matchms: added filters and test and fixed linter warnings

tools/export_to_path/export_to_path.xml

@@ -1,9 +1,9 @@
 <tool id="export_to_path" name="export to path" version="0.0.2">
+    <description>on a filesystem accessible to compute node</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="creator"/>
-    <description>on a filesystem accessible to compute node</description>
     <requirements>
         <requirement type="package" version="3.6">python</requirement>
     </requirements>

tools/filter_compounds/filter_compounds.xml

@@ -44,5 +44,8 @@
             @HELP@
         ]]>
     </help>
+    <citations>
+        <citation type="doi">https://doi.org/10.5281/zenodo.6035335</citation>
+    </citations>
 </tool>
 

tools/matchms/matchms_filtering.xml

@@ -69,16 +69,22 @@
         <conditional name="normalise_intensities">
             <param name="is_true" label="Normalize intensities" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
                    help="Normalize intensities of peaks (and losses) to unit height."/>
+            <when value="TRUE"></when>
+            <when value="FALSE"></when>
         </conditional>
 
         <conditional name="default_filters">
             <param name="is_true" label="Apply default filters" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
                    help="Collection of filters that are considered default and that do no require any (factory) arguments."/>
+            <when value="TRUE"></when>
+            <when value="FALSE"></when>
         </conditional>
 
         <conditional name="clean_metadata">
             <param name="is_true" label="Clean metadata" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
                    help="Apply all adding and cleaning filters if possible, so that the spectra have canonical metadata." />
+            <when value="TRUE"></when>
+            <when value="FALSE"></when>
         </conditional>
 
         <conditional name="relative_intensity">
@@ -88,6 +94,7 @@
                 <param label="Minimum intensity" name="from_intensity" value="0" type="float" help="Lower bound for intensity filter." />
                 <param label="Maximum intensity" name="to_intensity" value="1" type="float" help="Upper bound for intensity filter." />
             </when>
+            <when value="FALSE"></when>
         </conditional>
 
         <conditional name="mz_range">
@@ -97,16 +104,21 @@
                 <param label="Minimum m/z" name="from_mz" optional="true" type="float" help="Lower bound for m/z filter." />
                 <param label="Maximum m/z" name="to_mz" optional="true" type="float" help="Upper bound for m/z filter." />
             </when>
+            <when value="FALSE"></when>
         </conditional>
 
         <conditional name="require_smiles">
             <param name="is_true" label="Require SMILES" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
                    help="Remove spectra that does not contain SMILES." />
+            <when value="TRUE"></when>
+            <when value="FALSE"></when>
         </conditional>
 
         <conditional name="require_inchi">
             <param name="is_true" label="Require INCHI" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
                    help="Remove spectra that does not contain INCHI." />
+            <when value="TRUE"></when>
+            <when value="FALSE"></when>
         </conditional>
 
         <conditional name="reduce_to_top_n_peaks">
@@ -115,6 +127,7 @@
             <when value="TRUE">
                 <param label="Maximum number of peaks" name="n_max" value="5" type="integer" help="Maximum number of peaks. Remove peaks if more peaks are found." />
             </when>
+            <when value="FALSE"></when>
         </conditional>
 
     </inputs>

tools/matchms/matchms_formatter.xml

@@ -16,16 +16,16 @@
         <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>
 
     <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}
-    ]]></command>
-
     <configfiles>
         <configfile name="matchms_formatter_cli">
             python3 ${__tool_directory__}/formatter.py \
@@ -57,4 +57,8 @@
         @HELP_formatter@
         @HELP_matchms@
     </help>
+
+    <citations>
+        <citation type="doi">https://doi.org/10.5281/zenodo.6035335</citation>
+    </citations>
 </tool>

tools/matchms/matchms_metadata_export.xml

@@ -1,4 +1,4 @@
-<tool id="matchms_metadata_export" name="matchms metadata export " version="@TOOL_VERSION@+galaxy0" profile="21.09">
+<tool id="matchms_metadata_export" name="matchms metadata export" version="@TOOL_VERSION@+galaxy0" profile="21.09">
     <description>extract all metadata from mass spectra file to tabular format</description>
     <macros>
         <import>macros.xml</import>

tools/matchms/matchms_metadata_match.xml

@@ -12,14 +12,14 @@
         <requirement type="package" version="@TOOL_VERSION@">matchms</requirement>
     </requirements>
 
-    <environment_variables>
-        <environment_variable name="MPLCONFIGDIR">\$_GALAXY_JOB_TMP_DIR</environment_variable>
-    </environment_variables>
-
     <command detect_errors="exit_code"><![CDATA[
         python3 '${python_wrapper}'
     ]]> </command>
 
