--- a/sirius_csifingerid.xml	Fri Feb 11 10:05:21 2022 +0000
+++ b/sirius_csifingerid.xml	Wed Feb 16 16:11:55 2022 +0000
@@ -1,5 +1,5 @@
 <tool id="sirius_csifingerid" name="SIRIUS-CSI:FingerID"
-      version="4.9.8+galaxy3" profile="19.05">
+      version="4.9.8+galaxy4" profile="19.05">
     <description>is used to identify metabolites using single and
         tandem mass spectrometry</description>
     <requirements>
@@ -8,7 +8,7 @@
     </requirements>
     <command detect_errors="exit_code">
     <![CDATA[
-
+        export _JAVA_OPTIONS=-Duser.home=$__new_file_path__ &&
         python '$__tool_directory__/sirius_csifingerid.py'
             --input_pth '$input'
             --database $database
@@ -19,7 +19,9 @@
             --out_dir $__new_file_path__
             --canopus_result_pth canopus_all_summary.tsv
             --annotations_result_pth annotations_all_summary.tsv
+            --all_structures_result_pth structures_all_summary.tsv
             --cores_top_level 1
+            --cores_sirius \${GALAXY_SLOTS:-4}
             --meta_select_col $meta_select_col
             --min_MSMS_peaks $min_MSMS_peaks
             --schema $schema
@@ -47,9 +49,6 @@
                  #end if
             #end if
 
-            --rank_filter $rank_filter
-
-            --confidence_filter $confidence_filter
 
 
     ]]></command>
@@ -136,13 +135,13 @@
             </when>
         </conditional>
 
-        <param argument="--rank_filter" type="integer" value="0"
-               label="Only show the top ranked annotations less than or equal
-                      to this value (default to show all annotations)"/>
+<!--        <param argument="&#45;&#45;rank_filter" type="integer" value="0"-->
+<!--               label="Only show the top ranked annotations less than or equal-->
+<!--                      to this value (default to show all annotations)"/>-->
 
-        <param argument="--confidence_filter" type="float" value="0"
-               label="Only show annotations greater than or or equal
-                      to this value (default to show all annotations)"/>
+<!--        <param argument="&#45;&#45;confidence_filter" type="float" value="0"-->
+<!--               label="Only show annotations greater than or or equal-->
+<!--                      to this value (default to show all annotations)"/>-->
 
     </inputs>
     <outputs>
@@ -150,6 +149,8 @@
               from_work_dir="canopus_all_summary.tsv"/>
         <data name="annotation_results" format="tsv" label="${tool.name} on ${on_string}: Annotations"
               from_work_dir="annotations_all_summary.tsv"/>
+        <data name="structure_results" format="tsv" label="${tool.name} on ${on_string}: All structures"
+              from_work_dir="structures_all_summary.tsv"/>
     </outputs>
     <tests>
         <test>
@@ -195,13 +196,7 @@
             <output name="annotation_results" file="annotation_RP022611_result_all_adducts.tsv"/>
             <output name="canopus_results" file="canopus_RP022611_result_all_adducts.tsv"/>
         </test>
-        <test>
-            <!-- Test confidence filter  -->
-            <param name="input" value="generic.msp" ftype="msp"/>
-            <param name="confidence_filter" value="0.7"/>
-            <output name="annotation_results" file="cf_annotation_generic_msp_result.tsv"/>
-            <output name="canopus_results" file="cf_canopus_generic_msp_result.tsv"/>
-        </test>
+
     </tests>
     <help>
 ----------------