# HG changeset patch
# User cstrittmatter
# Date 1534368946 14400
# Node ID b82a1b3c5b61281124798f00c9ef400cb0cae403
# Parent  15be58c254f5dc2abd4a5a1dbeb1986c5e7a90bf
planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty

diff -r 15be58c254f5 -r b82a1b3c5b61 skesa.xml
--- a/skesa.xml	Wed Aug 15 09:33:27 2018 -0400
+++ b/skesa.xml	Wed Aug 15 17:35:46 2018 -0400
@@ -5,20 +5,29 @@
     <command detect_errors="exit_code"><![CDATA[
     #if $jobtype.select != "cl"
 	skesa
-      #if $jobtype.select == "asm"
-        -i $draft
+      #if $jobtype.select == "srr"
+        -sra_run $srrnum
+      #else if $jobtype.select == "asm"
+        --fasta $draft
       #else if $jobtype.select == "se"
         --fastq $fastq1
       #else if $jobtype.select == "pe"
 	--fastq $fastq1,$fastq2 --use_paired_ends
       #end if
-	> results.skesa.fasta
+      #if $cores != 0
+      --cores $cores
+      #end if
+      --memory $memory	> results.skesa.fasta
     #end if 
 
     ]]></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>
           <option value="se">Single-End Reads</option>
           <option value="pe">Paired-End Reads</option>
@@ -38,9 +47,10 @@
               <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>
       </conditional>
-   
-      <param name="percent_identity" type="integer" label="Percent identity required for an allele match [default 90]" value="90" />
-      <param name="percent_length" type="integer" label="Percent length required for an allele match [default 50]" value="50" />
+      <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" />
+      <param name="kmer" type="integer" label="Minimal kmer length for assembly [default 21] if non are specified " value="0" />
+      <param name="min_count" type="integer" label="Minimal count for kmers retained for comparing alternate choices [integer]" value="0" />
     
     </inputs>
     <outputs>
@@ -55,23 +65,30 @@
 
 A fasta assembly or single or paired end reads test or data set list of fastqs
 
-**PERCENTIDENTITY**
+**Memory available**
 
-Percentage of identity wanted to use against the database. From 0 to 100, default is 90%.
+--memory arg (=32)         Memory available (GB) [integer]
+     
 
-**PERCENTLENGTH**
+**Number of cores**
 
-Percentage of length wanted to use against the database. From 0 to 100, default is 50%.
+--cores arg (=0)           Number of cores to use (default all) [integer]
 
-https://github.com/phac-nml/ecoli_serotyping
+https://github.com/ncbi/ngs-tools/tree/master/tools/skesa/
 
     ]]></help>
      <citations>
         <citation type="bibtex">
         @misc{pope_dashnow_zobel_holt_raven_schultz_inouye_tomita_2014,
-        title={SRST2: ecyper wraps a standalone serotyping module for Escherichia coli. Supports fasta and fastq file formats.},
-        url={https://www.nml-lnm.gc.ca/},
-        author={National Microbiology Laboratory },
+        title={skesa: eSKESA is a de-novo sequence read assembler for cultured single isolate genomes
+    based on DeBruijn graphs. It uses conservative heuristics and is designed to
+    create breaks at repeat regions in the genome. This leads to excellent sequence
+    quality but not necessarily a large N50 statistic. It is a multi-threaded
+    application that scales well with the number of processors. For different runs
+    with the same inputs, including the order of reads, the order and orientation
+    of contigs in the output is deterministic. },
+        url={https://github.com/ncbi/ngs-tools/tree/master/tools/skesa/},
+        author={National Center for Biotechnology Information },
        }</citation>
     </citations>
 </tool>