Updated FASTK tool wrapper

tools/fastk/fastk.xml

@@ -6,28 +6,14 @@
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
         mkdir -p outfiles/tmpfiles && 
-        #if $infile.ext == "fasta":
-            ln -s '$infile' ./input.fasta &&
-            #set INPUTFILE="input.fasta"
-        #elif $infile.ext == "fasta.gz":
-            ln -s '$infile' ./input.fasta.gz &&
-            #set INPUTFILE="input.fasta.gz"
-        #elif $infile.is_of_type("fastq"):
-            ln -s '$infile' ./input.fastq &&
+        #if $infile.is_of_type("fastq"):
             #set INPUTFILE="input.fastq"
         #elif $infile.is_of_type("fastq.gz"):
-            ln -s '$infile' ./input.fastq.gz &&
             #set INPUTFILE="input.fastq.gz"
-        #elif $infile.ext == "cram":
-            ln -s '$infile' ./input.cram &&
-            #set INPUTFILE="input.cram"
-        #elif $infile.is_of_type("unsorted.bam"):
-            ln -s '$infile' ./input.bam &&
-            #set INPUTFILE="input.bam"
-        #elif $infile.ext == "sam":
-            ln -s '$infile' ./input.sam &&
-            #set INPUTFILE="input.sam"
-        #end if 
+        #else
+            #set INPUTFILE="input."+$infile.ext
+        #end if
+        ln -s '$infile' $INPUTFILE && 
         FastK $INPUTFILE 
         -k$kmer_size 
         #if $sorted_table.sorted_table_option == 'yes_with_default':
@@ -45,7 +31,7 @@
     ]]></command>
     <inputs>
         <param name="infile" type="data" format="fasta,fasta.gz,fastq,fastq.gz,cram,unsorted.bam,sam" label="Input file"/>   
-        <param name="kmer_size" type="integer" min="5" max="50" value="40" label="Enter desired k-mer size" help="Default: 40" />
+        <param name="kmer_size" argument="-k" type="integer" min="5" max="50" value="40" label="Enter desired k-mer size" help="Default: 40" />
         <conditional name="sorted_table">
             <param name="sorted_table_option" type="select" label="Sort table" help="Do you want a sorted table of all canonical k-mers and their counts? The sorted table is sorted lexicographically on the k-mer where a &lt; c &lt; g &lt; t.">
                 <option value="no">No</option>
@@ -66,7 +52,7 @@
         <data name="fastk_out" format="tar" from_work_dir="fastk.tar" label="${tool.name} on ${on_string}: FastK files"/>
         <data name="fastk_hist_out" format="fastk_hist" from_work_dir="outfiles/output.hist" label="${tool.name} on ${on_string}: FastK hist" />
         <data name="tabex_hist" format="txt"  label="${tool.name} on ${on_string}: Tabex output">
-            <filter> ( sorted_table['sorted_table_option'] == 'yes_with_default' or sorted_table['sorted_table_option'] == 'yes_with_custom' )</filter>
+            <filter> sorted_table['sorted_table_option'] != 'no' </filter>
         </data>
     </outputs>
     <tests>
@@ -111,13 +97,18 @@
     </tests>
     <help><![CDATA[
         FastK is a k‑mer counter that is optimized for processing high quality DNA assembly data sets such as those produced with an Illumina instrument or a PacBio run in HiFi mode.
+
+        The input data can be in CRAM, BAM, SAM, fasta, or fastq files.
 
-        FastK can produce the following outputs:
+        FastK produces the following outputs:
+
+        1. A .hist file in binary format containing histogram information detailing the frequency of occurrence for each k‑mer within the dataset.
+
+        2. A Tabex txt file comprising a table of k‑mer/count pairs, sorted lexicographically on the k‑mer sequence, followingthe order a < c < g < t
+
+        3. A tar file comprising of hidden .ktab files that can be used for downstream FASTK tools.
+
 
-        1. a histogram of the frequency with which each k‑mer in the data set occurs.
-        2. a table of k‑mer/count pairs sorted lexicographically on the k‑mer where a < c < g < t.
-        3. a k‑mer count profile of every sequence in the data set. A profile is the sequence of counts of the n-(k-1) consecutive k‑mers of a sequence of length n.
-        4. a relative profile of every sequence in the data set against a FastK table produced for another data set.
     ]]></help>
     <expand macro="citations"/>
 </tool>