Mercurial > repos > rnateam > segemehl

changeset 9:90b8941e5115 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 5d14c257183ec8dd0236bbbf63db4a890b9e954a
author bgruening
date Mon, 04 Sep 2017 10:12:30 -0400
parents 338ecc1500e4
children ee6a5ec6963c
files segemehl.tar.gz segemehl.xml
diffstat 2 files changed, 32 insertions(+), 19 deletions(-) [+]
line wrap: on
line diff
Binary file segemehl.tar.gz has changed
--- a/segemehl.xml	Wed Jul 26 15:30:57 2017 -0400
+++ b/segemehl.xml	Mon Sep 04 10:12:30 2017 -0400
@@ -10,7 +10,31 @@
            description="Execution halted." />
   </stdio>
   <command>
-    <![CDATA[
+	<!--
+        ## check for single/pair-end
+        #if str( $library.type ) == "single":
+            #set $query_list = list()
+        ## prepare inputs
+        #for $fastq in $library.input_query:
+            $query_list.append('%s' % $fastq )
+        #end for
+        -q "#echo ' '.join( $query_list )#"
+        #else
+            ## prepare inputs        
+            #set $mate1 = list()
+            #set $mate2 = list()
+            #for $mate_pair in $library.mate_list:
+                $mate1.append( str($mate_pair.first_strand_query) )
+                $mate2.append( str($mate_pair.second_strand_query) )
+            #end for
+        
+            -q #echo ','.join($mate1)
+            -p #echo ','.join($mate2)
+        
+            -I $library.maxinsertsize
+        #end if
+		-->
+	<![CDATA[
         ## prepare segemehl index if no reference genome is supplied
         #if $refGenomeSource.genomeSource == "history":
             mkdir ./temp_index/ &&
@@ -36,25 +60,13 @@
         
         ## check for single/pair-end
         #if str( $library.type ) == "single":
-            #set $query_list = list()
         ## prepare inputs
-        #for $fastq in $library.input_query:
-            $query_list.append('%s' % $fastq )
-        #end for
-        -q "#echo ' '.join( $query_list )#"
-        #else
-            ## prepare inputs        
-            #set $mate1 = list()
-            #set $mate2 = list()
-            #for $mate_pair in $library.mate_list:
-                $mate1.append( str($mate_pair.first_strand_query) )
-                $mate2.append( str($mate_pair.second_strand_query) )
-            #end for
+            -q ${library.input_query}
+        #else       
+            -q ${mate_pair.first_strand_query}
+            -p ${mate_pair.second_strand_query}
         
-            -q #echo ','.join($mate1)
-            -p #echo ','.join($mate2)
-        
-            -I $library.maxinsertsize
+            -I ${library.maxinsertsize}
         #end if
         -m $minsize
         -A $accuracy
@@ -116,7 +128,8 @@
         <option value="paired">Paired-end</option>
       </param>
       <when value="single">
-        <param name="input_query" type="data" multiple="True" format="fastqsanger,fastqillumina,fastq,fasta" label="Reads in FASTQ/FASTA files" />
+		<!--        <param name="input_query" type="data" multiple="True" format="fastqsanger,fastqillumina,fastq,fasta" label="Reads in FASTQ/FASTA files" /> -->
+		<param name="input_query" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Reads in FASTQ/FASTA files" />
       </when>
       <when value="paired">
         <!-- ToDo paired coolections -->