--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ramclustr.xml	Wed Jul 28 08:42:02 2021 +0000
@@ -0,0 +1,195 @@
+<tool id="ramclustr" name="RAMClustR" version="@TOOL_VERSION@+galaxy1">
+    <macros>
+        <import>ramclustr_macros.xml</import>
+    </macros>
+
+    <requirements>
+        <container type="docker">recetox/ramclustr:1.1.0-recetox0</container>
+    </requirements>
+
+    <command detect_errors="aggressive"><![CDATA[
+        Rscript
+            -e 'source("${__tool_directory__}/ramclustr_wrapper.R")'
+            #if $filetype.type_choice == "xcms":
+            -e 'x <- ramclustr_xcms(
+                input_xcms = "$filetype.input_xcms",
+            #else:
+            -e 'x <- ramclustr_csv(
+                ms="$filetype.ms_csv.ms",
+                idmsms="$filetype.ms_csv.idmsms",
+                feature_delimiter="$filetype.ms_csv.feature_delimiter",
+                sample_name_column = $filetype.ms_csv.sample_name_column,
+                retention_time_column= $filetype.ms_csv.retention_time_column,
+            #end if
+                sr = $filetype.required.sr,
+                deep_split = $filetype.required.deepSplit,
+                block_size = $filetype.required.blocksize,
+                mult = $filetype.required.mult,
+                hmax = $filetype.required.hmax,
+                collapse = $filetype.required.collapse,
+                use_pheno = $filetype.required.usePheno,
+                qc_inj_range = $filetype.required.qc_inj_range,
+                normalize = "$filetype.required.normalize",
+                min_module_size = $filetype.required.minModuleSize,
+                linkage = "$filetype.required.linkage",
+                mzdec = $filetype.required.mzdec,
+                cor_method = "$filetype.required.cor_method",
+                rt_only_low_n = $filetype.required.rt_only_low_n,
+                replace_zeros = $filetype.required.replace_zeros,
+            #if $filetype.type_choice == "xcms":
+                #if $filetype.optional.st
+                    st = $filetype.optional.st,
+                #end if
+            #else:
+                st = $filetype.ms_csv.st,
+            #end if
+                #if $filetype.optional.maxt
+                    maxt = $filetype.optional.maxt,
+                #end if
+                #if $filetype.optional.fftempdir
+                    fftempdir = $filetype.optional.fftempdir,
+                #end if
+                #if $filetype.metadata.batch_order_qc
+                    metadata_file = "${filetype.metadata.batch_order_qc}",
+                #end if
+                )'
+            -e 'store_output(x, "$result", "$method_metadata", $filetype.required.merge_msp, "$spec_abundance")'
+    ]]>
+    </command>
+
+    <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">
+                <param name="input_xcms" label="input_xcms" type="data" format="rdata.xcms.fillpeaks" help=": containing grouped feature data for clustering by ramclustR" />
+                <expand macro="parameters_required" />
+                <expand macro="parameters_optional_xcms" />
+                <expand macro="parameters_optional_metadata" />
+            </when>
+            <when value="csv">
+                <expand macro="parameters_csv" />
+                <expand macro="parameters_required" />
+                <expand macro="parameters_optional_csv" />
+                <expand macro="parameters_optional_metadata" />
+            </when>
+        </conditional>
+    </inputs>
+
+    <outputs>
+        <data label="${tool.name} on ${on_string}" name="result" format="RData" />
+        <data label="Spec Abundance of ${on_string}" name="spec_abundance" format="csv" />
+        <data label="Metadata for ${tool.name} on ${on_string}" name="method_metadata" format="txt"/>
+        <expand macro="output_msp"/>
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="type_choice" value="xcms"/>
+            <param name="input_xcms" value="xcmsObj_1.rdata.xcms.fillpeaks" ftype="rdata.xcms.fillpeaks"/>
+            <output name="result" file="ramclustObj_xcms_1.rdata" ftype="RData" compare="sim_size" delta="100"/>
+            <output_collection name="mass_spectra" type="list">
+                <element name="fill" file="fill_xcms_1.msp" ftype="msp" checksum="md5$d53ed06d6f888a88ff321f833e29bb47"/>
+            </output_collection>
+            <output name="method_metadata" file="metadata_xcms_1.txt" ftype="txt" checksum="md5$81db28b08860988e3966f585b0f44b0f"/>
+            <output name="spec_abundance" file="spec_abundance_xcms_1.csv" ftype="csv" compare="sim_size" delta="100"/>
+        </test>
+        <test>
+            <param name="type_choice" value="xcms"/>
+            <param name="input_xcms" value="xcmsObj_2.rdata.xcms.fillpeaks" ftype="rdata.xcms.fillpeaks"/>
+            <param name="batch_order_qc" value="sample_metadata_xcms_2.csv" ftype="csv" />
