diff skesa.xml @ 18:53d82924230b draft

Uploaded

--- a/skesa.xml	Thu Aug 16 14:48:35 2018 -0400
+++ b/skesa.xml	Thu Aug 16 14:54:58 2018 -0400
@@ -14,7 +14,7 @@
       #else if $jobtype.select == "pe"
 	--fastq $fastq1,$fastq2 --use_paired_ends
       #else if $jobtype.select == "rp"
-	--fastq '{$pairedf.forward}','{$pairedf.reverse}' --use_paired_ends
+	--fastq $jobtype.pairedf.forward,$jobtype.pairedf.reverse --use_paired_ends
       #end if
       #if $cores != 0
       --cores $cores
@@ -25,9 +25,6 @@
     ]]></command>
     <inputs>
       <conditional name="jobtype">
-        <when value="srr">
-         <param name="srrnum" type="text" label="Sra run number"/>
-         </when>
         <param name="select" type="select" label="Assembly or FASTQ Reads?">
           <option value="sra">SRR  number</option>
           <option value="asm">Genome Assembly</option>
@@ -36,6 +33,9 @@
           <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>
@@ -46,11 +46,11 @@
           <param name="fastq1" type="data" format="fastq" label="FASTQ" />
           <param name="fastq2" type="data" format="fastq" label="FASTQ" />
         </when>
-         <when value="cl">
-              <param type="data_collection" name="collection_files" format="fastq" collection_type="list" label="FASTQS: Must be a Data Set list built from multiple fastq files" />
+        <when value="cl">
+          <param name="collection_files" type="data_collection" format="fastq" collection_type="list" label="FASTQS: Must be a Data Set list built from multiple fastq files" />
         </when>
-         <when value="rp">
-              <param type="data_collection" collection_type="paired" name="pairedf" format="fastq" label="FASTQS: Must be a paired set of forward and reverse fastq files" />
+        <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" />