+    <environment_variables>
+        <environment_variable name="MPLCONFIGDIR">\$_GALAXY_JOB_TMP_DIR</environment_variable>
+    </environment_variables>
+
 <configfiles>
 <configfile name="python_wrapper">
 @init_logger@

tools/matchms/matchms_networking.xml

@@ -16,15 +16,15 @@
         <requirement type="package" version="@TOOL_VERSION@">matchms</requirement>
     </requirements>
 
+    <command detect_errors="aggressive"><![CDATA[
+        sh ${matchms_networking_cli}
+    ]]></command>
+
     <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_networking_cli}
-    ]]></command>
-
     <configfiles>
         <configfile name="matchms_networking_cli">
             python3 ${__tool_directory__}/matchms_networking_wrapper.py \
@@ -78,7 +78,7 @@
     </inputs>
 
     <outputs>
-        <data label="Similarity network of ${scores.name}" name="similarity_network_file">
+        <data label="Similarity network of ${scores.name}" name="similarity_network_file" format="graphml">
             <change_format>
                 <when input="graph_format" value="graphml" format="graphml"/>
                 <when input="graph_format" value="cyjs" format="cyjs"/>

tools/matchms/matchms_similarity.xml

@@ -13,14 +13,14 @@
         <requirement type="package" version="@TOOL_VERSION@">matchms</requirement>
     </requirements>
 
-    <environment_variables>
-        <environment_variable name="MPLCONFIGDIR">\$_GALAXY_JOB_TMP_DIR</environment_variable>
-    </environment_variables>
-
     <command detect_errors="exit_code"><![CDATA[
         sh ${matchms_python_cli}
     ]]> </command>
 
+    <environment_variables>
+        <environment_variable name="MPLCONFIGDIR">\$_GALAXY_JOB_TMP_DIR</environment_variable>
+    </environment_variables>
+
     <configfiles>
         <configfile name="matchms_python_cli">
             python3 ${__tool_directory__}/matchms_similarity_wrapper.py \
@@ -64,6 +64,7 @@
                 <param label="Reference spectra" name="references" type="data" format="msp,mgf"
                        help="Reference mass spectra to match against as library."/>
             </when>
+            <when value="TRUE"></when>
         </conditional>
         <param label="Scores array type" name="array_type" type="select" display="radio"
                help="Matrix type for storing scores objects. Sparse type more memory-efficient and better for large arrays.
@@ -113,6 +114,7 @@
                 <param label="tolerance" name="tolerance" type="float" value="60"
                        help="Peaks will be considered a match when less than tolerance apart."/>
             </when>
+            <when value="FALSE"></when>
         </conditional>
     </inputs>
 

tools/matchms/matchms_spectral_similarity.xml

@@ -12,14 +12,14 @@
         <requirement type="package" version="@TOOL_VERSION@">matchms</requirement>
     </requirements>
 
-    <environment_variables>
-        <environment_variable name="MPLCONFIGDIR">\$_GALAXY_JOB_TMP_DIR</environment_variable>
-    </environment_variables>
-
     <command detect_errors="exit_code"><![CDATA[
         python3 ${python_wrapper}
     ]]> </command>
 
+    <environment_variables>
+        <environment_variable name="MPLCONFIGDIR">\$_GALAXY_JOB_TMP_DIR</environment_variable>
+    </environment_variables>
+
 <configfiles>
 <configfile name="python_wrapper">
 @init_logger@

tools/msmetaenhancer/msmetaenhancer.xml

@@ -13,15 +13,15 @@
         <requirement type="package" version="@TOOL_VERSION@">msmetaenhancer</requirement>
     </requirements>
 
+    <command detect_errors="exit_code"><![CDATA[
+        sh ${msmetaenhancer_python_cli}
+    ]]> </command>
+
     <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="exit_code"><![CDATA[
-        sh ${msmetaenhancer_python_cli}
-    ]]> </command>
-
     <configfiles>
         <configfile name="msmetaenhancer_python_cli">
             python3 ${__tool_directory__}/msmetaenhancer_wrapper.py \
@@ -72,6 +72,7 @@
                         <option value="info" selected="true">INFO</option>
                     </param>
                 </when>
+                <when value="FALSE"></when>
             </conditional>
         </section>
     </inputs>
@@ -105,4 +106,8 @@
         ]]>
     </help>
 
