comparison matchms_similarity.xml @ 1:872d8040f713 draft default tip

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a

0:e5010b19d64d

<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>

    <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

    <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>

            </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"/>

        </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>

            <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="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@

1:872d8040f713

<tool id="matchms_similarity" name="matchms similarity" version="@TOOL_VERSION@+galaxy2" profile="21.09">
    <description>calculate the similarity score and matched peaks</description>

    <macros>
        <import>macros.xml</import>
        <import>help.xml</import>

    <requirements>
        <requirement type="package" version="0.8.0">spec2vec</requirement>
        <requirement type="package" version="@TOOL_VERSION@">matchms</requirement>
    </requirements>

    <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 \
            #if $ri_filtering.is_true == "TRUE"
            -r $ri_filtering.tolerance \
            #end if
            #if $symmetric.is_symmetric == "TRUE"
            -s \
            #else
            --ref "$references" \
            --ref_format "$references.ext" \
            #end if

    <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="select">
                <option value="FALSE" selected="true">FALSE</option>
                <option value="TRUE">TRUE</option>
            </param>
            <when value="FALSE">
                <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.
                    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>

            </when>
        </conditional>


        <conditional name="ri_filtering">
            <param name="is_true" label="Apply RI filtering" type="select">
                <option value="FALSE" selected="true">FALSE</option>
                <option value="TRUE">TRUE</option>
            </param>
            <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>
            <when value="FALSE"></when>
        </conditional>
    </inputs>

    <outputs>
        <data label="$metric.similarity_metric scores of ${on_string}" name="similarity_scores" format="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>

            <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="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="1000"/>
        </test>
    </tests>

    <help>
        @HELP_matchms@