velvet_optimizer: add missing kmer_step to command (galaxyproject#4227)

* add kmer_step to command which was missing

also add argument to all inputs

* add validators for odd/even integer params

* add min/max for kmer parameters

same as in velveth

tools/velvet_optimiser/velvetoptimiser.xml

@@ -1,4 +1,4 @@
-<tool id="velvetoptimiser" name="VelvetOptimiser" version="2.2.6+galaxy1">
+<tool id="velvetoptimiser" name="VelvetOptimiser" version="2.2.6+galaxy2">
     <description>Automatically optimize Velvet assemblies</description>
     <xrefs>
         <xref type="bio.tools">velvetoptimiser</xref>
@@ -18,6 +18,7 @@
             -t "\${GALAXY_SLOTS:-1}"
             -s $start_kmer
             -e $end_kmer
+            -x $kmer_step
             -d out
             -f "
             #for $i in $files:
@@ -64,22 +65,26 @@
             #end for
             "
 
-            ##if str($advanced.advanced_select) == "advanced"
-                $advanced.verbose
-                -k '$advanced.optFuncKmer'
-                -c '$advanced.optFuncCov'
-                #if str($advanced.velvetg_opts) != ""
-                    -o '$advanced.velvetg_opts'
-                #end if
-                -m $advanced.minCutoff
-                -z $advanced.maxCutoff
-            ##end if
+            $advanced.verbose
+            -k '$advanced.optFuncKmer'
+            -c '$advanced.optFuncCov'
+            #if str($advanced.velvetg_opts) != ""
+                -o '$advanced.velvetg_opts'
+            #end if
+            -m $advanced.minCutoff
+            -z $advanced.maxCutoff
 
     ]]></command>
     <inputs>
-        <param name="start_kmer" type="integer" value="31" label="Start k-mer size" help="Odd integer, Lower limit of k-mer size range to search for optimum value" />
-        <param name="end_kmer" type="integer" value="191" label="End k-mer size" help="Odd integer, Upper limit of k-mer size range to search for optimum value" />
-        <param name="kmer_step" type="integer" value="2" label="K-mer search step size" help="Even integer, the k-mer value step size when searching the range" />
+        <param name="start_kmer" argument="-s" type="integer" value="31"  min="11" max="191" label="Start k-mer size" help="Odd integer, Lower limit of k-mer size range to search for optimum value">
+            <validator type="expression" message="Value needs to be odd">int(value) % 2 == 1</validator>
+        </param>
+        <param name="end_kmer" argument="-e" type="integer" value="191"  min="11" max="191" label="End k-mer size" help="Odd integer, Upper limit of k-mer size range to search for optimum value">
+            <validator type="expression" message="Value needs to be odd">int(value) % 2 == 1</validator>
+        </param>
+        <param name="kmer_step" argument="-x" type="integer" value="2"  min="2" max="189" label="K-mer search step size" help="Even integer, the k-mer value step size when searching the range">
+            <validator type="expression" message="Value needs to be even">int(value) % 2 == 0</validator>
+        </param>
 
         <repeat name="files" title="Input files" min="1">
             <param name="filetype" label="Input file type" type="select" help="Input file type">
@@ -111,12 +116,12 @@
         </repeat>
 
