--- a/matchms_formatter.xml	Wed Sep 21 15:29:51 2022 +0000
+++ b/matchms_formatter.xml	Tue Oct 18 11:02:18 2022 +0000
@@ -7,9 +7,15 @@
     <expand macro="creator"/>
 
     <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">matchms</requirement>
         <requirement type="package" version="1.1.4">pandas</requirement>
         <requirement type="package" version="8.0.1">click</requirement>
     </requirements>
+    
+    <environment_variables>
+        <environment_variable name="MPLCONFIGDIR">\$_GALAXY_JOB_TMP_DIR</environment_variable>
+        <environment_variable name="XDG_CACHE_HOME">\$_GALAXY_JOB_TMP_DIR</environment_variable>
+    </environment_variables>
 
     <command detect_errors="aggressive"><![CDATA[
         sh ${matchms_formatter_cli}
@@ -19,7 +25,6 @@
         <configfile name="matchms_formatter_cli">
             python3 ${__tool_directory__}/formatter.py \
             --sf "$scores" \
-            --mf "$matches" \
             --o "$output" \
             $method.selection \
             #if $method.selection == "get-thresholded-data"
@@ -32,9 +37,7 @@
     </configfiles>
 
     <inputs>
-        <param label="Scores Table" name="scores" type="data" format="tsv" help="Scores output table." />
-        <param label="Matches Table" name="matches" type="data" format="tsv" help="Scores output table." />
-
+        <param label="Scores object" name="scores" type="data" format="json" help="MatchMS Scores json file." />
 
         <conditional name="method">
             <param name="selection" type="select" label="Formatting method">
@@ -59,53 +62,23 @@
 
     <tests>
         <test>
-            <param name="scores" value="scores_test2_out.tsv" ftype="tsv"/>
-            <param name="matches" value="matches_test2_out.tsv" ftype="tsv"/>
+            <param name="scores" value="similarity/scores_test2_out.json" ftype="json"/>
             <param name="selection" value="get-thresholded-data"/>
             <param name="scores_threshold" value="0.4"/>
             <param name="matches_threshold" value="2"/>
             <output name="output" file="formatter/test2_threshold_formatting.tsv" ftype="tsv"
-                    checksum="md5$8929cdac47252da638f066261ffc16b7"/>
+                checksum="md5$db18b3f3dd5d8dea4db0fc1d59d3db3b"/>
         </test>
         <test>
-            <param name="scores" value="scores_test2_out.tsv" ftype="tsv"/>
-            <param name="matches" value="matches_test2_out.tsv" ftype="tsv"/>
+            <param name="scores" value="similarity/scores_test2_out.json" ftype="json"/>
             <param name="selection" value="get-top-k-data"/>
             <param name="k" value="3"/>
             <output name="output" file="formatter/test2_topk_formatting.tsv" ftype="tsv"
-                    checksum="md5$a9186721aa2df2f9dbdef5021aa6bc26"/>
+                checksum="md5$ff827ec7413acac3d2394330935ace99"/>
         </test>
     </tests>
 
     <help><![CDATA[
-    Usage
-        This tool creates user friendly tables from the data matrices produces by matchms.
-        The tool can be operated on two modes based on (i) thresholds or (ii) top k matches.
-
-    Input Table Format
-        The tool expects two data matrices with the format as depicted below.
-        The tool assumes the reference compound labels as row labels and the query labels as column labels (as naturally outputted by matchms).
-
-        +----------+------+------+-----+
-        |          | C001 | C002 | ... |
-        +==========+======+======+=====+
-        | Perylene | 0.1  | 0.0  | ... |
-        +----------+------+------+-----+
-        | Glycine  | 0.5  | 0.34 | ... |
-        +----------+------+------+-----+
-        |   ...    | ...  | ...  | ... |
-        +----------+------+------+-----+
-
-    Output Table Format
-        +----------+-----------+---------+--------+
-        | query    | reference | matches | scores |
-        +==========+===========+=========+========+
-        | C001     | Glycine   |      6  | 0.5    |
-        +----------+-----------+---------+--------+
-        | C002     | Glycine   |     3   | 0.34   |
-        +----------+-----------+---------+--------+
-        |   ...    | ...       | ...     | ...    |
-        +----------+-----------+---------+--------+
-
+        @HELP_formatter@
     ]]></help>
 </tool>