# HG changeset patch
# User nml
# Date 1740582874 0
# Node ID ac93c8247a7f74637b81ad7e4c3974752c393e2e
# Parent  f081459f2a151efc76e2691d593d0ab4f8322b60
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob-suite commit bc53cd0c79b976fc17f854ede446e61d6c9bb49a

diff -r f081459f2a15 -r ac93c8247a7f mob_recon.xml
--- a/mob_recon.xml	Fri Feb 21 18:41:02 2025 +0000
+++ b/mob_recon.xml	Wed Feb 26 15:14:34 2025 +0000
@@ -138,7 +138,7 @@
     </collection>
   </outputs>
   <tests>
-    <test>
+    <test expect_num_outputs="4">
       <param name="input" value="Ecoli_strain_KV7_complete_LT795502.fasta" ftype="fasta"/>
       <section name="adv_param">
         <param name="unicycler_contigs" value="True"/>
diff -r f081459f2a15 -r ac93c8247a7f mob_typer.xml
--- a/mob_typer.xml	Fri Feb 21 18:41:02 2025 +0000
+++ b/mob_typer.xml	Wed Feb 26 15:14:34 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="mob_typer" name="MOB-Typer" version="@VERSION@+galaxy0">
+<tool id="mob_typer" name="MOB-Typer" version="@VERSION@+galaxy1">
   <description>Get the plasmid type and mobility given its sequence</description>
   <macros>
     <import>macros.xml</import>
@@ -65,8 +65,7 @@
    #if $adv_param.biomarker_report_file
    --biomarker_report_file biomarker_report.txt
    #end if
-   
-
+  
    --out_file plasmid_report.txt;
 
   ]]>
@@ -74,9 +73,8 @@
   <inputs>
     <param name="input" type="data" format="fasta" label="Input" help="FASTA file with contig(s)"/>
     <section name="adv_param" title="Advanced parameters" expanded="False">
-      <param name="multi" type="boolean" truevalue="true" falsevalue="" checked="false" label="Treat each input sequence as an independent plasmid?" help="Treat each sequence in the FASTA file as a separate input (--multi)" />
-      <param name="biomarker_report_file" type="boolean" truevalue="true" falsevalue="" checked="false" label="Output BLAST biomarker report?" help="The report will report all biomarkers identified in a given query plasmid (--biomarker_report_file)" />
-
+      <param name="multi" type="boolean"  checked="false" label="Treat each input sequence as an independent plasmid?" help="Treat each sequence in the FASTA file as a separate input (--multi)" />
+      <param name="biomarker_report_file" type="boolean" checked="true" label="Output BLAST biomarker report?" help="The report will report all biomarkers identified in a given query plasmid (--biomarker_report_file)" />
       <param name="min_rep_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for replicon blastn" help="(--min_rep_evalue)"/> 
       <param name="min_mob_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for relaxase tblastn" help="(--min_mob_evalue)"/> 
       <param name="min_con_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for contig blastn" help="(--min_con_evalue)"/> 
@@ -101,10 +99,12 @@
   </inputs>
   <outputs>
     <data name="plasmid_report" from_work_dir="plasmid_report.txt" label="${tool.name}: Plasmid report on ${input.element_identifier}"  format="tabular" />
-    <data name="biomarker_report" from_work_dir="biomarker_report.txt" label="${tool.name}: Biomarker report on ${input.element_identifier}"  format="tabular" />
+    <data name="biomarker_report" from_work_dir="biomarker_report.txt" label="${tool.name}: Biomarker report on ${input.element_identifier}"  format="tabular">
+     <filter>adv_param["biomarker_report_file"]</filter> 
+    </data>
   </outputs>
   <tests>
-    <test>
+    <test expect_num_outputs="2">
       <param name="input" value="plasmid_476.fasta" ftype="fasta"/>
       <output name="plasmid_report">
         <assert_contents>