changeset 3:4a9da2b6c2e3 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ commit fed92935f1f0b52173d2fddbdd2bbf44e802b51e"

--- a/kraken2.xml	Wed May 08 08:23:47 2019 -0400
+++ b/kraken2.xml	Mon Nov 23 20:50:12 2020 +0000
@@ -35,9 +35,7 @@
             --threads \${GALAXY_SLOTS:-1}
             --db '${kraken2_database.fields.path}'
 
-            #if $quick:
-                --quick
-            #end if
+            $quick
 
             #if $single_paired.single_paired_selector == "yes"
                 --paired 
@@ -63,19 +61,15 @@
 
             --confidence '${confidence}'
             --minimum-base-quality '${min_base_quality}'
+            --minimum-hit-groups '${minimum_hit_groups}'
 
-            #if $use_names:
-                --use-names
-            #end if
+            $use_names
 
             #if $report.create_report:
                 --report '${report_output}'
-                #if $report.use_mpa_style:
-                    --use-mpa-style
-                #end if
-                #if $report.report_zero_counts:
-                    --report-zero-counts
-                #end if
+                $report.use_mpa_style
+                $report.report_zero_counts:
+                $report.report_minimizer_data:
             #end if
 
             > '${output}'
@@ -98,18 +92,18 @@
                 <param format="@INTYPES@" label="Input sequences" name="input_sequences" type="data"/>
             </when>
         </conditional>
-        <param name="use_names" type="boolean" label="Print scientific names instead of just taxids"/>
-        <param name="confidence"  type="float" label="Confidence" value="0.0" help="Confidence score threshold. Must be in [0, 1]">
-            <validator type="in_range" min="0.0" max="1.0" message="Confidence score threshold should be between 0 and 1" />
-        </param>
-        <param name="min_base_quality" type="integer" label="Minimum Base Quality" value="0" help="Minimum base quality used in classification (only effective with FASTQ input)"/>
-        <param name="quick" type="boolean" label="Enable quick operation" help="Quick operation (use first hit)"/>
+        <param argument="--use-names" type="boolean" truevalue="--use-names" falsevalue="" label="Print scientific names instead of just taxids"/>
+        <param argument="--confidence" type="float" label="Confidence" value="0.0" min="0" max="1" help="Confidence score threshold. Must be in [0, 1]"/>
+        <param argument="--minimum-base-quality" name="min_base_quality" type="integer" label="Minimum Base Quality" value="0" help="Minimum base quality used in classification (only effective with FASTQ input)"/>
+        <param argument="--minimum-hit-groups" type="integer" label="Minimum hit goups" value="2" help="Number of overlapping k-mers sharing the same minimizer needed to make a call" />
+        <param argument="--quick" type="boolean" truevalue="--quick" falsevalue="" label="Enable quick operation" help="Quick operation (use first hit)"/>
         <param name="split_reads" type="boolean" label="Split classified and unclassified outputs?" help="Sets --unclassified-out and --classified-out"/>
 
         <section name="report" title="Create Report" expanded="false">
-            <param name="create_report" type="boolean"  label="Print a report with aggregrate counts/clade to file" help="--report" optional="true"/>
-            <param name="use_mpa_style" type="boolean" label="Format report output like Kraken 1's kraken-mpa-report" help="--use-mpa-style" optional="true"/>
-            <param name="report_zero_counts" type="boolean" label="Report counts for ALL taxa, even if counts are zero" help="--report-zero-counts" optional="true"/>
+            <param name="create_report" type="boolean"  label="Print a report with aggregrate counts/clade to file" help="--report" />
+            <param argument="--use-mpa-style" type="boolean" truevalue="--use-mpa-style" falsevalue="" label="Format report output like Kraken 1's kraken-mpa-report" />
+            <param argument="--report-zero-counts" type="boolean" truevalue="--report-zero-counts" falsevalue="" label="Report counts for ALL taxa, even if counts are zero" />
+            <param argument="--report-minimizer-data" type="boolean" truevalue="--report-minimizer-data" falsevalue="" label="Report minimizer data" help="Report minimizer and distinct minimizer count information in addition to normal Kraken report" />
         </section>
 
         <expand macro="input_database"/>  

--- a/macros.xml	Wed May 08 08:23:47 2019 -0400
+++ b/macros.xml	Mon Nov 23 20:50:12 2020 +0000
@@ -1,9 +1,7 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">2.0.8_beta</token>
-    <token name="@INTYPES@">
-        fasta,fastq,fasta.gz,fasta.bz2,fastq.gz,fastq.bz2,fastqsanger
-    </token>
+    <token name="@TOOL_VERSION@">2.1.1</token>
+    <token name="@INTYPES@">fasta,fastq,fasta.gz,fasta.bz2,fastq.gz,fastq.bz2</token>
     <xml name="input_database">
         <param label="Select a Kraken2 database" name="kraken2_database" type="select">
             <options from_data_table="kraken2_databases">