diff matchms_similarity.xml @ 0:e5010b19d64d draft

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/matchms_similarity.xml	Tue Jun 27 14:26:29 2023 +0000
@@ -0,0 +1,190 @@
+<tool id="matchms_similarity" name="matchms similarity" version="@TOOL_VERSION@+galaxy0" profile="21.09">
+    <description>calculate the similarity score and matched peaks</description>
+
+    <macros>
+        <import>macros.xml</import>
+        <import>help.xml</import>
+    </macros>
+    <expand macro="creator"/>
+    <expand macro="bio.tools"/>
+
+    <requirements>
+        <requirement type="package" version="0.8.0">spec2vec</requirement>
+        <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>
+
+    <configfiles>
+        <configfile name="matchms_python_cli">
+            python3 ${__tool_directory__}/matchms_similarity_wrapper.py \
+            #if $ri_filtering.is_true
+            -r $ri_filtering.tolerance \
+            #end if
+            #if $symmetric.is_symmetric
+            -s \
+            #else
+            --ref "$references" \
+            --ref_format "$references.ext" \
+            #end if
+            --array_type "$array_type" \
+            #if $metric.similarity_metric == "Spec2Vec"
+            --spec2vec_model "$metric.model_metadata" \
+            --spec2vec_weights "$metric.model_weights" \
+            --allow_missing_percentage $metric.algorithm.allow_missing_percentage \
+            #end if
+            "$queries" \
+            "$queries.ext" \
+            "$metric.similarity_metric" \
+            #if $metric.similarity_metric == "Spec2Vec"
+            0 \
+            0 \
+            #else
+            $metric.algorithm.tolerance \
+            $metric.algorithm.mz_power \
+            #end if
+            $metric.algorithm.intensity_power \
+            "$similarity_scores"
+        </configfile>
+    </configfiles>
+
+    <inputs>
+        <param label="Queries spectra" name="queries" type="data" format="msp,mgf"
+               help="Query mass spectra to match against references."/>
+        <conditional name="symmetric">
+            <param name="is_symmetric" label="Symmetric" type="boolean" truevalue="TRUE" falsevalue="FALSE"
+                   checked="false"/>
+            <when value="FALSE">
+                <param label="Reference spectra" name="references" type="data" format="msp,mgf"
+                       help="Reference mass spectra to match against as library."/>
+            </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.
+                    Note that whatever is selected the output might still be sprase array if scores have too much 0-entries.">
+            <option value="numpy" selected="true">dense</option>
+            <option value="sparse">sparse</option>
+        </param>
+        <conditional name="metric">
+            <param label="Similarity metric" name="similarity_metric" type="select" display="radio"
+                help="Similarity metric to use for score computation.">
+                <expand macro="similarity_metrics"/>
+                <option value="Spec2Vec">Spec2Vec</option>
+            </param>
+            <when value="CosineGreedy">
+                <expand macro="similarity_algorithm_params"/>
+            </when>
+            <when value="CosineHungarian">
+                <expand macro="similarity_algorithm_params"/>
+            </when>
+            <when value="ModifiedCosine">
+                <expand macro="similarity_algorithm_params"/>
+            </when>
+            <when value="NeutralLossesCosine">
+                <expand macro="similarity_algorithm_params"/>
+            </when>
+            <when value="Spec2Vec">
+                <param label="Model JSON file" name="model_metadata" type="data" format="json"
+                       help="Model JSON file to use for Spec2Vec similarity computing."/>
+                <param label="Model NPY file" name="model_weights" type="data" format="binary"
+                       help="Model NPY file to use for Spec2Vec similarity computing."/>
+
+                <section name="algorithm" title="Algorithm Parameters" expanded="true">
+                    <param label="intensity_power" name="intensity_power" type="float" value="0.0"
+                           help="Spectrum vectors are a weighted sum of the word vectors. The given word intensities will be raised to the given power.
