# HG changeset patch
# User cstrittmatter
# Date 1536845662 14400
# Node ID a368d48a4562f92f17349d87ebdaeda1f476775f
# Parent  abb622c228c45ad15c2afe646f513db99ef6b3aa
planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty

diff -r abb622c228c4 -r a368d48a4562 run_skesa_collection.py
--- a/run_skesa_collection.py	Mon Aug 27 08:59:02 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,43 +0,0 @@
-import sys
-
-from pathlib import Path
-
-path1 = sys.argv[1]
-
-cores = sys.argv[2]
-
-memory = sys.argv[2]
-
-print(path1)
-
-#print(path2)
-
-pathlist = Path(path1).glob('*fastq*')
-
-i = 0
-skcmd = []
-
-skcmd.append("skesa ")
-
-for path in pathlist:
-    # because path is object not string-wq
-    i += 1
-    path_in_str = str(path)
-    if i == 2:
-        skcmd.append("," + path_in_str)
-        #print("," + path_in_str)
-        i = 0
-    if i == 1:
-        skcmd.append(" --fastq " + path_in_str)
-        #print(" --fastq " + path_in_str) 
-
-    
-
-if cores != 0:
-    skcmd.append(" --cores " + cores)
-    
-
-skcmd.append(" --memory " + memory)
-
-skcmds = ''.join(skcmd)
-print(skcmds) 
diff -r abb622c228c4 -r a368d48a4562 skesa.xml
--- a/skesa.xml	Mon Aug 27 08:59:02 2018 -0400
+++ b/skesa.xml	Thu Sep 13 09:34:22 2018 -0400
@@ -1,40 +1,22 @@
 <tool id="skesa" name="skesa" version="0.1">
     <requirements>
-      	<requirement type="package" version="2.2">skesa</requirement>
-	<requirement type="package" >python</requirement>
+      <requirement type="package" version="2.2">skesa</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-    
-
-      #if $jobtype.select != "cl"
+    #if $jobtype.select != "cl"
 	skesa
-       #if $jobtype.select == "asm"
+      #if $jobtype.select == "asm"
         --fasta $draft
-       #else if $jobtype.select == "se"
+      #else if $jobtype.select == "se"
         --fastq $fastq1
-       #else if $jobtype.select == "pe"
-	--fastq $fastq1,$fastq2 --use_paired_ends
-       #else if $jobtype.select == "rp"
-	--fastq $jobtype.pairedf.forward,$jobtype.pairedf.reverse --use_paired_ends
-       #if $cores != 0
-        --cores $cores
-       #end if
-        --memory $memory > results.skesa.fasta
+      #else if $jobtype.select == "pe"
+	    --fastq $fastq1,$fastq2 --use_paired_ends
       #end if
-
-
-      #if $jobtype.select == "cl"
-	
-	#set $pathOuput = 0
-	mkdir temp_data;
-        #for $collection_file in $jobtype.collection_files
-             	#silent sys.stderr.write($collection_file+"\n")
-	 	cp $collection_file temp_data/.;
-	     
-        #end for
-	
-
+      #if $cores != 0
+      --cores $cores
       #end if
+      --memory $memory	> results.skesa.fasta
+    #end if 
 
     ]]></command>
     <inputs>
@@ -43,12 +25,7 @@
           <option value="asm">Genome Assembly</option>
           <option value="se">Single-End Reads</option>
           <option value="pe">Paired-End Reads (Separate Files)</option>
-          <option value="rp">Paired-End Reads (Paired Data Set)</option>
-          <option value="cl">Collection of Reads</option>
         </param>
-        <when value="srr">
-          <param name="srrnum" type="text" label="Sra run number"/>
-        </when>
         <when value="asm">
           <param name="draft" type="data" format="fasta" label="FASTA" />
         </when>
@@ -59,16 +36,10 @@
           <param name="fastq1" type="data" format="fastq" label="FASTQ" />
           <param name="fastq2" type="data" format="fastq" label="FASTQ" />
         </when>
-        <when value="cl">
-          <param name="collection_files" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" collection_type="paired" label="FASTQS: Must be a Data Set list built from multiple fastq files" />
-        </when>
-        <when value="rp">
-          <param name="pairedf" type="data_collection" collection_type="paired" format="fastq" label="FASTQS: Must be a paired set of forward and reverse fastq files" />
-        </when>
       </conditional>
       <param name="memory" type="integer" label="Memory available (GB) [integer]" value="16" />
       <param name="cores" type="integer" label="Number of cores to use (default all) [integer]" value="0" />
-    
+     
     </inputs>
     <outputs>
             <data format="fasta" label="skesa Results" name="${input.name}.skesa.fasta" from_work_dir="*.fasta"/>