--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/matchms_formatter.xml	Sat Oct 30 13:48:25 2021 +0000
@@ -0,0 +1,107 @@
+<tool id="matchms_formatter" name="matchms output formatter" version="0.1.0+galaxy0" python_template_version="3.5">
+    <description>reformat output tables of matchms</description>
+
+    <creator>
+        <organization url="https://www.recetox.muni.cz/" name="RECETOX MUNI" />
+    </creator>
+
+    <requirements>
+        <requirement type="package" version="1.1.4">pandas</requirement>
+        <requirement type="package" version="8.0.1">click</requirement>
+    </requirements>
+
+    <command detect_errors="aggressive"><![CDATA[
+        sh ${matchms_formatter_cli}
+    ]]></command>
+
+    <configfiles>
+        <configfile name="matchms_formatter_cli">
+            python3 ${__tool_directory__}/formatter.py \
+            --sf "$scores" \
+            --mf "$matches" \
+            --o "$output" \
+            $method.selection \
+            #if $method.selection == "get-thresholded-data"
+                --st $method.scores_threshold \
+                --mt $method.matches_threshold
+            #else
+                --k $method.k
+            #end if
+        </configfile>
+    </configfiles>
+
+    <inputs>
+        <param label="Scores Table" name="scores" type="data" format="tsv" help="Scores output table." />
+        <param label="Matches Table" name="matches" type="data" format="tsv" help="Scores output table." />
+
+        <conditional name="method">
+            <param name="selection" type="select" label="Formatting method">
+                <option value="get-thresholded-data" selected="true">Thresholding</option>
+                <option value="get-top-k-data">Top K Matches</option>
+            </param>
+            <when value="get-thresholded-data">
+                <param label="Scores Threshold" name="scores_threshold" type="float" value="0.6" min="0.0" max="1.0"
+                help="Threshold for matching score." />
+                <param label="Matches Threshold" name="matches_threshold" type="integer" value="3" min="0"
+                help="Threshold for number of matches ions." />
+            </when>
+            <when value="get-top-k-data">
+                <param label="Top K" name="k" type="integer" value="5" help="K for top k match selection." />
+            </when>
+        </conditional>
+
+    </inputs>
+    <outputs>
+        <data label="${tool.name} (${method.selection}) on ${on_string}" name="output" format="tsv" />
+    </outputs>
+
+    <tests>
+        <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-thresholded-data"/>
+            <param name="scores_threshold" value="0.4"/>
+            <param name="matches_threshold" value="2"/>
+            <output name="output" file="test2_threshold_formatting.tsv" ftype="tsv" checksum="md5$8929cdac47252da638f066261ffc16b7"/>
+        </test>
+        <test>
+            <param name="scores" value="scores_test2_out.tsv" ftype="tsv"/>
+            <param name="matches" value="matches_test2_out.tsv" ftype="tsv"/>
+            <param name="selection" value="get-top-k-data"/>
+            <param name="k" value="3"/>
+            <output name="output" file="test2_topk_formatting.tsv" ftype="tsv" checksum="md5$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>
+</tool>
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