# HG changeset patch
# User iuc
# Date 1710259822 0
# Node ID 766d5f63b0f4a81946a079aebeab120f17ffae59
# Parent  aec58624706f5afb3e6fef9288307a097177f308
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ commit 3a94fbf6a188ea81441ef2f654ba5a74bff56f22

diff -r aec58624706f -r 766d5f63b0f4 kraken.xml
--- a/kraken.xml	Wed Dec 04 06:51:45 2019 -0500
+++ b/kraken.xml	Tue Mar 12 16:10:22 2024 +0000
@@ -6,6 +6,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="xrefs"/>
     <expand macro="requirements" />
     <expand macro="version_command" />
     <command detect_errors="exit_code">
@@ -66,7 +67,7 @@
             </param>
             <when value="collection">
                 <param format="fasta,fastq" name="input_pair" type="data_collection" collection_type="paired" label="Collection of paired reads" help="FASTA or FASTQ datasets" />
-                <param name="check_names" argument="--check-names" type="boolean" checked="False" truevalue="--paired --check-names" falsevalue="--paired" label="Verify read names match"/>
+                <param argument="--check-names" type="boolean" checked="False" truevalue="--paired --check-names" falsevalue="--paired" label="Verify read names match"/>
             </when>
             <when value="yes">
                 <param format="fasta,fastq" name="forward_input" type="data" label="Forward strand" help="FASTA or FASTQ dataset"/>
@@ -87,13 +88,13 @@
                 <option selected="True" value="no">No</option>
             </param>
             <when value="yes">
-                <param name="min_hits" argument="--min-hits" type="integer" value="1" label="Number of hits required for classification"
+                <param argument="--min-hits" type="integer" value="1" label="Number of hits required for classification"
                        help="min-hits will allow you to require multiple hits before declaring a sequence classified, which can be especially useful with custom databases when testing to see if sequences either do or do not belong to a particular genome; default=1"/>
             </when>
             <when value="no"/><!-- Do absolutely nothing -->
         </conditional>
 
-        <param name="only_classified_output" argument="--only-classified-output" type="boolean" checked="False" truevalue="--only-classified-output" falsevalue=""
+        <param argument="--only-classified-output" type="boolean" checked="False" truevalue="--only-classified-output" falsevalue=""
                label="Print no Kraken output for unclassified sequences"/>
 
         <expand macro="input_database" />
@@ -110,7 +111,7 @@
     </outputs>
 
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <param name="single_paired_selector" value="no"/>
             <param name="input_sequences" value="kraken/kraken_test1.fa" ftype="fasta"/>
             <param name="split_reads" value="false"/>
@@ -119,7 +120,7 @@
             <param name="kraken_database" value="old_style_test_entry"/>
             <output name="output" file="kraken/kraken_test1_output.tab" ftype="tabular"/>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="single_paired_selector" value="no"/>
             <param name="input_sequences" value="kraken/kraken_test1.fa" ftype="fasta"/>
             <param name="split_reads" value="false"/>
diff -r aec58624706f -r 766d5f63b0f4 macros.xml
--- a/macros.xml	Wed Dec 04 06:51:45 2019 -0500
+++ b/macros.xml	Tue Mar 12 16:10:22 2024 +0000
@@ -6,6 +6,11 @@
             <requirement type="package" version="1.1.1">kraken</requirement>
         </requirements>
     </xml>
+    <xml name="xrefs">
+        <xrefs>
+            <xref type="bio.tools">kraken</xref>
+        </xrefs>
+    </xml>
     <xml name="version_command">
         <version_command><![CDATA[
             export LC_ALL=C && kraken --version