+    <citations>
+        <citation type="doi">https://doi.org/10.21105/joss.04494</citation>
+    </citations>
+
 </tool>

tools/msp_merge/msp_merge.xml

@@ -40,4 +40,8 @@
     <help><![CDATA[
         MSPmerge handles input/output files in MSP format using the matchms.importing and matchms.exporting modules (https://matchms.readthedocs.io/en/latest/index.html).
     ]]></help>
+
+    <citations>
+        <citation type="doi">https://doi.org/10.5281/zenodo.6035335</citation>
+    </citations>
 </tool>

tools/mzml_validator/mzml_validator.xml

@@ -63,4 +63,8 @@
         **mzML Schema Validator** validates mzML files against XML Schema Definition (XSD) developed by HUPO Proteomics Standard Initiative
         (https://www.psidev.info/mzML).
     ]]></help>
+
+    <citations>
+        <citation type="doi">https://doi.org/10.5281/zenodo.6035335</citation>
+    </citations>
 </tool>

tools/query/query.xml

@@ -5,11 +5,11 @@
     <expand macro="creator"/>
 
     <requirements>
-        <requirement type="package">click</requirement>
-        <requirement type="package">pyarrow</requirement>
-        <requirement type="package">pytables</requirement>
-        <requirement type="package">pandas</requirement>
-        <requirement type="package">pandasql</requirement>
+        <requirement type="package" version="7.0">click</requirement>
+        <requirement type="package" version="0.15.1">pyarrow</requirement>
+        <requirement type="package" version="3.6.1">pytables</requirement>
+        <requirement type="package" version="1.3.5">pandas</requirement>
+        <requirement type="package" version="0.7.3">pandasql</requirement>
         <requirement type="package" version="3.7">python</requirement>
     </requirements>
 
@@ -88,11 +88,15 @@
             </param>
             <expand macro="internal_name" format="h5"/>
             <expand macro="internal_name" format="sqlite"/>
+            <when value="csv"></when>
+            <when value="tsv"></when>
+            <when value="feather"></when>
+            <when value="parquet"></when>
         </conditional>
     </inputs>
 
     <outputs>
-        <data name="output">
+        <data name="output" format="h5">
             <change_format>
                 <when input="result.format" value="h5" format="h5"/>
                 <when input="result.format" value="csv" format="csv"/>
@@ -121,4 +125,13 @@
             <output name="output" file="ab.csv" ftype="csv"/>
         </test>
     </tests>
+
+    <help>
+    Query tool simplifies data handling by offering seamless conversion between different tabular data types and the execution of SQL SELECT 
+    and JOIN operations on various input file formats. Additionally, it allows you to customize the output format to meet your specific requirements.
+    </help>
+
+    <citations>
+        <citation type="doi">https://doi.org/10.5281/zenodo.6035335</citation>
+    </citations>
 </tool>

tools/ramclustr/macros.xml

@@ -39,10 +39,13 @@
         <edam_topics>
                <edam_topic>topic_3520</edam_topic>       
         </edam_topics>
+     </xml>
+
+    <xml name="refs">
         <xrefs>
                <xref type="bio.tools">ramclustr</xref>
         </xrefs>
-     </xml>
+    </xml>
 
     <xml name="parameters_csv">
         <section name="ms_csv" title="Input MS Data as CSV" expanded="true">

tools/ramclustr/ramclustr.xml

@@ -3,13 +3,14 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro='annotation'/>
     <edam_operations>
         <edam_operation>operation_3557</edam_operation>
         <edam_operation>operation_3435</edam_operation>
         <edam_operation>operation_3432</edam_operation>
         <edam_operation>operation_3465</edam_operation>
     </edam_operations>
-    <expand macro='annotation'/>
+    <expand macro="refs"/>
     <expand macro="creator"/>
 
     <requirements>

tools/ramclustr/ramclustr_define_experiment.xml

@@ -3,10 +3,11 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro='annotation'/>
     <edam_operations>
         <edam_operation>operation_3429</edam_operation>
     </edam_operations>
-    <expand macro='annotation'/>
+    <expand macro="refs"/>
     <expand macro="creator"/>
 
     <command detect_errors="exit_code"><![CDATA[

tools/recetox_aplcms/macros.xml

@@ -13,6 +13,9 @@
               <edam_topic>topic_0091</edam_topic>
               <edam_topic>topic_3520</edam_topic>       
        </edam_topics>
+    </xml>
+
+    <xml name="refs">
        <xrefs>
               <xref type="bio.tools">recetox-aplcms</xref>
        </xrefs>
@@ -89,6 +92,7 @@
                     <param name="sd_cut_max" type="float" value="500" label="Maximal standard deviation"
                             help="The maximum standard deviation - features with a standard deviation greater than this number are eliminated." />
                 </when>
+                <when value="FALSE"></when>
             </conditional>
             <conditional name="peak_estim">
                 <param name="peak_estim_method" type="select" display="radio" label="Peak estimation method"
@@ -100,6 +104,7 @@
                     <param name="moment_power" type="float" value="1" label="Moment power"
                            help="The power parameter for data transformation when fitting the bi-Gaussian mixture model in an EIC." />
                 </when>
+                <when value="EM"></when>
             </conditional>
         </section>
     </xml>