--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mykrobe_predict.xml	Sat Jan 13 09:02:31 2018 -0500
@@ -0,0 +1,117 @@
+<tool id="mykrobe_predict" name="mkyrobe predict" version="0.5.6" >
+  <description>Antibiotic resistance predictions</description>
+  <macros>
+    <import>macro.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <command detect_errors="exit_code">
+<![CDATA[
+         @select_inputs@
+
+         mykrobe predict 
+         '$name'
+         $select_species.species
+
+
+        #if $select_species.species =='tb':
+          --panel $select_species.panel
+        #end if
+
+
+
+        #if $kmer:
+          --kmer $kmer
+        #end if
+
+        #if $min_variant_conf:
+          --min_variant_conf $min_variant_conf
+        #end if
+
+
+        #if $expected_depth:
+          --expected_depth $expected_depth
+        #end if
+
+
+        #if $min_gene_conf:
+          --min_gene_conf $min_gene_conf
+        #end if
+
+
+
+        #if $min_gene_percent_covg_threshold:
+          --min_gene_percent_covg_threshold $min_gene_percent_covg_threshold
+        #end if
+
+
+        #if $min_depth:
+          --min_depth $min_depth
+        #end if
+
+
+        #if $expected_error_rate:
+          --expected_error_rate $expected_error_rate
+        #end if
+
+        $report_all_calls
+
+        $ont
+        -q
+        -t "\${GALAXY_SLOTS:-1}"
+
+        -1
+        #if $type == 'fastq':
+          *.fastq
+        #else
+          *.bam
+        #end if
+         > $json
+]]>
+  </command>
+  <inputs>
+    <expand macro="inputs" />
+    <conditional name="select_species">
+      <param name="species" type="select" label="Specify Species for AMR">
+        <option value="tb">Mycobacterium tuberculosis (tb)</option>
+        <option value="staph">Staphylococcus aureus (staph)</option>
+      </param>
+      <when value="staph"/>
+      <when value="tb">
+        <param name="panel" type="select" label="Select panel for TB only">
+          <option value="bradley-2015">Bradely 2015</option>
+          <option value="walker-2015">Walker 2015</option>            
+        </param>
+      </when>
+    </conditional>      
+    <param name="kmer" argument="--kmer" optional="True" type="integer" min="0" label="Kmer length" value="21" help="default = 21"/>
+    <param name="expected_error_rate" argument="--expected_error_rate" optional="True" type="float" label="Expected Error Rate"  help="Expected sequencing error rate. Set to 0.15 for ONT genotyping"/>
+    <param name="expected_depth" argument="--expected_depth" optional="True" type="integer" min="0" label="Expected Depth"  help=""/>
+    <param name="min_depth" argument="--min_depth" optional="True" type="integer" min="0" label="Minimum Depth"  help=""/>
+    <param name="report_all_calls" argument="--report_all_calls"  type="boolean" truevalue="--report_all_calls" falsevalue="" label="report all calls"  help=""/>
+    <param name="ont" argument="--ont"  type="boolean" truevalue="--ont" falsevalue="" label="Set default for ONT data"  help=""/>
+    <param name="min_variant_conf" argument="--min_variant_conf" optional="True" type="integer" min="0" label="Minimum genotype confidence for variant genotyping"  help=""/>      
+    <param name="min_gene_conf" argument="--min_gene_conf" optional="True" type="integer" min="0" label="minimum genotype confidence for gene genotyping"  help=""/>
+    <param name="min_gene_percent_covg_threshold" argument="--min_gene_percent_covg_threshold" optional="True" type="integer" min="0" label="Minimum Gene predict coverage"  help="all genes alleles found above this percent coverage will be reported (default 100 (only best allelesreported))"/>      
+  </inputs>
+
+  <outputs>
+    <data name="json" format="json" label="JSON prediction"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="type" value="single"/>
+      <param name="fastq_input1" value="reads.fastq"/>
+      <param name="species" value="tb"/>
+      <param name="panel" value="bradley-2015"/>
+      <output name="json">
+        <assert_contents>
+          <has_text_matching expression="variant_calls"/>
+        </assert_contents>
+      </output>
+    </test>
+  </tests>
+  <help>
+    @ATTRIBUTION@
+  </help>
+  <expand macro="citation" />
+</tool>