# HG changeset patch
# User estrain
# Date 1534443094 14400
# Node ID 1581b4e8d9938559358f6c7db6fcc66c48742f9a
# Parent  a28a417429900dc0b86ac95da2768ebd5392c14d
Uploaded

diff -r a28a41742990 -r 1581b4e8d993 skesa.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/skesa.xml	Thu Aug 16 14:11:34 2018 -0400
@@ -0,0 +1,100 @@
+<tool id="skesa" name="skesa" version="0.1">
+    <requirements>
+      <requirement type="package" version="2.2">skesa</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+    #if $jobtype.select != "cl"
+	skesa
+      #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
+      #else if $jobtype.select == "rp"
+	--fastq $pairedf.forward,$pairedf.reverse --use_paired_ends
+      #end if
+      #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 (Separate Files)</option>
+          <option value="rp">Paired-End Reads (Paired Data Set)</option>
+          <option value="cl">Collection of Reads</option>
+        </param>
+        <when value="asm">
+          <param name="draft" type="data" format="fasta" label="FASTA" />
+        </when>
+        <when value="se">
+          <param name="fastq1" type="data" format="fastq" label="FASTQ" />
+        </when>
+        <when value="pe">
+          <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>
+         <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>
+      </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" />
+      <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>
+            <data format="fasta" label="skesa Results" name="${input.name}.skesa.fasta" from_work_dir="*.fasta"/>
+    </outputs>
+
+    <help><![CDATA[
+    
+**Usage: skesa**
+
+**INPUT**
+
+A fasta assembly or single or paired end reads test or data set list of fastqs
+
+**Memory available**
+
+--memory arg (=32)         Memory available (GB) [integer]
+     
+
+**Number of cores**
+
+--cores arg (=0)           Number of cores to use (default all) [integer]
+
+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={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>