+            <output name="result" file="ramclustObj_xcms_2.rdata" ftype="RData" compare="sim_size" delta="200"/>
+            <output_collection name="mass_spectra" type="list">
+                <element name="fill" file="fill_xcms_2.msp" ftype="msp" lines_diff="10"/>
+            </output_collection>
+            <output name="method_metadata" file="metadata_xcms_2.txt" ftype="txt" checksum="md5$286e4aa53c38c99e92202584d7407406"/>
+            <output name="spec_abundance" file="spec_abundance_xcms_2.csv" ftype="csv" compare="sim_size" delta="100"/>
+        </test>
+        <test>
+            <param name="type_choice" value="csv"/>
+            <param name="ms" value="csv_test-input_1_2.csv" ftype="csv"/>
+            <param name="sample_name_column" value="1"/>
+            <param name="feature_delimiter" value="_"/>
+            <param name="retention_time_column" value="2"/>
+            <param name="st" value="5.0"/>
+            <param name="sr" value="0.5"/>
+            <param name="deepSplit" value="False"/>
+            <param name="blocksize" value="1000"/>
+            <param name="mult" value="1"/>
+            <param name="hmax" value="0.3"/>
+            <param name="collapse" value="True"/>
+            <param name="usePheno" value="True"/>
+            <param name="normalize" value="none"/>
+            <param name="qc_inj_range" value="20"/>
+            <param name="minModuleSize" value="2"/>
+            <param name="linkage" value="average"/>
+            <param name="mzdec" value="3"/>
+            <param name="cor_method" value="pearson"/>
+            <param name="rt_only_low_n" value="True"/>
+            <param name="replace_zeros" value="True"/>
+            <param name="Merge MSP Files" value="True"/>
+            <param name="maxt" value="1"/>
+            <output name="result" file="ramclustObj_csv_1.rdata"/>
+            <output name="spec_abundance" file="spec_abundance_csv_1.csv" ftype="csv"/>
+            <output name="method_metadata" file="metadata_csv_1.txt" ftype="txt"/>
+            <output_collection name="mass_spectra" type="list">
+                <element name="fill" file="spectra_csv_1.msp" ftype="msp"/>
+            </output_collection>
+        </test>
+        <test>
+            <param name="type_choice" value="csv"/>
+            <param name="ms" value="csv_test-input_1_2.csv" ftype="csv"/>
+            <param name="sample_name_column" value="1"/>
+            <param name="feature_delimiter" value="_"/>
+            <param name="retention_time_column" value="2"/>
+            <param name="batch_order_qc" value="sample_metadata_csv_2.csv" ftype="csv" />
+            <output name="result" file="ramclustObj_csv_2.rdata"/>
+            <output name="spec_abundance" file="spec_abundance_csv_2.csv" ftype="csv"/>
+            <output name="method_metadata" file="metadata_csv_2.txt" ftype="txt"/>
+            <output_collection name="mass_spectra" type="list">
+                <element name="fill" file="spectra_csv_2.msp" ftype="msp" lines_diff="10"/>
+            </output_collection>
+        </test>
+    </tests>
+
+    <help>
+    Documentation
+        For documentation on the tool see https://github.com/cbroeckl/RAMClustR/blob/master/vignettes/RAMClustR.Rmd
+
+    Upstream Tools
+        +-------+----------------------+----------------------+------------+
+        | Name  | Output File          | Format               | Parameter  |
+        +=======+======================+======================+============+
+        | xcms  | xset.fillPeaks.RData | rdata.xcms.fillpeaks | xcmsObj    |
+        +-------+----------------------+----------------------+------------+
+
+        The tool takes an **xcmsSet** object as input and extracts all relevant information.
+
+        +-------+------------------------+--------+------------+
+        | Name  | Output File            | Format | Parameter  |
+        +=======+========================+========+============+
+        | ???   | Feature Table with MS1 | csv    | ms         |
+        +-------+------------------------+--------+------------+
+        | ???   | Feature Table with MS2 | csv    | idmsms     |
+        +-------+------------------------+--------+------------+
+
+        Alternatively, the tool takes a **csv** table as input which has to fulfill the following requirements
+
+        (1) no more than one sample (or file) name column and one feature name row;
+        (2) feature names that contain the mass and retention times, separated by a constant delimiter; and
+        (3) features in columns and samples in rows.
+
+    Downstream Tools
+        +---------+--------------+----------------------+
+        | Name    | Output File  | Format               |
+        +=========+==============+======================+
+        | matchMS | Mass Spectra | collection (tgz/msp) |
+        +---------+--------------+----------------------+
+
+    @GENERAL_HELP@
+    </help>
+
+    <expand macro="citations" />
+</tool>