer" type="boolean" label="Run a whole-genome HMMer analysis" truevalue="--full-hmmer" falsevalue="" checked="false" />
         <param name="full_blast" type="boolean" label="Run a whole-genome BLAST analysis" truevalue="--full-blast" falsevalue="" checked="false" />
 
-        <param name="pfam_database" type="select" label="Covariance models">
+        <param name="pfam_database" type="select" label="Pfam database" help="Pfam Covariance models">
             <options from_file="antismash.loc">
               <column name="value" index="0"/>
               <column name="name" index="1"/>
@@ -50,58 +51,33 @@
         </param>
 
         <param name="types" type="select" display="checkboxes" multiple="true" label="Gene cluster types to search">
-            <option value="1" selected="True">all</option>
-            <option value="2">type I polyketide synthases</option>
-            <option value="3">type II polyketide synthases</option>
-            <option value="4">type III polyketide synthases</option>
-            <option value="5">nonribosomal peptide synthetases</option>
-            <option value="6">terpene synthases</option>
-            <option value="7">lantibiotics</option>
-            <option value="8">bacteriocins</option>
-            <option value="9">beta-lactams</option>
-            <option value="10">aminoglycosides / aminocyclitols</option>
-            <option value="11">aminocoumarins</option>
-            <option value="12">siderophores</option>
-            <option value="13">ectoines</option>
-            <option value="14">butyrolactones</option>
-            <option value="15">indoles</option>
-            <option value="16">nucleosides</option>
-            <option value="17">phosphoglycolipids</option>
-            <option value="18">melanins</option>
-            <option value="19">others</option>
+            <option value="t1pks" selected="True">type I polyketide synthases</option>
+            <option value="t2pks" selected="True">type II polyketide synthases</option>
+            <option value="t3pks" selected="True">type III polyketide synthases</option>
+            <option value="t4pks" selected="True">type IV polyketide synthases</option>
+            <option value="transatpks" selected="True">trans-AT PKS</option>
+            <option value="nrps" selected="True">nonribosomal peptide synthetases</option>
+            <option value="terpene" selected="True">terpene synthases</option>
+            <option value="lantipeptide" selected="True">lantipeptides</option>
+            <option value="bacteriocin" selected="True">bacteriocins</option>
+            <option value="blactam" selected="True">beta-lactams</option>
+            <option value="amglyccycl" selected="True">aminoglycosides / aminocyclitols</option>
+            <option value="aminocoumarin" selected="True">aminocoumarins</option>
+            <option value="siderophore" selected="True">siderophores</option>
+            <option value="ectoine" selected="True">ectoines</option>
+            <option value="butyrolactone" selected="True">butyrolactones</option>
+            <option value="indole" selected="True">indoles</option>
+            <option value="nucleoside" selected="True">nucleosides</option>
+            <option value="phosphoglycolipid" selected="True">phosphoglycolipids</option>
+            <option value="oligosaccharide" selected="True">oligosaccharides</option>
+            <option value="furan" selected="True">furans</option>
+            <option value="hserlactone" selected="True">hserlactones</option>
+            <option value="thiopeptide" selected="True">thiopeptides</option>
+            <option value="phenazine" selected="True">phenazines</option>
+            <option value="phosphonate" selected="True">phosphonates</option>
+            <option value="others" selected="True">others</option>
         </param>
 