+                            The default is 0, which means that no weighing will be done."/>
+                    <param label="Maximum share of new peaks" name="allow_missing_percentage" type="float" value="0.1" max="1.0" min="0.0"
+                           help="Maximum allowed share of the peaks that are new to the model in relation to the whole peak corpus."/>
+                </section>
+            </when>
+        </conditional>
+
+
+        <conditional name="ri_filtering">
+            <param name="is_true" label="Apply RI filtering" type="boolean" truevalue="TRUE" falsevalue="FALSE"
+                   checked="false"/>
+            <when value="TRUE">
+                <param label="tolerance" name="tolerance" type="float" value="60"
+                       help="Peaks will be considered a match when less than tolerance apart."/>
+            </when>
+        </conditional>
+    </inputs>
+
+    <outputs>
+        <data label="$metric.similarity_metric scores of ${on_string}" name="similarity_scores" format="json"/>
+    </outputs>
+
+    <tests>
+        <test> <!-- TEST #1: Test scoring of different file formats. -->
+            <param name="references" value="similarity/fill.mgf" ftype="mgf"/>
+            <param name="queries" value="similarity/fill2.msp" ftype="msp"/>
+            <conditional name="metric">
+                <param name="similarity_metric" value="CosineGreedy"/>
+            </conditional>
+            <output name="similarity_scores" file="similarity/scores_test1_out.json" ftype="json"/>
+        </test>
+        <test> <!-- TEST #2: Test scoring of the same file formats. -->
+            <param name="references" value="similarity/RECETOX_Exposome_pesticides_HR_MS_20220323.msp" ftype="msp"/>
+            <param name="queries" value="similarity/fill2.msp" ftype="msp"/>
+            <conditional name="metric">
+                <param name="similarity_metric" value="CosineGreedy"/>
+            </conditional>
+            <output name="similarity_scores" file="similarity/scores_test2_out.json" ftype="json"/>
+        </test>
+        <test> <!-- TEST #3: Test scoring with applying RI filtering  -->
+            <param name="references" value="similarity/fill.mgf" ftype="mgf"/>
+            <param name="queries" value="similarity/fill2.msp" ftype="msp"/>
+            <conditional name="ri_filtering">
+                <param name="is_true" value="True"></param>
+                <param name="tolerance" value="60.0" />
+            </conditional>
+            <conditional name="metric">
+                <param name="similarity_metric" value="CosineHungarian"/>
+            </conditional>
+            <output name="similarity_scores" file="similarity/scores_test3_out.json" ftype="json"/>
+        </test>
+        <test> <!-- TEST #4: Test symmetric scoring. -->
+            <param name="queries" value="similarity/recetox_gc-ei_ms_20201028.msp" ftype="msp"/>
+            <param name="is_symmetric" value="TRUE"/>
+            <conditional name="metric">
+                <param name="similarity_metric" value="NeutralLossesCosine"/>
+            </conditional>
+            <output name="similarity_scores" file="similarity/scores_test4_out.json" ftype="json"/>
+        </test>
+        <test> <!-- TEST #5: Test symmetric scoring with applying RI filtering. -->
+            <param name="queries" value="similarity/recetox_gc-ei_ms_20201028.msp" ftype="msp"/>
+            <conditional name="metric">
+                <param name="similarity_metric" value="ModifiedCosine"/>
+            </conditional>
+            <param name="is_symmetric" value="TRUE" />
+            <conditional name="ri_filtering">
+                <param name="is_true" value="True"></param>
+                <param name="tolerance" value="60.0" />
+            </conditional>
+            <output name="similarity_scores" file="similarity/scores_test5_out.json" ftype="json"/>
+        </test>
+        <test> <!-- TEST #6: Test Spec2Vec. -->
+            <param name="references" value="similarity/spec2vec/inp_filtered_library.msp" ftype="msp"/>
+            <param name="queries" value="similarity/spec2vec/inp_filtered_spectra.msp" ftype="msp"/>
+            <conditional name="metric">
+                <param name="similarity_metric" value="Spec2Vec"/>
+                <param name="model_metadata" value="similarity/spec2vec/model.json" ftype="json"/>
+                <param name="model_weights" value="similarity/spec2vec/weights_100.binary" ftype="auto"/>
+                <param name="allow_missing_percentage" value="1.0"/>
+            </conditional>
+            <output name="similarity_scores" file="similarity/scores_test6_out.json" ftype="json" compare="sim_size" delta="100000"/>
+        </test>
+    </tests>
+
+    <help>
+        @HELP_matchms@
+    </help>
+
+    <expand macro="citations"/>
+</tool>