--- a/galaxy/tools/LC-MSMS/XSeekerPreparator.xml	Thu Nov 19 14:28:46 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,343 +0,0 @@
-<tool id="xseeker_preparator"
-      name="XSeeker Preparator"
-      version="1.0.1"
-      profile="20.04"
->
-    <description>Prepare RData file from CAMERA to be visualized in XSeeker</description>
-    
-    <edam_operations>
-        <edam_operation>operation_1812</edam_operation>
-        <edam_operation>operation_0335</edam_operation>
-    </edam_operations>
-    
-    <requirements>
-        <requirement type="set_environment">R_SCRIPT_PATH</requirement>
-        <!-- 
-        <requirement type="package" version="4.0.0">R</requirement>
-        -->
-        <requirement type="package" version="4.0.0">R</requirement>
-        <requirement type="package" version="1.6.6">optparse</requirement>
-        <requirement type="package" version="3.10.2">xcms</requirement>
-        <requirement type="package" version="1.2.1">blob</requirement>
-        <requirement type="package" version="0.9.4">fst</requirement>
-        <requirement type="package" version="1.4.0">stringr</requirement>
-        <requirement type="package">DBModelR</requirement>
-    </requirements>
-    
-    <stdio>
-
-        <exit_code 
-            range="1"
-            level="warning"
-            description="Selected samples have no data associated to them."
-        />
-
-        <exit_code 
-            range="2"
-            level="warning"
-            description="Some samples have no data associated to them."
-        />
-
-    </stdio>
-
-    <version_command>
-        R_SCRIPT_PATH '$__tool_directory__/XSeekerPreparator.R' -v
-    </version_command>
-
-    <command>
-        <![CDATA[
-
-            R_SCRIPT_PATH '$__tool_directory__/XSeekerPreparator.R'
-
-                -P
-
-                --input '$input'
-                --output '$output'
-
-                #if $samples.selected
-                    --samples '${",".join(samples.selected)}'
-                #end if
-
-                #if $database.archetypes
-                    --archetype '${",".join($database.archetypes)}'
-                #end if
-
-                #if $database.base.kind == "tabular"
-                    --compounds-csv '${database.base.tabular}'
-                #else if $database.base.kind == "sql"
-                    --database '${database.base.sql}'
-                #end if
-
-                #if $database.models.kind == "default"
-                    --models '${base_config}'
-                #else
-                    --models '${database.models.url}'
-                #end if
-
-        ]]>
-
-    </command>
-
-    <inputs>
-        <param 
-            name="input"
-            type="data"
-            multiple="false"
-            label="Rdata to prepare"
-            optional="false"
-            format="rdata"
-        >
-        </param>
-        <section name="samples" title="Samples Options" expanded="false">
-            <param 
-                name="selected"
-                type="data"
-                multiple="true"
-                label="Samples to visualize"
-                optional="true"
-                format="mzml"
-            >
-            </param>
-        </section>
-
-        <section name="database" title="Database Options" expanded="false">
-            <param
-                name="archetypes"
-                type="select"
-                multiple="true"
-                label="Molecule family (for database's compounds enrichment)"
-            >
-                <option value="G" selected="true">General</option>
-                <option value="H">Halogenates</option>
-            </param>
-
-            <conditional name="base">
-                <param name="kind" type="select" label="File containing compound's type">
-                    <option value="none" selected="true">None (deafult)</option>
-                    <option value="tabular">tabular</option>
-                    <option value="sql">sql</option>
-                </param>
-                <when value="tabular">
-                    <param
-                        name="tabular"
-                        type="data"
-                        multiple="true"
-                        label="Tabular file containing compound to use in XSeeker"
-                        optional="true"
-                        format="tabular"
-                    >
-                    </param>
-                </when>
-                <when value="sql">
-                    <param
-                        name="sql"
-                        type="data"
-                        multiple="true"
-                        label="SQL file containing compound to use in XSeeker"
-                        optional="true"
-                        format="sql"
-                    >
-                    </param>
-                </when>
-            </conditional>
-
-            <conditional name="models">
-                <param name="kind" type="select" label="How is the database's model defined">
-                    <option value="default" selected="true">Default (regular XSeeker Database)</option>
-                    <option value="url">Download model file</option>
-                    <option value="git">Get versionned model file</option>
-                </param>
-                <when value="url">
-                    <param name="url" type="text" format="url" label="File URL"/>
-                </when>
-                <when value="git">
-                    <param name="url" type="text" format="url" label="Repo URL"/>
-                </when>
-            </conditional>
-        </section>
-    </inputs>
-
-
-    <outputs>
-        <data format="xseeker.sqlite" name="output" />
-    </outputs>
-
-    <configfiles>
-        <configfile name="base_config">
-tryCatch({
-    DBModelR::ModelDefinition(table="yui", fields=list(yui="INTEGER"))
-}, error=function(e) {
-    stop("Please, install DBModelR before you source this file.")
