--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ramclustr_xcms.xml	Mon Dec 07 22:14:20 2020 +0000
@@ -0,0 +1,93 @@
+<tool id="ramclustr_xcms" name="RAMClustR (XCMS)" version="@TOOL_VERSION@+galaxy0">
+    <macros>
+        <import>ramclustr_macros.xml</import>
+    </macros>
+
+    <requirements>
+        <container type="docker">recetox/ramclustr:1.1.0-recetox0</container>
+    </requirements>
+
+    <inputs>
+        <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" />
+    </inputs>
+
+    <command detect_errors="aggressive"><![CDATA[
+        Rscript
+            -e 'source("${__tool_directory__}/ramclustr_wrapper.R")'
+            -e 'x <- ramclustr_xcms(
+                input_xcms = "$input_xcms",
+                sr = $required.sr,
+                deep_split = $required.deepSplit,
+                block_size = $required.blocksize,
+                mult = $required.mult,
+                hmax = $required.hmax,
+                collapse = $required.collapse,
+                use_pheno = $required.usePheno,
+                qc_inj_range = $required.qc_inj_range,
+                normalize = "$required.normalize",
+                min_module_size = $required.minModuleSize,
+                linkage = "$required.linkage",
+                mzdec = $required.mzdec,
+                cor_method = "$required.cor_method",
+                rt_only_low_n = $required.rt_only_low_n,
+                replace_zeros = $required.replace_zeros,
+                #if $optional.st
+                    st = $optional.st,
+                #end if
+                #if $optional.maxt
+                    maxt = $optional.maxt,
+                #end if
+                #if $optional.fftempdir
+                    fftempdir = $optional.fftempdir,
+                #end if
+                )'
+            -e 'store_output(x, "$result", "$method_metadata", $required.merge_msp, "$spec_abundance")'
+    ]]>
+    </command>
+
+    <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 ${on_string}" name="method_metadata" format="txt"/>
+        <expand macro="output_msp"/>
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="input_xcms" value="xcmsObj.rdata.xcms.fillpeaks" ftype="rdata.xcms.fillpeaks"/>
+            <output name="result" file="ramclustObj.rdata" ftype="RData" compare="sim_size" delta="100"/>
+            <output_collection name="mass_spectra" type="list">
+                <element name="fill" file="fill.msp" ftype="msp" checksum="md5$d53ed06d6f888a88ff321f833e29bb47"/>
+            </output_collection>
+            <output name="method_metadata" file="metadata.txt" ftype="txt" checksum="md5$81db28b08860988e3966f585b0f44b0f"/>
+            <output name="spec_abundance" file="spec_abundance.csv" ftype="csv" compare="sim_size" delta="100"/>
+        </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.
+
+    Downstream Tools
+        +---------+--------------+----------------------+
+        | Name    | Output File  | Format               |
+        +=========+==============+======================+
+        | matchMS | Mass Spectra | collection (tgz/msp) |
+        +---------+--------------+----------------------+
+
+    @GENERAL_HELP@
+    </help>
+
+    <expand macro="citations" />
+</tool>