# HG changeset patch
# User iuc
# Date 1710765131 0
# Node ID 81cea47ec685d6b7b3db39fcce625611c2edf286
# Parent  46c5d7a0393bb4482c8e5fce0d748588d7fdf52d
planemo upload for repository https://github.com/katholt/srst2 commit 13ef9da7b3f4b7a06deb5b3ce7331ae127ec7aba

diff -r 46c5d7a0393b -r 81cea47ec685 macros.xml
--- a/macros.xml	Tue Sep 06 14:18:05 2022 +0000
+++ b/macros.xml	Mon Mar 18 12:32:11 2024 +0000
@@ -10,10 +10,15 @@
             <yield/>
         </requirements>
     </xml>
+    <xml name="xrefs">
+        <xrefs>
+            <xref type="bio.tools">srst2</xref>
+        </xrefs>
+    </xml>
     <xml name="read_type_options">
         <param argument="--read_type" type="select" label="Read file type">
             <option value="q" selected="true">fastq</option>
             <option value="f">fasta</option>
         </param>
     </xml>
-</macros>
\ No newline at end of file
+</macros>
diff -r 46c5d7a0393b -r 81cea47ec685 srst2.xml
--- a/srst2.xml	Tue Sep 06 14:18:05 2022 +0000
+++ b/srst2.xml	Mon Mar 18 12:32:11 2024 +0000
@@ -4,6 +4,7 @@
         <import>macros.xml</import>
         <token name="@FAST_A_Q_FORMATS@">fasta,fasta.gz,fastq,fastq.gz,fastqsanger,fastqsanger.gz</token>
     </macros>
+    <expand macro="xrefs"/>
     <expand macro="requirements"/>
     <version_command>srst2 --version</version_command>
     <command detect_errors="exit_code"><![CDATA[
@@ -288,7 +289,7 @@
                 <has_n_lines n="2"/>
             </assert_contents>
         </output>
-        <output_collection name="new_consensus" type="list">
+        <output_collection name="new_consensus" type="list" count="1">
             <element name="49__AmpC1_Ecoli_Bla__AmpC1__1670.output__input.0-gene_db.pileup">
                 <assert_contents>
                     <has_text text="49__AmpC1_Ecoli_Bla__AmpC1__1670"/>
@@ -296,7 +297,7 @@
                 </assert_contents>
             </element>
         </output_collection>
-        <output_collection name="samtools_pileup_alignment" type="list">
+        <output_collection name="samtools_pileup_alignment" type="list" count="1">
             <element name="output__input.0-gene_db.pileup">
                 <assert_contents>
                     <has_text text="49__AmpC1_Ecoli_Bla__AmpC1__1670"/>
@@ -304,7 +305,7 @@
                 </assert_contents>
             </element>
         </output_collection>
-        <output_collection name="bowtie2_alignment_output" type="list">
+        <output_collection name="bowtie2_alignment_output" type="list" count="1">
             <element name="output__input.0-gene_db.sorted.bam">
                 <assert_contents>
                     <has_size value="18500" delta="1000"/>
@@ -347,14 +348,10 @@
                 <has_size value="0" delta="0"/>
             </assert_contents>
         </output>
-        <output_collection name="new_consensus" type="list">
-        </output_collection>
-        <output_collection name="samtools_pileup_alignment" type="list">
-        </output_collection>
-        <output_collection name="bowtie2_alignment_output" type="list">
-        </output_collection>
-        <output_collection name="scores_ofEachAllele" type="list">
-        </output_collection>
+        <output_collection name="new_consensus" type="list" count="0"/>
+        <output_collection name="samtools_pileup_alignment" type="list" count="0"/>
+        <output_collection name="bowtie2_alignment_output" type="list" count="0"/>
+        <output_collection name="scores_ofEachAllele" type="list" count="0"/>
         <output name="log_output">
             <assert_contents>
                 <has_text text="Total paired readsets found:1"/>
@@ -383,4 +380,4 @@
     <citations>
         <citation type="doi">10.1186/s13073-014-0090-6</citation>
     </citations>
- </tool>
\ No newline at end of file
+ </tool>