-<!--
-t1pks   (PKS_KS & PKS_AT) or (ene_KS & PKS_AT) or (mod_KS & PKS_AT) or (hyb_KS & PKS_AT) or (itr_KS & PKS_AT) or (tra_KS & PKS_AT)      20      20
-transatpks      (PKS_KS & ATd) or (ene_KS & ATd) or (mod_KS & ATd) or (hyb_KS & ATd) or (itr_KS & ATd) or (tra_KS & ATd)        20      20
-t2pks   t2ks or t2clf or t2pks2 20      20
-t3pks   Chal_sti_synt_C or Chal_sti_synt_N      20      20
-t4pks   hglE or hglD    20      20
-nrps    (Condensation & AMP-binding) or (Condensation & A-OX) or cluster(Condensation,AMP-binding)      20      20
-terpene Terpene_Synth or Terpene_synth_C or phytoene_synt or Lycopene_cycl or terpene_cyclase or NapT7 or fung_ggpps or fung_ggpps2 or dmat or trichodiene_synth        20      10
-lantipeptide    (Lant_dehyd_N & Lant_dehyd_C) or cluster(LANC_like,Flavoprotein) or cluster(LANC_like,Trp_halogenase) or cluster(LANC_like,p450) or (LANC_like & Pkinase) or (LANC_like & DUF4135) or cluster(LANC_like,Lant_dehyd_N) or cluster(LANC_like,Lant_dehyd_C) or cluster(LANC_like,adh_short) or cluster(LANC_like,adh_short_C2) or TIGR03731 or Antimicr18 or Gallidermin or L_biotic_A or TIGR03731 or leader_d or leader_eh or leader_abc or mature_d or mature_ab or mature_a or mature_b or mature_ha or mature_h_beta or lacticin_l or lacticin_mat or LD_lanti_pre or strep_PEQAXS    20      10
-bacteriocin     strepbact or Antimicrobial14 or Bacteriocin_IId or BacteriocIIc_cy or Bacteriocin_II or Bacteriocin_IIi or Lactococcin or Antimicrobial17 or Lactococcin_972 or Bacteriocin_IIc or LcnG-beta or Bacteriocin_Iii or Subtilosin_A or Cloacin or Linocin_M18 or TIGR03603 or TIGR03604 or TIGR03605 or TIGR03651 or TIGR03678 or TIGR03693 or TIGR03798 or TIGR03882 or TIGR03601 or TIGR03602 or TIGR03795 or TIGR03793 or TIGR03975 or mvnA or thiostrepton or subtilosin or cypemycin or mvd or lasso or DUF692 or micJ25 or mcjC or glycocin or botH or skfc or thuricin or sublancin  20      5
-blactam BLS or CAS or tabtoxin  20      10
-amglyccycl      strH or strK1 or strK2 or NeoL or DOIS or ValA or SpcFG or SpcDK_glyc or salQ   20      10
-aminocoumarin   novK or novJ or novI or novH or SpcDK_cou       20      10
-siderophore     IucA_IucC       20      5
-ectoine ectoine_synt    20      5
-butyrolactone   AfsA    20      5
-indole  indsynth        20      10
-nucleoside      LipM or LipU or LipV or LipU or ToyB or TunD or pur6 or pur10 or nikJ or nikO   20      10
-phosphoglycolipid       MoeO5 or moeGT  20      10
-melanin melC    20      5
-oligosaccharide minimum(3,[Glycos_transf_1,Glycos_transf_2,Glyco_transf_28,MGT,MGT2,DUF1205], [MGT2])   20      10
-furan   mmyO    20      5
-hserlactone     Autoind_synth   20      10
-thiopeptide     cluster(Lant_dehyd_C,YcaO) or cluster(Lant_dehyd_N,YcaO)        20      10
-phenazine       phzB    20      10
-phosphonate     phosphonates    20      20
-other   (PP-binding & AMP-binding) or (PP-binding & A-OX) or (NAD_binding_4 & A-OX) or (NAD_binding_4 & AMP-binding) or LmbU or goadsporin_like or Neocarzinostat or cyanobactin_synth or cycdipepsynth or fom1 or bcpB or frbD or mitE or vlmB or prnB or CaiA or bacilysin or cypI    20      20
-
--->
-
-
     </inputs>
     <outputs>
         <data format="fasta" name="geneclusterprots" label="${tool.name} on ${on_string} (Gen Cluster Proteins)" />
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Wed Oct 09 10:05:11 2013 -0400
@@ -0,0 +1,8 @@
+<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc-->
+<tables>
+    <!-- Locations of indexes in the AntiSmash Pfam database -->
+    <table name="antismash_pfam" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/antismash.loc" />
+    </table>
+</tables>
--- a/tool_dependencies.xml	Wed Oct 09 04:14:07 2013 -0400
+++ b/tool_dependencies.xml	Wed Oct 09 10:05:11 2013 -0400
@@ -1,13 +1,13 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="blast+" version="2.2.28">
-        <repository changeset_revision="d794cb2b0f45" name="package_blast_plus_2_2_28" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="5a449da71d08" name="package_blast_plus_2_2_28" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="hmmer " version="2.3.2">
         <repository changeset_revision="64510d86d77d" name="package_hmmer_2_3_2" owner="lionelguy" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="hmmer" version="3.0">
-        <repository changeset_revision="3bc37773c609" name="package_hmmer_3_0" owner="jjohnson" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="a44693e3a2c4" name="package_hmmer_3_0" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="muscle" version="3.8.31">
         <repository changeset_revision="ce304c51f69b" name="package_muscle_3_8_31" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu" />