--- a/macro.xml	Tue Aug 10 11:29:58 2021 +0000
+++ b/macro.xml	Thu Aug 26 20:38:36 2021 +0000
@@ -1,121 +1,102 @@
-<?xml version="1.1"?>
 <macros>
-  <token name="@TOOL_VERSION@">0.10.0</token>
-  <xml name="requirements">
-    <requirements>
-      <requirement type="package" version="@TOOL_VERSION@">mykrobe</requirement>
-    </requirements>    
-  </xml>
-  <token name="@select_inputs@">
-    <![CDATA[
-         #set $name='sample'
-    ]]>
-  </token>
-
-  <token name="@shared_options@">
-    <![CDATA[
-        #if $kmer:
-          --kmer '${kmer}'
-        #end if
-        #if $expected_depth:
-          --expected_depth '${expected_depth}'
-        #end if
-
-        $ont
-
-        $report_all_calls
+    <token name="@TOOL_VERSION@">0.10.0</token>
+    <token name="@PROFILE@">20.09</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">mykrobe</requirement>
+      </requirements>
+    </xml>
 
-        #if $expected_error_rate:
-          --expected_error_rate '${expected_error_rate}'
-        #end if
-
-        #if $min_variant_conf:
-          --min_variant_conf '${min_variant_conf}'
-        #end if
-
-        #if $min_gene_conf:
-          --min_gene_conf '${min_gene_conf}'
-        #end if
-
-        #if $min_proportion_expected_depth:
-          --min_proportion_expected_depth '${min_proportion_expected_depth}'
-        #end if
-
-        #if $min_gene_percent_covg_threshold:
-          --min_gene_percent_covg_threshold  '${min_gene_percent_covg_threshold}'
-        #end if
-
-        $guess_sequence_method
-
-        $ignore_minor_calls
-
-        #if $ignore_filtered:
-          --ignore_filtered '${ignore_filtered}'
-        #end if
-
-        #if $model:
-          --model '${model}'
-        #end if
+    <token name="@shared_options@">
+        <![CDATA[
+            #if $kmer:
+                --kmer ${kmer}
+            #end if
+            #if $expected_depth:
+                --expected_depth ${expected_depth}
+            #end if
+            $ont
+            $report_all_calls
+            #if $expected_error_rate:
+                --expected_error_rate ${expected_error_rate}
+            #end if
+            #if $min_variant_conf:
+                --min_variant_conf ${min_variant_conf}
+            #end if
+            #if $min_gene_conf:
+                --min_gene_conf ${min_gene_conf}
+            #end if
+            #if $min_proportion_expected_depth:
+                --min_proportion_expected_depth ${min_proportion_expected_depth}
+            #end if
+            #if $min_gene_percent_covg_threshold:
+                --min_gene_percent_covg_threshold  ${min_gene_percent_covg_threshold}
+            #end if
+            $guess_sequence_method
+            $ignore_minor_calls
+            #if $ignore_filtered:
+                --ignore_filtered '${ignore_filtered}'
+            #end if
+            #if $model:
+                --model '${model}'
+            #end if
+            #if $ploidy:
+                --ploidy '${ploidy}'
+            #end if
+        ]]>
+    </token>
 
-        #if $ploidy:
-          --ploidy '${ploidy}'
-        #end if
-    ]]>
-  </token>
-
-  <xml name="inputs">
-    <conditional name="data_type">
-      <param name="type" type="select" label="Specify the read type.">
-        <option value="single">Single-end Data</option>
-        <option value="paired">Paired-end Data</option>
-        <option value="collection">Collection Paired-end Data</option>
-      </param>
-      <when value="single">
-        <param name="seq1" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz,fasta,fasta.gz,bam" label="Single end read file(s)"/>
-      </when>
-      <when value="paired">
-        <param name="seq1" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" label="Forward paired-end read file"/>
-        <param name="seq2" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" label="Reverse paired-end read file"/>
-      </when>
-      <when value="collection">
-        <param name="collection1" type="data_collection" label="Paired-end reads collection" optional="false" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" collection_type="paired" />
-      </when>
-    </conditional>
-  </xml>
+    <xml name="inputs">
+        <conditional name="data_type">
+            <param name="type" type="select" label="Specify the read type.">
+                <option value="single">Single-end Data</option>
+                <option value="paired">Paired-end Data</option>
+                <option value="collection">Collection Paired-end Data</option>
+            </param>
+            <when value="single">
+                <param name="seq1" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz,fasta,fasta.gz,bam" label="Single end read file(s)"/>
+            </when>
+            <when value="paired">
+                <param name="seq1" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" label="Forward paired-end read file"/>
+                <param name="seq2" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" label="Reverse paired-end read file"/>
+            </when>
+            <when value="collection">
+                <param name="collection1" type="data_collection" label="Paired-end reads collection" optional="false" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" collection_type="paired" />
+            </when>
+        </conditional>
+    </xml>
 
