Mercurial > repos > iuc > staramr

changeset 3:59d308975e63 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/staramr commit e62bb361f68ef29164b43337da3b3f4a09a98836
author iuc
date Thu, 20 Mar 2025 12:31:44 +0000
parents d0a2e0a9c853
children
files staramr_search.xml
diffstat 1 files changed, 12 insertions(+), 13 deletions(-) [+]
line wrap: on
line diff
--- a/staramr_search.xml	Thu Feb 27 16:29:20 2025 +0000
+++ b/staramr_search.xml	Thu Mar 20 12:31:44 2025 +0000
@@ -2,7 +2,7 @@
     <description>Scans genome assemblies against the ResFinder, PlasmidFinder, and PointFinder databases searching for AMR genes</description>
     <macros>
         <token name="@TOOL_VERSION@">0.11.0</token>
-        <token name="@VERSION_SUFFIX@">1</token>
+        <token name="@VERSION_SUFFIX@">2</token>
         <token name="@PROFILE@">22.05</token>
         <xml name="element_assert" token_name="" token_text="">
             <element name="@NAME@">
@@ -13,7 +13,7 @@
             </element>
         </xml>
     </macros>
-     <xrefs>
+    <xrefs>
         <xref type="bio.tools">staramr</xref>
     </xrefs>
     <requirements>
@@ -306,16 +306,16 @@
             </param>
         </section>
         <section name="output_files" title="Selection of the output files" expanded="true" >
-          <param name="output_selection" type="select" display="checkboxes" multiple="true"  label="Output files selection">
-              <option value="mlst_table" selected="true">MLST report</option>
-              <option value="summary_table" selected="true">AMR genes/mutations summary</option>
-              <option value="detailed_summary_table" selected="true">AMR genes/mutations/plasmids detailed summary</option>
-              <option value="resfinder_table" selected="true">AMR gene report from ResFinder</option>
-              <option value="plasmidfinder_table" selected="true">AMR gene report from PlasmidFinder</option>
-              <option value="pointfinder_table" selected="true">AMR gene report from PointFinder</option>
-              <option value="settings_output" selected="false">Settings file</option>
-              <option value="excel_output" selected="false">Excel spreadsheet</option>
-          </param>
+            <param name="output_selection" type="select" display="checkboxes" multiple="true"  label="Output files selection">
+                <option value="mlst_table" selected="true">MLST report</option>
+                <option value="summary_table" selected="true">AMR genes/mutations summary</option>
+                <option value="detailed_summary_table" selected="true">AMR genes/mutations/plasmids detailed summary</option>
+                <option value="resfinder_table" selected="true">AMR gene report from ResFinder</option>
+                <option value="plasmidfinder_table" selected="true">AMR gene report from PlasmidFinder</option>
+                <option value="pointfinder_table" selected="true">AMR gene report from PointFinder</option>
+                <option value="settings_output" selected="false">Settings file</option>
+                <option value="excel_output" selected="false">Excel spreadsheet</option>
+            </param>
         </section> 
     </inputs>
     <outputs>
@@ -335,7 +335,6 @@
             <filter>output_files['output_selection'] and "plasmidfinder_table" in output_files['output_selection']</filter>
         </data>
         <data format="tabular" name="pointfinder" label="${tool.name} on ${on_string}: AMR point mutation report from PointFinder">
-            <filter>pointfinder_organism != "disabled"</filter>
             <filter>output_files['output_selection'] and "pointfinder_table" in output_files['output_selection']</filter>
         </data>
         <data format="txt" name="settings" label="${tool.name} on ${on_string}: Settings file" >