--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ramclustr.xml	Tue Mar 22 16:09:16 2022 +0000
@@ -0,0 +1,175 @@
+<tool id="ramclustr" name="RAMClustR" version="@TOOL_VERSION@+galaxy2">
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="creator"/>
+
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">r-ramclustr</requirement>
+        <requirement type="package" version="3.14.0">bioconductor-xcms</requirement>
+    </requirements>
+
+    <command detect_errors="aggressive"><![CDATA[
+        Rscript
+            -e 'source("${__tool_directory__}/ramclustr_wrapper.R")'
+            -e 'source("${ramclustr_method}")'
+    ]]>
+    </command>
+    <configfiles>
+        <configfile name="ramclustr_method">
+            store_output(
+                #if $filetype.type_choice == "xcms":
+                ramclustr_xcms(
+                    input_xcms = "$filetype.xcms.input_xcms",
+                    use_pheno = $filetype.xcms.usePheno,
+                #else:
+                ramclustr_csv(
+                    ms = "$filetype.ms_csv.ms",
+                    idmsms = "$filetype.ms_csv.idmsms",
+                #end if
+                    sr = $filetype.required.sr,
+                    #if $filetype.type_choice == "xcms":
+                        #if $filetype.required.st
+                            st = $filetype.required.st,
+                        #end if
+                    #else:
+                        st = $filetype.required.st,
+                    #end if
+                    cor_method = "$filetype.required.cor_method",
+                    maxt = $filetype.required.maxt,
+                    linkage = "$clustering.linkage",
+                    min_module_size = $clustering.minModuleSize,
+                    hmax = $clustering.hmax,
+                    deep_split = "$clustering.deepSplit",
+                    normalize = "$normalisation.normalisation_method.normalize",
+                    #if "$normalisation.normalisation_method.normalize" == "batch.qc":
+                        metadata_file = "$normalisation.normalisation_method.batch_order_qc",
+                        qc_inj_range = $normalisation.normalisation_method.qc_inj_range,
+                    #end if
+                    block_size = $performance.blocksize,
+                    mult = $performance.mult,
+                    mzdec = $msp_output_details.mzdec,
+                    rt_only_low_n = $extras.rt_only_low_n,
+                    replace_zeros = $extras.replace_zeros,
+                    #if $extras.ExpDes:
+                        exp_design = "${$extras.ExpDes}"
+                    #end if
+                ),
+                $msp_output_details.merge_msp,
+                "$spec_abundance",
+            #if $msp_output_details.merge_msp:
+                "$mass_spectra_merged"
+            #else:
+                NULL
+            #end if
+                )
+        </configfile>
+    </configfiles>
+    <inputs>
+        <conditional name="filetype">
+            <param name="type_choice" type="select" label="Choose input format:">
+                <option value="xcms" selected="true">XCMS</option>
+                <option value="csv">CSV</option>
+            </param>
+            <when value="xcms">
+                <expand macro="parameters_xcms" />
+                <section name="required" title="General parameters" expanded="true">
+                    <param label="Sigma t" name="st" type="float" optional="true" help="Retention time similarity (optional).
+                           A recommended starting point is half the value of your average chromatographic peak width at half max (seconds))."/>
+                    <expand macro="parameters_required" />
+                </section>
+            </when>
+            <when value="csv">
+                <expand macro="parameters_csv" />
+                <section name="required" title="General parameters" expanded="true">
+                    <param label="Sigma t" name="st" type="float" value="1" help="Retention time similarity.
+                           A recommended starting point is half the value of your average chromatographic peak width at half max (seconds))."/>
+                    <expand macro="parameters_required" />
+                </section>
+            </when>
+        </conditional>
+        <expand macro="main_parameters" />
+    </inputs>
+
+    <outputs>
+        <data label="Spec Abundance of ${on_string}" name="spec_abundance" format="csv" />
+        <expand macro="output_msp"/>
+    </outputs>
+
+    <tests>
+        <test><!-- TEST 1 -->
+            <section name="filetype">
+                <param name="type_choice" value="xcms"/>
+                <section name="xcms">
+                    <param name="input_xcms" value="test1_xcmsObj_1.rdata.xcms.fillpeaks" ftype="rdata.xcms.fillpeaks"/>
+                </section>
+                <section name="required">
+                    <param name="maxt" value="259.8"/>
+                </section>
+            </section>
+            <section name="extras">
+                <param name="ExpDes" value="lc-ramclustr-define-experiment.csv" ftype="csv"/>
+            </section>
+            <output name="mass_spectra_merged" file="test1_fill_xcms_1.msp" ftype="msp"/>
+            <output name="spec_abundance" file="test1_spec_abundance_xcms_1.csv" ftype="csv" compare="sim_size" delta="100"/>
+        </test>
+        <test><!-- TEST 2 -->
+            <section name="filetype">
+                <param name="type_choice" value="xcms"/>
+                <section name="xcms">
+                    <param name="input_xcms" value="test2_xcmsObj_2.rdata.xcms.fillpeaks" ftype="rdata.xcms.fillpeaks"/>
+                </section>
+                <section name="required">
+                    <param name="maxt" value="78.4"/>
+                </section>
+            </section>
+            <section name="normalisation">
+                <section name="normalisation_method">
+                    <param name="batch_order_qc" value="test2_sample_metadata_xcms_2.csv" ftype="csv" />
+                </section>
+            </section>
+            <output name="mass_spectra_merged" file="test2_fill_xcms_2.msp" ftype="msp" compare="diff" lines_diff="10"/>
+            <output name="spec_abundance" file="test2_spec_abundance_xcms_2.csv" ftype="csv" compare="sim_size" delta="100"/>
+        </test>
+        <test><!-- TEST 3 -->
+            <section name="filetype">
+                <param name="type_choice" value="csv"/>
+                <section name="ms_csv">
+                    <param name="ms" value="test3_csv_test-input_1_2.csv" ftype="csv"/>
+                </section>
+                <section name="required">
+                    <param name="st" value="5.0"/>
+                    <param name="maxt" value="1"/>
+                </section>
+            </section>
+            <section name="performance">
+                <param name="blocksize" value="1000"/>
+                <param name="mult" value="1"/>
+            </section>
+            <output name="mass_spectra_merged" file="test3_spectra_csv_1.msp" ftype="msp"/>
+            <output name="spec_abundance" file="test3_spec_abundance_csv_1.csv" ftype="csv"/>
+        </test>
+        <test><!-- TEST 4 -->
+            <section name="filetype">
+                <param name="type_choice" value="csv"/>
+                <section name="ms_csv">
+                    <param name="ms" value="test3_csv_test-input_1_2.csv" ftype="csv"/>
+                </section>
+            </section>
+            <output name="mass_spectra_merged" file="test4_spectra_csv_2.msp" ftype="msp" lines_diff="10"/>
+        </test>
+    </tests>
+
+    <help>
+        <![CDATA[
+            @HELP@
+
+        .. rubric:: **Footnotes**
+        .. [1] Correlation, Variance and Covariance - `stats::cor <https://www.rdocumentation.org/packages/stats/versions/3.6.2/topics/cor>`_
+        .. [2] Hierarchical Clustering - `stats::hclust <https://www.rdocumentation.org/packages/stats/versions/3.6.2/topics/hclust>`_
+        .. [3] Dynamic Dendrogram Pruning Based on Dendrogram Only - `dynamicTreeCut::cutreeDynamicTree <https://www.rdocumentation.org/packages/dynamicTreeCut/versions/1.63-1/topics/cutreeDynamicTree>`_
+        ]]>
+    </help>
+
+    <expand macro="citations" />
+</tool>