# HG changeset patch
# User recetox
# Date 1644575628 0
# Node ID da32f57b4f88b8fb7d75492826085458023f6391
# Parent  e2a1dbeba19698ab9365a9c70f14362f3f3c511a
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5b13d8883fe18bee3aa992c2e34aa1fa79419442"

diff -r e2a1dbeba196 -r da32f57b4f88 matchms_formatter.xml
--- a/matchms_formatter.xml	Fri Jan 28 16:23:30 2022 +0000
+++ b/matchms_formatter.xml	Fri Feb 11 10:33:48 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="matchms_formatter" name="matchms output formatter" version="0.1.1" python_template_version="3.5">
+<tool id="matchms_formatter" name="matchms output formatter" version="0.1.2" python_template_version="3.5">
     <description>reformat output tables of matchms</description>
 
     <macros>
@@ -32,8 +32,9 @@
     </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,tabular,tsv" help="Scores output table." />
+        <param label="Matches Table" name="matches" type="data" format="csv,tabular,tsv" help="Scores output table." />
+
 
         <conditional name="method">
             <param name="selection" type="select" label="Formatting method">
@@ -76,9 +77,35 @@
         </test>
     </tests>
 
-    <help>
-        <![CDATA[
-            @HELP_formatter@
-        ]]>
-    </help>
+    <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>
 </tool>