# HG changeset patch
# User estrain
# Date 1539637933 14400
# Node ID 9448df7c25a0055b4b11ef31c52ce880af86a032
# Parent  8bafd3d18864eb1253d30d9dab64ce791d17eb41
Uploaded

diff -r 8bafd3d18864 -r 9448df7c25a0 skesa.xml
--- a/skesa.xml	Mon Sep 17 06:49:22 2018 -0400
+++ b/skesa.xml	Mon Oct 15 17:12:13 2018 -0400
@@ -1,77 +1,136 @@
-<tool id="skesa" name="skesa" version="0.1">
+<tool id="skesa" name="skesa" version="0.23">
     <requirements>
-      <requirement type="package" version="2.2">skesa</requirement>
+      <requirement type="package" version="2.3.0">skesa</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-   
-	skesa
-      #if $jobtype.select == "asm"
-        --fasta $draft
-      #else if $jobtype.select == "se"
-        --fastq $fastq
-      #else if $jobtype.select == "cl"
-        #set forward=$jobtype.coll.forward
-        #set reverse=$jobtype.coll.reverse
-	    --fastq $forward,$reverse --use_paired_ends
-      #else if $jobtype.select == "pe"
-	    --fastq $forward,$reverse --use_paired_ends
+
+      skesa
+
+      #if $jobtype.select == "fasta_single"
+        #set outname = $jobtype.fasta.name
+        --fasta $jobtype.fasta 
+      #else if $jobtype.select == "fastq_single"
+        #set outname = $jobtype.fastq1.name
+        --fastq $jobtype.fastq1 
+      #else if $jobtype.select == "fastq_fr"
+        #set outname = $jobtype.fastq1.name
+        --fastq $jobtype.fastq1 --fastq $jobtype.fastq2
+      #else if $jobtype.select == "fastq_pair"
+        #set outname = $jobtype.coll.name
+        --fastq $jobtype.coll.forward --fastq $jobtype.coll.reverse
+      #end if
 
+      #if $options.select=="advanced"
+        #if $options.cores
+          --cores $options.cores
+        #end if
+        #if $options.memory
+          --memory $options.memory
+        #end if
+        #if $options.hash_count
+          --hash_count
+        #end if
+        #if $options.estimated_kmers
+          --estimated_kmers $options.estimated.kmers
+        #end if
+        #if $options.skip
+         --skip_bloom_filter
+        #end if
+        #if $options.kmer
+         --kmer $options.kmer 
+        #end if
+        #if $options.min_count
+         --min_count $options.min_count 
+        #end if
+        #if $options.max_kmer_count
+         --max_kmer_count $options.max_kmer_count 
+        #end if
+        #if $options.vector_percent
+         --vector_percent $options.vector_percent 
+        #end if
+        #if $options.insert_size
+         --insert_size $options.insert.size 
+        #end if
+        #if $options.steps
+         --steps $options.steps 
+        #end if
+        #if $options.fraction
+         --fraction $options.fraction 
+        #end if
+        #if $options.max_snp_len
+         --max_snp_len $options.max_snp_len 
+        #end if
+        #if $options.min_contig
+         --min_contig $options.min_contig 
+        #end if
+        #if $options.allow_snps
+         --allow_snps 
+        #end if
+      #else if $options.select =="basic"
+        --cores \${GALAXY_SLOTS:-4} 
+        --memory 16
       #end if
-      #if $cores != 0
-      --cores $cores
-      #end if
-      --memory $memory	> results.skesa.fasta
-   
+
+      > ${outname}.fasta 
 
     ]]></command>
     <inputs>
       <conditional name="jobtype">
-        <param name="select" type="select" label="Assembly or FASTQ Reads?">
-          <option value="asm">Genome Assembly</option>
-          <option value="se">Single-End Reads</option>
-          <option value="pe">Paired-End Reads (Separate Files)</option>
-          <option value="cl">Paired collection from your history</option>
+        <param name="select" type="select" label="Select Input">
+          <option value="fasta_single">Single FASTA</option>
+          <option value="fastq_single">Single FASTQ</option>
+          <option value="fastq_fr">Forward and Reverse FASTQ</option>
+          <option value="fastq_pair">Paired FASTQ Collection</option>
         </param>
-        <when value="asm">
-          <param name="draft" type="data" format="fasta" label="FASTA" />
+        <when value="fasta_single">
+          <param name="fasta" type="data" format="fasta" label="FASTA" />
         </when>
-        <when value="se">
-          <param name="fastq" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" label="FASTQ" />
+        <when value="fastq_single">
+          <param name="fastq1" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" label="FASTQ" />
         </when>
-        <when value="cl">
-          <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" collection_type="paired" />
+        <when value="fastq_fr">
+          <param name="fastq1" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" label="Forward FASTQ" />
+          <param name="fastq2" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" label="Reverse FASTQ" />
         </when>
-        <when value="pe">
-          <param name="forward" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" label="FASTQ" />
-          <param name="reverse" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" label="FASTQ" />
+        <when value="fastq_pair">
+          <param name="coll" label="Paired FASTQ" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" collection_type="paired" />
         </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" />
-     
+  
+      <conditional name="options">
+        <param name="select" type="select" label="Options Type">
+          <option value="basic">Basic</option>
+          <option value="advanced">Advanced</option>
+        </param>
+        <when value="advanced">
+          <param name="cores" type="integer" label="Number of cores to use" value="1"/>
+          <param name="memory" type="integer" label="Memory available (GB, only for sorted counter)" value="16"/>
+          <param name="hash_count" type="boolean" label="hash counter"/>
+          <param name="estimated_kmers" type="integer" label="Estimated number of unique kmers for bloom filter" value="100"/>
+          <param name="skip" type="boolean" label="skip bloom filter, use estimate kmers as the hash"/>
+          <param name="kmer" type="integer" label="Minimal kmer length for assembly" value="21"/>
+          <param name="min_count" type="integer" label="Minimal count for kmers retained for comparing alternate choices" value=""/>
+          <param name="max_kmer_count" type="integer" label="Minimum acceptable average count for estimating the maximal kmer length in reads" value=""/>
+          <param name="vector_percent" type="float" label="Count for  vectors as a fraction of the read number (1=disabled)" value="1">
+            <validator type="in_range" message="Must be float(0,1)." min="0" max="1"/>
+          </param>
+          <param name="insert_size" type="integer" label="Expected insert size for paired reads (if not provided, it will be estimated)" value=""/>
+          <param name="steps" type="integer" label="Number of assembly iterations from minimal to maximal kmer length in reads" value="11"/>
+          <param name="fraction" type="float" label="Maximum noise to signal ratio acceptable for extension" value="0.1">
+            <validator type="in_range" message="Must be float(0,1)." min="0" max="1"/>
+          </param>
+          <param name="max_snp_len" type="integer" label="Maximal snp length" value="150"/>
+          <param name="min_contig" type="integer" label="Minimal contig length reported in output" value="200"/>
+          <param name="allow_snps" type="boolean" label="Turn SNP discovery" value="false"/>
+        </when>
+        <when value="basic"/>
+      </conditional>
     </inputs>
     <outputs>
-            <data format="fasta" label="skesa Results" name="${input.name}.skesa.fasta" from_work_dir="*.fasta"/>
+      <data format="fasta" name="results.skesa.fasta" label="${tool.name} on ${on_string}: Contigs" 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>