diff antismash.xml @ 25:99435bb90725 draft

Uploaded

--- a/antismash.xml	Tue Oct 15 04:19:33 2013 -0400
+++ b/antismash.xml	Fri Oct 18 03:35:17 2013 -0400
@@ -2,14 +2,18 @@
     <description>and Antibiotics Analysis (antiSMASH)</description>
     <requirements>
         <requirement type="package" version="3.0">hmmer</requirement>
+        <requirement type="package">hmmer</requirement>
         <requirement type="package" version="2.2.28">blast+</requirement>
+        <requirement type="package">blast+</requirement>
         <requirement type="package" version="3.8.31">muscle</requirement>
+        <requirement type="package">muscle</requirement>
         <requirement type="package" version="1.4.0-post-1">straight.plugin</requirement>
         <requirement type="package" version="1.62">biopython</requirement>
         <requirement type="package" version="1.2.6">pyquery</requirement>
         <requirement type="package" version="0.1.2">helperlibs</requirement>
         <requirement type="package" version="0.9">cssselect</requirement>
         <requirement type="package" version="2.0.2">antismash</requirement>
+        <requirement type="package">antismash</requirement>
     </requirements>
     <command>
         #import os, glob
@@ -24,7 +28,7 @@
         ln -s $infile #echo 'input_tempfile.' + $file_extension#;
         mkdir -p $outputfolder;
         run_antismash.py 
-            --cpus 4
+            --cpus 12
             --enable $types
             --input-type 'nucl'
             $smcogs
@@ -33,11 +37,15 @@
             $inclusive
             $full_hmmer
             $full_blast
+            $eukaryotic
+
 
             #if str($pfam_database) != "None":
                 --pfamdir $pfam_database.fields.path
             #end if
 
+            --debug
+
             --disable-embl
             --outputfolder $outputfolder
 
@@ -47,49 +55,63 @@
             ##--from START          Start analysis at nucleotide specified
             ##--to END
 
-        ;
+        2>&#38;1
+
+        ##
         ## shuffling files to create the correct outputs for Galaxy
-        
+        ##
+
         ## html output
-        #if 'html' in str($outputs).split(','):
-            cp #echo os.path.join($outputfolder, 'index.html')# $html 2>/dev/null;
-        #end if
+        ;
+        cp #echo os.path.join($outputfolder, 'index.html')# $html 2> /dev/null
         
         ## gene clusters
         #if 'geneclusterprots_tabular' in str($outputs).split(','):
-            cp #echo os.path.join($outputfolder, 'geneclusters.txt')# $geneclusterprots_tabular 2>/dev/null;
+            ;
+            cp #echo os.path.join($outputfolder, 'geneclusters.txt')# $geneclusterprots_tabular 2> /dev/null
         #end if
 
         #if 'geneclusterprots_fasta' in str($outputs).split(','):
-            cp #echo os.path.join($outputfolder, '*_genecluster_proteins.fa')# $geneclusterprots_fasta 2>/dev/null;
+            ;
+            cp #echo os.path.join($outputfolder, '*_genecluster_proteins.fa')# $geneclusterprots_fasta 2> /dev/null
         #end if
 
 
         ##SVG images
         #if 'archive_svgs' in str($outputs).split(','):
-            cd #echo os.path.join($outputfolder, 'svg')#;
+            ;
+            cd #echo os.path.join($outputfolder, 'svg')#
             #if $clusterblast:
-                tar cfz $archive_svgs *_all.svg genecluster* 2>/dev/null;
+                ;
+                tar cfz $archive_svgs *_all.svg genecluster* 2> /dev/null
             #else:
-                tar cfz $archive_svgs genecluster*;
+                ;
+                tar cfz $archive_svgs genecluster*
             #end if
         #end if
 
         ##all files in a archive
         #if 'archive' in str($outputs).split(','):
+            ;
             cd $outputfolder;
-            tar cf $archive *.zip 2>/dev/null;
+            tar cf $archive *.zip 2> /dev/null
         #end if
 
         ## genbank
         #if 'gb' in str($outputs).split(','):
-            cat #echo os.path.join($outputfolder, '*.gbk')# > $genbank 2>/dev/null;
+            ;
+            cat #echo os.path.join($outputfolder, '*.gbk')# > $genbank 2> /dev/null
         #end if
 
     </command>
     <inputs>
         <param name="infile" type="data" format="genbank" label="Nucleotide sequence file in GenBank format"/>
 
+        <param name="eukaryotic" type="select" label="Origin of DNA">
+            <option value="" selected="True">Prokaryotic</option>
+            <option value="--eukaryotic">Eukaryotic</option>
+        </param>
+
         <param name="clusterblast" type="boolean" label="BLAST identified clusters against known clusters"
             help="(--clusterblast)"
             truevalue="--clusterblast" falsevalue="" checked="True" />
@@ -146,10 +168,9 @@
             <option value="other" selected="True">others</option>
         </param>
 
-        <param name="outputs" type="select" multiple="true" label="Output formats">
+        <param name="outputs" type="select" multiple="true" label="Additional outputs">
             <option value="geneclusterprots_fasta" selected="True">Gene cluster proteins (FASTA)</option>
             <option value="geneclusterprots_tabular">Gene cluster proteins (Tabular)</option>
-            <option value="html" selected="True">Interactive summary page (html)</option>
             <option value="archive_svgs">All clusters as image (compressed)</option>
             <option value="archive">All files compressed</option>
             <option value="gb">Annotated genome (GenBank)</option>
@@ -170,7 +191,9 @@
           <filter>'archive_svgs' in outputs</filter>
         </data>
         <data format="html" name="html" label="${tool.name} on ${on_string} (html report)">
+          <!-- html is default output at any time.
           <filter>'html' in outputs</filter>
+          -->
         </data>
         <data name="genbank" format="genbank" label="${tool.name} on ${on_string} (genbank)">
           <filter>'gb' in outputs</filter>
@@ -217,5 +240,8 @@
 
 http://antismash.secondarymetabolites.org/help.html
 
+
+Bjoern A. Gruening: https://github.com/bgruening/galaxytools/tree/master/antismash
+
   </help>
 </tool>