         <section name="advanced" title="Advanced Options" expanded="false">
-            <param name="verbose" type="boolean" checked="false" truevalue="-v" falsevalue="" label="Verbose" help="Include verbose velvet output in log file" />
-            <param name="optFuncKmer" type="text" value="n50" label="K-mer optimisation function" help="See help below for possibilities!"/>
-            <param name="optFuncCov" type="text" value="Lbp" label="Coverage cutoff optimisation function" help="See help below for possibilities!"/>
-            <param name="velvetg_opts" type="text" value="" label="Other velvetg options" help="Add any other required velvetg options from the advanced set"/>
-            <param name="minCutoff" type="integer" value="0" label="Minimum coverage cutoff" help="The minimum coverage cutoff to consider in the optimisation"/>
-            <param name="maxCutoff" type="float" value="0.8" label="Maximum coverage cutoff" help="The maximum coverage cutoff to consider expressed as a fraction of the calculated expected coverage."/>
+            <param name="verbose" argument="-v" type="boolean" checked="false" truevalue="-v" falsevalue="" label="Verbose" help="Include verbose velvet output in log file" />
+            <param name="optFuncKmer" argument="-k" type="text" value="n50" label="K-mer optimisation function" help="See help below for possibilities!"/>
+            <param name="optFuncCov" argument="-c" type="text" value="Lbp" label="Coverage cutoff optimisation function" help="See help below for possibilities!"/>
+            <param name="velvetg_opts" argument="-o" type="text" value="" label="Other velvetg options" help="Add any other required velvetg options from the advanced set"/>
+            <param name="minCutoff" argument="-m" type="integer" value="0" label="Minimum coverage cutoff" help="The minimum coverage cutoff to consider in the optimisation"/>
+            <param name="maxCutoff" argument="-z" type="float" value="0.8" label="Maximum coverage cutoff" help="The maximum coverage cutoff to consider expressed as a fraction of the calculated expected coverage."/>
         </section>
     </inputs>
 
@@ -239,10 +244,12 @@
 
       The hash length, also known as k-mer length, corresponds to the length, in base pairs, of the words being hashed.
 
-      The hash length is the length of the k-mers being entered in the hash table. Firstly, you must observe three technical constraints::
-        - it must be an odd number, to avoid palindromes. If you put in an even number, Velvet will just decrement it and proceed.
-        - it must be below or equal to MAXKMERHASH length (cf. 2.3.3, by default 31bp), because it is stored on 64 bits
-        - it must be strictly inferior to read length, otherwise you simply will not observe any overlaps between reads, for obvious reasons.
+      The hash length is the length of the k-mers being entered in the hash table. Firstly, you must observe three technical constraints:
+
+      - it must be an odd number, to avoid palindromes. If you put in an even number, Velvet will just decrement it and proceed.
+      - it must be below or equal to MAXKMERHASH length (cf. 2.3.3, by default 31bp), because it is stored on 64 bits
+      - it must be strictly inferior to read length, otherwise you simply will not observe any overlaps between reads, for obvious reasons.
+
 
       Now you still have quite a lot of possibilities. As is often the case, it's a trade-off between specificity and sensitivity. Longer kmers bring you more specificity (i.e. less spurious overlaps) but lowers coverage (cf. below)... so there's a sweet spot to be found with time and experience.
       We like to think in terms of "k-mer coverage", i.e. how many times has a k-mer been seen among the reads. The relation between k-mer coverage Ck and standard (nucleotide-wise) coverage C is Ck = C * (L - k + 1)/L where k is your hash length, and L you read length.
@@ -277,21 +284,15 @@
       Velvet works mainly with fasta and fastq formats. For paired-end reads, the assumption is that each read is next to its mate
       read. In other words, if the reads are indexed from 0, then reads 0 and 1 are paired, 2 and 3, 4 and 5, etc.
 
-      Supported file formats are::
-
-          fasta
-          fastq
-          bam
-
-      Read categories are::
-
-          short (default)
-          shortPaired
-          long (for Sanger, 454 or even reference sequences)
-          longPaired
-          reference (for pre-mapped sam or bam files - see Velvet manual for details on how to use this option)
-
+      Supported file formats are: fasta, fastq, bam
 
+      Read categories are: 
+      
+      - short (default)
+      - shortPaired
+      - long (for Sanger, 454 or even reference sequences)
+      - longPaired
+      - reference (for pre-mapped sam or bam files - see Velvet manual for details on how to use this option)
     ]]></help>
     <citations>
         <citation type="bibtex">@UNPUBLISHED{GLADMAN2012,