diff tools/mentalist_call/mentalist_call.xml @ 1:c6a98b93e569 draft

planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 83ebe793451a5ccbfeff873eda359f699e14ae1e

--- a/tools/mentalist_call/mentalist_call.xml	Wed Dec 20 17:36:03 2017 -0500
+++ b/tools/mentalist_call/mentalist_call.xml	Sat Mar 24 23:12:21 2018 -0400
@@ -1,16 +1,23 @@
-<tool id="mentalist_call" name="MentaLiST MLST Analysis" version="0.1.3">
+<tool id="mentalist_call" name="MentaLiST MLST Analysis" version="0.2.2">
   <requirements>
-    <requirement type="package" version="0.1.3">mentalist</requirement>
+    <requirement type="package" version="0.2.2">mentalist</requirement>
   </requirements>
+  <edam_operations>
+    <edam_operation>operation_3840</edam_operation>
+  </edam_operations>
   <command detect_errors="exit_code"><![CDATA[
     mentalist
     call
     -o '$output_file'
     --db '$kmer_db.fields.path'
+    --mutation_threshold '$mutation_threshold'
+    --kt '$kmer_threshold'
+    $output_votes
+    $output_special
     #if $input_type.sPaired == "paired":
-       -s $input_type.pInput1.name $input_type.pInput1 $input_type.pInput2
+       -s $input_type.pInput1.name -1 $input_type.pInput1 -2 $input_type.pInput2
     #elif $input_type.sPaired == "collections":
-       -s $input_type.fastq_collection.name $input_type.fastq_collection.forward $input_type.fastq_collection.reverse
+       -s $input_type.fastq_collection.name -1 $input_type.fastq_collection.forward -2 $input_type.fastq_collection.reverse
     #end if
   ]]></command>
   <inputs>
@@ -32,13 +39,27 @@
 	<validator type="no_options" message="No MentaLiST databases are available" />
       </options>
     </param>
+    <param name="mutation_threshold" type="integer" label="Mutation threshold"
+	   help="Maximum number of mutations when looking for novel alleles."
+	   value="6" min="1" max="25" />
+    <param name="kmer_threshold" type="integer" label="Kmer threshold"
+	   help="Minimum number of times a kmer is seen to be considered present in the sample."
+	   value="10" min="1" max="25" />
+    <param name="output_votes" type="boolean" label="Output votes"
+	   argument="--output_votes" truevalue="--output_votes" falsevalue=""
+	   help="Outputs the results for the original voting algorithm" />
+    <param name="output_special" type="boolean" label="Output special"
+	   argument="--output_special" truevalue="--output_special" falsevalue=""
+	   help="Outputs a fasta file with the alleles from special cases such as incomplete coverage, novel and multiple alleles." />
   </inputs>
   <outputs>
-    <data name="output_file" format="tabular"/>
+    <data name="output_file" format="tabular" />
+    <data name="coverage_file" format="tabular" />
   </outputs>
   <help><![CDATA[
   ]]></help>
   <citations>
     <citation type="doi">10.1101/172858</citation>
+    <citation type="doi">10.1099/mgen.0.000146</citation>
   </citations>
 </tool>