--- a/skesa.xml	Thu Aug 16 14:05:56 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,100 +0,0 @@
-<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>