-  <xml name="options">
-    <param argument="--kmer" optional="True" type="integer" min="0" label="Kmer length" value="21" help="default = 21"/>
-    <param 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 argument="--expected_depth" optional="True" type="integer" min="0" label="Expected depth"  help=""/>
-    <param argument="--ont" type="boolean" truevalue="--ont" falsevalue="" label="Set default for ONT data"  help=""/>
-    <param argument="--min_variant_conf" optional="True" type="integer" min="0" label="Minimum genotype confidence for variant genotyping"  help=""/>      
-    <param argument="--min_gene_conf" optional="True" type="integer" min="0" label="Minimum genotype confidence for gene genotyping"  help=""/>
-    <param 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 alleles reported))"/>      
-    <param argument="--min_proportion_expected_depth" optional="True" type="float" label="Minimum depth required on the sum of both alleles" help="Default 0.3 (30%)"/>
-    <param argument="--model" optional="True" type="data" format="txt" label="Genotype model used" help="default kmer_count. Options kmer_count, median_depth"/>
-    <param argument="--ploidy" optional="True" type="select" label="Diploid or Haploid" help="Use a diploid (includes 0/1 calls) or haploid genotyping model">
-      <option value="diploid">diploid</option>
-      <option value="haploid">haploid</option>
-    </param>
-    <param argument="--report_all_calls" type="boolean" truevalue="--report_all_calls" falsevalue="" label="Report all calls"  help=""/>
-    <param argument="--ignore_minor_calls" type="boolean" truevalue="--ignore_minor_calls" falsevalue="" label="Ignore minor calls"  help="Ignore minor calls when running resistance prediction"/>
-    <param argument="--ignore_filtered" type="data" format="txt" label="Ignore filtered" optional="True" help="Don't include filtered genotypes"/>
-    <param argument="--guess_sequence_method" type="boolean" truevalue="--guess_sequence_method" falsevalue="" label="Guess sequence method"  help="Guess if ONT or Illumia based on error rate. If error rate is > 10%, ploidy is set to haploid and a confidence threshold is used"/>
-  </xml>
+    <xml name="options">
+        <param argument="--kmer" optional="True" type="integer" min="0" label="Kmer length" value="21" help="default = 21"/>
+        <param 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 argument="--expected_depth" optional="True" type="integer" min="0" label="Expected depth"  help=""/>
+        <param argument="--ont" type="boolean" truevalue="--ont" falsevalue="" label="Set default for ONT data"  help=""/>
+        <param argument="--min_variant_conf" optional="True" type="integer" min="0" label="Minimum genotype confidence for variant genotyping"  help=""/>
+        <param argument="--min_gene_conf" optional="True" type="integer" min="0" label="Minimum genotype confidence for gene genotyping"  help=""/>
+        <param 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 alleles reported))"/>
+        <param argument="--min_proportion_expected_depth" optional="True" type="float" label="Minimum depth required on the sum of both alleles" help="Default 0.3 (30%)"/>
+        <param argument="--model" optional="True" type="data" format="txt" label="Genotype model used" help="default kmer_count. Options kmer_count, median_depth"/>
+        <param argument="--ploidy" optional="True" type="select" label="Diploid or Haploid" help="Use a diploid (includes 0/1 calls) or haploid genotyping model">
+            <option value="diploid">diploid</option>
+            <option value="haploid">haploid</option>
+        </param>
+        <param argument="--report_all_calls" type="boolean" truevalue="--report_all_calls" falsevalue="" label="Report all calls"  help=""/>
+        <param argument="--ignore_minor_calls" type="boolean" truevalue="--ignore_minor_calls" falsevalue="" label="Ignore minor calls"  help="Ignore minor calls when running resistance prediction"/>
+        <param argument="--ignore_filtered" type="data" format="txt" label="Ignore filtered" optional="True" help="Don't include filtered genotypes"/>
+        <param argument="--guess_sequence_method" type="boolean" truevalue="--guess_sequence_method" falsevalue="" label="Guess sequence method"  help="Guess if ONT or Illumia based on error rate. If error rate is > 10%, ploidy is set to haploid and a confidence threshold is used"/>
+    </xml>
 
-  <token name="@ATTRIBUTION@">
-    <![CDATA[
-             
-             **MyKrobe predict - Antibiotic resistance predictions**
-             
-             Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis
-             using Bruijn graph.
-    ]]>      
-  </token>
+    <token name="@ATTRIBUTION@">
+        <![CDATA[
+            **MyKrobe predict - Antibiotic resistance predictions**
+            Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis
+            using Bruijn graph.
+        ]]>
+    </token>
 
-  <xml name="citation">
-    <citations>
-      <citation type="doi">10.1038/ncomms10063</citation>
-    </citations>
-  </xml>
+    <xml name="citation">
+        <citations>
+            <citation type="doi">10.1038/ncomms10063</citation>
+        </citations>
+    </xml>
 </macros>