diff kat_sect.xml @ 1:ab2cf85b9ae8 draft

planemo upload commit f86fb54b98f0dbed260735675219e64882f08efe

--- a/kat_sect.xml	Mon Feb 06 12:36:09 2017 -0500
+++ b/kat_sect.xml	Mon Mar 13 15:36:43 2017 -0400
@@ -1,14 +1,16 @@
-<tool id="kat_sect" name="KAT Sect" version="1.3.0">
-  <description> SEquence Coverage estimator Tool. Estimates the coverage of each sequence in a file using K-mers from another sequence file.</description>
-  <requirements>
-    <requirement type="package" version="2.3.1">kat</requirement>
-  </requirements>
-  <stdio>
-    <exit_code range="1:" />
-  </stdio>
+<?xml version='1.0' encoding='utf-8'?>
+<tool id="kat_@EXECUTABLE@" name="KAT @EXECUTABLE@" version="@VERSION@.1">
+  <description> Estimates the coverage of each sequence in a file using K-mers from another sequence file(s).</description>
+  <macros>
+    <token name="@EXECUTABLE@">sect</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <expand macro="stdio" />
+  <expand macro="version_command" />
   <command><![CDATA[
 
-  ln "$db" db.fasta &&
+  cp "$db" db.fasta &&
   #if $single_or_paired.type == "single"
     ln "$input_se" "$single_or_paired.input_se.element_identifier".fastq && 
     kat sect 'db.fasta'
@@ -22,45 +24,46 @@
     kat sect 'db.fasta'
     "$single_or_paired.fastq_collection.forward.name"_1.fastq "$single_or_paired.fastq_collection.forward.name"_2.fastq
   #end if  
-  --threads \${GALAXY_SLOTS:-4}
-  -o reads
+
+  @THREADS@
+  
+  $keep_counts
+  
+  -o results
   
   ]]></command>
   <inputs>
-    <conditional name="single_or_paired">
-      <param name="type" type="select" label="Read type">
-        <option value="single">Single-end</option>
-        <option value="paired">Paired-end</option>
-        <option value="collection">Collection Paired-end</option>
-      </param>
-      <when value="single">
-        <param name="input_se" type="data" format="fastqsanger" label="Single end read file(s)"/>
-      </when>
-      <when value="paired">
-        <param name="forward_pe" type="data" format="fastqsanger" label="Forward paired-end read file"/>
-        <param name="reverse_pe" type="data" format="fastqsanger" label="Reverse paired-end read file"/>
-      </when>
-      <when value="collection">
-        <param name="fastq_collection" type="data_collection" label="Paired-end reads collection" optional="false" format="fastqsanger" collection_type="paired" />
-      </when>
-    </conditional>
+    <expand macro="macro_input" />
+
     <param name="db" type="data" format="fasta" label="Fasta file of targeted regions"/>
+    <expand macro="macro_kmers" />
+    <param name="keep_counts" type="boolean" falsevalue='--no_count_stats' truevalue='' checked='False' label="Fasta Count File" help="Produce a fasta style representation of the input sequence file containing K-mer coverage counts mapped across each sequence"/>
   </inputs>
   <outputs>
-    <data format="tabular" name="reads" label='Reads' from_work_dir="reads-stats.tsv" />
+    <data format="tabular" name="stats" label='Stats' from_work_dir="results-stats.tsv" />
+    <data format="txt" name="counts" label='Counts' from_work_dir="results-counts.cvg">
+      <filter>keep_counts</filter>
+    </data>
   </outputs>
   <tests>
     <test>
-      <param name="input" value="input.fastq" />
+      <param name="input_se" value="input.fastq" />
       <param name="db" value="db.fasta" />
-      <output file="matched.fastq" ftype="fastqsanger" name="reads" />
+      <param name="keep_counts" value="False" />
+      <output file="kat-sect-stats.tsv" name="stats" />
     </test>
+    <test>
+      <param name="input_se" value="input.fastq" />
+      <param name="db" value="db.fasta" />
+      <param name="keep_counts" value="True" />
+      <output file="kat-sect-stats.tsv" name="stats" />
+      <output file="kat-sect-counts.cvg" name="counts" />
+    </test>    
   </tests>
   <help><![CDATA[
-http://kat.readthedocs.io/en/latest/using.html#filtering-tools
+  https://kat.readthedocs.io/en/latest/using.html#sect
 ]]>
   
   </help>
-  <citations>
-  </citations>
+  <expand macro="citations" />
 </tool>