# HG changeset patch
# User nml
# Date 1735581489 0
# Node ID 4b4a7d9f7c9e70734a73c3c4423cb0072b2a3115
# Parent  954b1b1ef3fbdd49eabd2bfe56dccc6087473fe6
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/ectyper commit 20e805e46acfc9171da5e3281f3248295b6f8018

diff -r 954b1b1ef3fb -r 4b4a7d9f7c9e ectyper.xml
--- a/ectyper.xml	Wed Dec 18 22:36:31 2024 +0000
+++ b/ectyper.xml	Mon Dec 30 17:58:09 2024 +0000
@@ -1,10 +1,13 @@
-<tool id="ectyper" name="ectyper" version="1.0.0">
+<tool id="ectyper" name="ectyper" version="@VERSION@+galaxy0">
   <description>ectyper is a standalone serotyping module for Escherichia coli. It supports fasta and fastq file formats.</description>
-  <xrefs>
+  <macros>
+        <token name="@VERSION@">2.0.0</token>
+  </macros>
+   <xrefs>
     <xref type="bio.tools">ectyper</xref>
   </xrefs>
   <requirements>
-     <requirement type="package" version="1.0.0">ectyper</requirement>
+     <requirement type="package" version="@VERSION@">ectyper</requirement>  
   </requirements>
   <command detect_errors="exit_code">
   <![CDATA[
@@ -48,25 +51,46 @@
     --refseq mash_sketch.msh
   #end if
 
+  #if $adv_param.pathotype
+    --pathotype
+    -pathpid $adv_param.pathotype_adv_param.pathpid
+    -pathpcov $adv_param.pathotype_adv_param.pathpcov 
+  #end if
+
   #if $adv_param.db_input
     --dbpath custom_db.json
   #end if
 
+  #if $adv_param.longreadsmode
+    --longreads
+  #end if
+
+  #if $adv_param.debugmode
+    --debug
+  #end if
+
   --output '.'
   ]]>
   </command>
   <inputs>
     <param name="input" type="data"  format="fastq,fasta" label="Genome(s) input(s)" help="FASTA or FASTQ file(s)"/>
     <section name="adv_param" title="Advanced parameters" expanded="False">
-      <param name="opid" label="O antigen minimum %identity" type="integer" value="90" min="1" max="100"/>
+      <param name="opid" label="O antigen minimum %identity" type="integer" value="95" min="1" max="100"/>
       <param name="opcov" label="O antigen minimum %coverage" type="integer" value="90" min="1" max="100"/>
       <param name="hpid" label="H antigen minimum %identity" type="integer" value="95" min="1" max="100"/>
       <param name="hpcov" label="H antigen minimum %coverage" type="integer" value="50" min="1" max="100"/>
-      <param name="verifyEcoli" type="boolean" checked="true" label="Enable E. coli species verification"/>
+      <param name="verifyEcoli" type="boolean" checked="false" label="Enable E. coli species and results QC verification"/>
       <param name="blastresults" type="boolean" checked="false"  label="Include BLAST allele alignment results tab-delim file in the outputs?" />
       <param name="logging" type="boolean" checked="false"  label="Include log file in the run outputs?" />
       <param name="mash_input" type="data" optional="true" format="binary" label="Mash genome sketches (Optional)" help="Optionally provide custom MASH genome sketch to help with species identification (otherwise default RefSeq sketch is used)"/>
-      <param name="db_input" type="data" optional="true" format="json" label="Custom database of alleles (Optional)" help="Optionally provide custom database of alleles in JSON format"/>
+      <param name="pathotype" type="boolean" checked="true" label="Enable E.coli pathotyping and Shiga toxin (stx) subtyping (Recommended)"/>
+      <section name="pathotype_adv_param" title="Advanced parameters (pathoyping and shiga toxin subtyping)" expanded="False"> 
+        <param name="pathpid" label="Minimum %identity required for a pathotype/toxin database reference allele match" type="integer" value="90" min="1" max="100"/>
+        <param name="pathpcov" label="Minimum %coverage required for a pathotype/toxin database reference allele match" type="integer" value="50" min="1" max="100"/>
+      </section>
+      <param name="longreadsmode" type="boolean" checked="false" label="Enable long read mapping mode (Optional)" help="Enable this mode if no typing results are obtained"/>
+      <param name="db_input" type="data" optional="true" format="json" label="Custom database of O and H antigen alleles (Optional)" help="Optionally provide custom database of alleles in JSON format"/>
+      <param name="debugmode" type="boolean" checked="false" label="Enable debug mode with high log messages verbosity"/>
     </section>
   </inputs>
   <outputs>
@@ -80,17 +104,25 @@
   </outputs>
   <tests>
     <test expect_num_outputs="1">
-      <param name="input" value="Escherichia2.fastq"/>
-      <assert_stderr>
-            <has_text text="O22"/> 
-            <has_text text="H8"/> 
-      </assert_stderr>
+      <param name="input" value="Escherichia2.fastq" ftype="fastq"/> 
       <output name="output_result" ftype="tabular" >
           <assert_contents>
               <has_text_matching expression="O22"/>
+              <has_text text="H8"/> 
          </assert_contents>
       </output>
     </test>
+    <test expect_num_outputs="1">
+      <param name="input" value="Escherichia1.fasta" ftype="fasta"/>
+      <output name="output_result" ftype="tabular">
+          <assert_contents>
+              <has_text text="O103:H2"/>
+              <has_text text="EHEC-STEC"/>
+              <has_text text="stx1a;stx2a"/>
+              <has_text text="eae,ehxA,hlyE,stx1,stx2"/>  
+         </assert_contents>
+      </output>
+    </test>  
   </tests>
 
   <help>