--- a/matchms_formatter.xml	Mon Jan 24 11:15:28 2022 +0000
+++ b/matchms_formatter.xml	Fri Jan 28 16:23:30 2022 +0000
@@ -1,9 +1,10 @@
-<tool id="matchms_formatter" name="matchms output formatter" version="0.1.0+galaxy0" python_template_version="3.5">
+<tool id="matchms_formatter" name="matchms output formatter" version="0.1.1" python_template_version="3.5">
     <description>reformat output tables of matchms</description>
 
-    <creator>
-        <organization url="https://www.recetox.muni.cz/" name="RECETOX MUNI" />
-    </creator>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="creator"/>
 
     <requirements>
         <requirement type="package" version="1.1.4">pandas</requirement>
@@ -22,17 +23,17 @@
             --o "$output" \
             $method.selection \
             #if $method.selection == "get-thresholded-data"
-                --st $method.scores_threshold \
-                --mt $method.matches_threshold
+            --st $method.scores_threshold \
+            --mt $method.matches_threshold
             #else
-                --k $method.k
+            --k $method.k
             #end if
         </configfile>
     </configfiles>
 
     <inputs>
-        <param label="Scores Table" name="scores" type="data" format="csv,tsv" help="Scores output table." />
-        <param label="Matches Table" name="matches" type="data" format="csv,tsv" help="Scores output table." />
+        <param label="Scores Table" name="scores" type="data" format="csv,tsv" help="Scores output table."/>
+        <param label="Matches Table" name="matches" type="data" format="csv,tsv" help="Scores output table."/>
 
         <conditional name="method">
             <param name="selection" type="select" label="Formatting method">
@@ -41,18 +42,18 @@
             </param>
             <when value="get-thresholded-data">
                 <param label="Scores Threshold" name="scores_threshold" type="float" value="0.6" min="0.0" max="1.0"
-                help="Threshold for matching score." />
+                       help="Threshold for matching score."/>
                 <param label="Matches Threshold" name="matches_threshold" type="integer" value="3" min="0"
-                help="Threshold for number of matches ions." />
+                       help="Threshold for number of matches ions."/>
             </when>
             <when value="get-top-k-data">
-                <param label="Top K" name="k" type="integer" value="5" help="K for top k match selection." />
+                <param label="Top K" name="k" type="integer" value="5" help="K for top k match selection."/>
             </when>
         </conditional>
 
     </inputs>
     <outputs>
-        <data label="${tool.name} (${method.selection}) on ${on_string}" name="output" format_source="scores" />
+        <data label="${tool.name} (${method.selection}) on ${on_string}" name="output" format_source="scores"/>
     </outputs>
 
     <tests>
@@ -62,46 +63,22 @@
             <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"/>
+            <output name="output" file="formatter/test2_threshold_formatting.tsv" ftype="tsv" 
+                    checksum="md5$8929cdac47252da638f066261ffc16b7"/>
         </test>
         <test>
             <param name="scores" value="scores_test2_out.tsv" ftype="tsv"/>
             <param name="matches" value="matches_test2_out.tsv" ftype="tsv"/>
             <param name="selection" value="get-top-k-data"/>
             <param name="k" value="3"/>
-            <output name="output" file="formatter/test2_topk_formatting.tsv" ftype="tsv" checksum="md5$a9186721aa2df2f9dbdef5021aa6bc26"/>
+            <output name="output" file="formatter/test2_topk_formatting.tsv" ftype="tsv"
+                    checksum="md5$a9186721aa2df2f9dbdef5021aa6bc26"/>
         </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>
+    <help>
+        <![CDATA[
+            @HELP_formatter@
+        ]]>
+    </help>
 </tool>