diff matchms_convert.xml @ 3:4216e42a5534 draft default tip

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e

--- a/matchms_convert.xml	Thu May 25 09:04:26 2023 +0000
+++ b/matchms_convert.xml	Tue Jun 27 14:21:13 2023 +0000
@@ -1,11 +1,20 @@
-<tool id="matchms_convert" name="matchms convert" version="0.19.0+galaxy0" profile="21.05">
-    <description>convert between mass spectral library formats using matchms</description>
+<tool id="matchms_convert" name="matchms convert" version="@TOOL_VERSION@+galaxy0" profile="21.05">
+    <description>convert between mass spectral library formats (.mgf/.msp/.json) using matchms</description>
+    
     <macros>
         <import>macros.xml</import>
+        <import>help.xml</import>
     </macros>
+
     <expand macro="creator"/>
+
+    <edam_operations>
+        <edam_operation>operation_3434</edam_operation>
+    </edam_operations>
+    <expand macro="bio.tools"/>
+
     <requirements>
-        <requirement type="package" version="0.19.0">matchms</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">matchms</requirement>
     </requirements>
 
     <command detect_errors='aggressive'><![CDATA[
@@ -14,6 +23,8 @@
 
 <configfiles>
 <configfile name="matchms_python_cli">
+@init_logger@
+
 from matchms.importing import load_from_msp, load_from_mgf, load_from_json
 from matchms.exporting import save_as_msp, save_as_mgf, save_as_json
 spectra = list(load_from_${spectral_library.ext}("${spectral_library}", ${harmonization_metadata}))
@@ -31,7 +42,7 @@
 
         <param label="Harmonization metadata" name="harmonization_metadata" type="boolean" truevalue="True" falsevalue="False"
             checked="true"
-            help="Set to False if metadata harmonization to default keys is not desired. The default is True." />
+            help="Apply metadata harmonization, parsing certain keys required by additional filters or initializing other attributes. The default is True." />
 
         <conditional name="output_file">
             <param label="Spectral library format" name="output_format" type="select"
@@ -43,9 +54,9 @@
             <when value="msp">
                 <param label="Export peak comments" name="export_peak_comments" type="boolean"
                     truevalue="True" falsevalue="False" checked="true"
-                    help="Writes peak comments to individual peaks after the respective mz/intensity pair when selected." />
+                    help="Retain peak comments from individual peaks after the respective mz and intensity pairs when selected." />
                 <param label="Export style" name="export_style" type="select"
-                    help="Converts the keys to required Export style. One of ['matchms', 'massbank', 'nist', 'riken', 'gnps']. Default is 'matchms'">
+                    help="Converts the keys to a specific style - see [1] for details.. One of ['matchms', 'massbank', 'nist', 'riken', 'gnps']. Default is 'matchms'.">
                     <option value="matchms" selected="true">matchms</option>
                     <option value="massbank">massbank</option>
                     <option value="nist">nist</option>
@@ -53,6 +64,8 @@
                     <option value="gnps">gnps</option>
                 </param>
             </when>
+            <when value="mgf" />
+            <when value="json" />
         </conditional>
     </inputs>
 
@@ -106,14 +119,15 @@
 
 
     <help><![CDATA[
-    Documentation
-        Mass spectral libraries are often stored in various formats, such as `msp`, `mgf` or `json`.
-        This tool can be used to convert from one library format to another.
+        Description
+            Mass spectral libraries are often stored in various formats, such as `msp`, `mgf` or `json`.
+            This tool can be used to convert from one library format to another.
+            Some of the metadata keywords might change during the conversion process, as they are harmonized internally with matchms.
 
-        Please note that peak comments in `RIKEN` style `msp` files are lost upon conversion.
-        Additionally, some of the metadata keywords might change during the conversion process, as they are harmonized internally with matchms.
+            .. rubric:: **Footnotes**
+            .. [1] Export styles - see this `table <https://github.com/matchms/matchms/blob/master/matchms/data/export_key_conversions.csv>`_ for supported key conversions and detailed description of the export styles.
 
-        For more documentation on the matchms library see https://github.com/matchms/matchms/blob/master/README.rst and https://matchms.readthedocs.io/en/latest/.
+            @HELP_matchms@
     ]]></help>