--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ramclustr_csv.xml	Mon Dec 07 22:14:48 2020 +0000
@@ -0,0 +1,92 @@
+<tool id="ramclustr_csv" name="RAMClustR (CSV)" version="@TOOL_VERSION@+galaxy0">
+    <macros>
+        <import>ramclustr_macros.xml</import>
+    </macros>
+
+    <requirements>
+        <container type="docker">recetox/ramclustr:1.1.0-recetox0</container>
+    </requirements>
+
+    <inputs>
+        <expand macro="parameters_csv" />
+        <expand macro="parameters_required" />
+        <expand macro="parameters_optional" />
+    </inputs>
+
+    <command detect_errors="aggressive"><![CDATA[
+        Rscript
+            -e 'source("${__tool_directory__}/ramclustr_wrapper.R")'
+            -e 'x <- ramclustr_csv(
+                ms="$ms_csv.ms",
+                idmsms="$ms_csv.idmsms",
+                feature_delimiter="$ms_csv.feature_delimiter",
+                sample_name_column = $ms_csv.sample_name_column,
+                retention_time_column= $ms_csv.retention_time_column,
+                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>
+
+    <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  |
+        +=======+========================+========+============+
+        | ???   | Feature Table with MS1 | csv    | ms         |
+        +-------+------------------------+--------+------------+
+        | ???   | Feature Table with MS2 | csv    | idmsms     |
+        +-------+------------------------+--------+------------+
+
+        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>