-})
-
-list(
-    adduct=DBModelR::ModelDefinition(
-        table="adduct",
-        fields=list(
-            name="TEXT",
-            mass="FLOAT",
-            charge="INTEGER",
-            multi="INTEGER",
-            formula_add="TEXT",
-            formula_ded="TEXT",
-            sign="TEXT",
-            oidscore="INTEGER",
-            quasi="INTEGER",
-            ips="FLOAT"
-        )
-    ),
-    cluster=DBModelR::ModelDefinition(
-        table="cluster",
-        fields=list(
-            clusterID="INTEGER",
-            formula="TEXT",
-            annotation="TEXT",
-            coeff="FLOAT",
-            r_squared="FLOAT",
-            charge="INTEGER",
-            mean_rt="FLOAT",
-            score="FLOAT",
-            deviation="FLOAT",
-            status="TEXT",
-            adduct="TEXT",
-            curent_group="INTEGER",
-            pc_group="INTEGER",
-            align_group="INTEGER",
-            xcms_group="INTEGER"
-        ),
-        one=list("sample", "compound")
-    ),
-    compound=DBModelR::ModelDefinition(
-        table="compound",
-        fields=list(
-            name="TEXT",
-            common_name="TEXT",
-            formula="TEXT",
-            charge="INTEGER",
-            date="TEXT",
-            mz="FLOAT"
-        )
-    ),
-    feature=DBModelR::ModelDefinition(
-        table="feature",
-        fields=list(
-            featureID="INTEGER",
-            mz="FLOAT",
-            mz_min="FLOAT",
-            mz_max="FLOAT",
-            rt="FLOAT",
-            rt_min="FLOAT",
-            rt_max="FLOAT",
-            int_o="FLOAT",
-            int_b="FLOAT",
-            max_o="FLOAT",
-            iso="TEXT",
-            abundance="FLOAT"
-        ),
-        one=list("cluster")
-    ),
-    instrument=DBModelR::ModelDefinition(
-        table="instrument",
-        fields=list(
-            model="TEXT",
-            manufacturer="TEXT",
-            analyzer="TEXT",
-            detector_type="TEXT",
-            ion_source="TEXT"
-        )
-    ),
-    instrument_config=DBModelR::ModelDefinition(
-        table="instrument_config",
-        fields=list(
-            resolution="TEXT",
-            agc_target="TEXT",
-            maximum_IT="TEXT",
-            number_of_scan_range="TEXT",
-            scan_range="TEXT",
-            version="TEXT"
-        )
-    ),
-    project=DBModelR::ModelDefinition(
-        table="project",
-        fields=list(
-            name="TEXT",
-            comment="TEXT"
-        ),
-        one=list("sample")
-    ),
-    sample=DBModelR::ModelDefinition(
-        table="sample",
-        fields=list(
-            name="TEXT",
-            path="TEXT",
-            polarity="TEXT",
-            kind="TEXT", ## rdata or mxml or enriched_rdata
-            raw="BLOB"
-        ),
-        one=list(
-            "peak_picking_parameters",
-            "pairing_parameters",
-            "alignmenmt_parameters",
-            "camera_parameters",
-            "instrument",
-            "instrument_config",
-            "software",
-            "smol_xcms_set"
-        )
-    ),
-    smol_xcms_set=DBModelR::ModelDefinition(
-        table="smol_xcms_set",
-        fields=list(
-            raw="BLOB"
-        )
-    ),
-    software=DBModelR::ModelDefinition(
-        table="software",
-        fields=list(
-            name="TEXT",
-            version="TEXT"
-        )
-    ),
-    peak_picking_parameters=DBModelR::ModelDefinition(
-        table="peak_picking_parameters",
-        fields=list(
-            ppm="FLOAT",
-            peakwidth="TEXT",
-            snthresh="TEXT",
-            prefilterStep="TEXT",
-            prefilterLevel="TEXT",
-            mzdiff="TEXT",
-            fitgauss="TEXT",
-            noise="TEXT",
-            mzCenterFun="TEXT",
-            integrate="INTEGER",
-            firstBaselineCheck="TEXT",
-            snthreshIsoROIs="TEXT",
-            maxCharge="INTEGER",
-            maxIso="INTEGER",
-            mzIntervalExtension="TEXT"
-        )
-    ),
-    alignmenmt_parameters=DBModelR::ModelDefinition(
-        table="alignmenmt_parameters",
-        fields=list(
-            binSize="TEXT",
-            centerSample="TEXT",
-            response="TEXT",
-            distFun="TEXT",
-            gapInit="TEXT",
-            gapExtend="TEXT",
-            factorDiag="TEXT",
-            factorGap="TEXT",
-            localAlignment="INTEGER",
-            initPenalty="TEXT",
-            bw="TEXT",
-            minFraction="TEXT",
-            minSamples="TEXT",
-            maxFeatures="TEXT"
-        )
-    )
-)
-        </configfile>
-    </configfiles>
-</tool>