changeset 4:9b91d26ee080 draft

Uploaded

--- a/antismash.xml	Fri Oct 04 04:22:38 2013 -0400
+++ b/antismash.xml	Fri Oct 04 04:27:10 2013 -0400
@@ -1,22 +1,31 @@
 <tool id="antismash" name="Secondary Metabolites" version="2.0.2.0">
-  <description>and Antibiotics Analysis (antiSMASH)</description>
-  <command>run_antismash.py 
+    <description>and Antibiotics Analysis (antiSMASH)</description>
+    <requirements>
+        <requirement type="package" version="3.0">hmmer</requirement>
+        <requirement type="package" version="2.3.2">hmmer</requirement>
+        <requirement type="package" version="2.2.28">blast+</requirement>
+        <requirement type="package" version="3.8.31">muscle</requirement>
+        <requirement type="package" version="2.0.2">antismash</requirement>
+    </requirements>
+    <command>
+        run_antismash.py 
 
-    --input $infile
-    --cpus 4
-    #set $type_list = ','.join([$type for $type in $types])
-    --enable $type_list
-    --input-type nucl
-    $smcogs
-    $clusterblast
-    $subclusterblast
-    $inclusive
-    $full_hmmer
-    $full_blast
+            --input $infile
+            --cpus 4
+            #set $type_list = ','.join([$type for $type in $types])
+            --enable $type_list
+            --input-type nucl
+            $smcogs
+            $clusterblast
+            $subclusterblast
+            $inclusive
+            $full_hmmer
+            $full_blast
 
+            --pfamdir  $pfam_database.fields.path
 
-  ##--from START          Start analysis at nucleotide specified
-  ##--to END  
+              ##--from START          Start analysis at nucleotide specified
+              ##--to END  
 
     </command>
     <inputs>
@@ -30,6 +39,14 @@
         <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">
+            <options from_file="antismash.loc">
+              <column name="value" index="0"/>
+              <column name="name" index="1"/>
+              <column name="path" index="2"/>
+            </options>
+        </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>

--- a/readme.txt	Fri Oct 04 04:22:38 2013 -0400
+++ b/readme.txt	Fri Oct 04 04:27:10 2013 -0400
@@ -44,6 +44,14 @@
 </section>
 
 
+external Data
+=============
+
+The antismash.loc file contains the path to a PFAM database.
+For any other tool that also uses a PFAM database *.log file, you can sync or link both *.loc files.
+
+
+
 History
 =======
 

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/antismash.loc.sample	Fri Oct 04 04:27:10 2013 -0400
@@ -0,0 +1,16 @@
+#This is a sample file distributed with Galaxy that is used to define a
+#list of PFAM hmms, using three columns tab separated
+#(longer whitespace are TAB characters):
+#
+#The entries are as follows:
+#
+#<unique_id>	<PFAM name>	<path>
+#
+#Your antismash.loc file should include an entry per line.  For example:
+#
+#pfam01	PFAM 27 08 Aug 2013	/data/0/galaxy_data/antismash/pfam/08_08_2013/
+#
+#...etc...
+#
+
+