--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dimsPredictPuritySingle.xml	Wed Nov 27 13:42:05 2019 -0500
@@ -0,0 +1,164 @@
+<tool id="mspurity_dimspredictpuritysingle" name="msPurity.dimsPredictPuritySingle" version="@TOOL_VERSION@+galaxy@GALAXY_TOOL_VERSION@">
+    <description>Calculate the anticipated precursor ion purity from a DIMS dataset.</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        Rscript '$__tool_directory__/dimsPredictPuritySingle.R'
+            #if $mzML_data.format == 'mzML_file'
+                --mzML_file '$mzML_data.source'
+            #elif $mzML_data.format == 'library'
+                --mzML_file '$__app__.config.user_library_import_dir/$__user_email__/$mzML_data.source'
+            #elif $mzML_data.format == 'mzML_data_collection'
+                --mzML_files='
+                #for $i in $mzML_data.source
+                    $i,
+                #end for
+                '
+                --galaxy_names='
+                #for $i in $mzML_data.source
+                    $i.name,
+                #end for
+                '
+                --mzML_filename=' $mzML_data.mzML_filename'
+
+            #end if
+            --peaks_file='$peaks_file'
+            --out_dir='.'
+            --minoffset=$minoffset
+            --maxoffset=$maxoffset
+            --ppm=$ppm
+            --iwNorm=$iw_norm
+            --ilim=$ilim
+            #if $sim
+                --sim
+            #end if
+            #if $remove_NAs
+                --remove_nas
+            #end if
+            #if $dimspy_usage.usage == "dimspy"
+                --dimspy
+                --file_num_dimspy $dimspy_usage.file_num_dimspy
+            #end if
+            #if $isotopes.isotopes == "exclude_default":
+                --exclude_isotopes
+            #elif $isotopes.isotopes == "user"
+                --exclude_isotopes
+                --isotope_matrix = '$isotopes.im'
+            #end if
+    ]]></command>
+    <inputs>
+
+        <param argument="--peaks_file"  type="data" format="tsv, tabular"
+                help="tsv or tabular file with one column containing the mz values (column header should be either
+                      mz)"/>
+
+        <conditional name="mzML_data">
+            <param name="format" type="select" label="Choose the source for the dataset" >
+                <option value="mzML_file" selected="true">A single .mzML files to check purity from</option>
+                <option value="library">Library directory name (to be used with dimspy workflows) or path to
+                                        to an individual .mzML file</option>
+                <option value="mzML_data_collection" selected="true">A data collection of .mzML files</option>
+            </param>
+            <when value="mzML_file">
+                <param argument="--mzML_file" name="source" type="data" format="mzml" label="Single *.mzML"  >
+                    <validator type="empty_field" />
+                </param>
+            </when>
+            <when value="mzML_data_collection">
+                <param argument="--mzML_files" name="source" type="data_collection" 
+                label="Data collection containing *.mzml files" >
+                    <validator type="empty_field" />
+                </param>
+                <param argument="--mzML_filename" type="text" label="Name of file to to calculate purity from" help=""/>
+            </when>
+
+            <when value="library">
+                <param  argument="--mzML_file" name="source" type="text"
+                       size="40" label="Library directory containing *.mzml files (dimspy input only)
+                                                                 or path to an individual .mzML file">
+                    <validator type="empty_field" />
+                </param>
+            </when>
+
+        </conditional>
+
+        <expand macro="general_params" />
+        <expand macro="offsets" />
+
+        <param argument="--ppm" type="float" label="ppm" min="0" value="10"
+                    help="ppm tolerance to compare between mz values"/>
+        <param argument="--remove_NAs" type="boolean" label="Remove rows where mz value is NA or NaN?" help=""/>
+        <param argument="--sim" type="boolean" label="SIM-Stitch experiment?" help=""/>
+        <conditional name="dimspy_usage">
+            <param name="usage" type="select" label="dimspy peak matrix text file usage?">
+                <option value="no_dimspy" selected="true">dimspy not used to prepare the mz text file</option>
+                <option value="dimspy">dimspy used to prepare mz file</option>
+            </param>
+            <when value="no_dimspy">
+            </when>
+            <when value="dimspy">
+                <param argument="--file_num_dimspy" type="integer" label="File number" min="0" value="1"
+                    help="Choose the file number from the dimspy matrix to use to calculate the precursor ion
+                          purity metric (order based on column order). This file will then be looked for in the
+                          library folder to calculate the metric.
+                         "/>
+            </when>
+        </conditional>
+
+    </inputs>
+    <outputs>
+	    <data name="dimsPredictPuritySingle_output"  format="tsv" label="${tool.name} on ${on_string}"
+              from_work_dir="dimsPredictPuritySingle_output.tsv" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="mzML_data|format" value="mzML_file"   />
+            <param name="mzML_data|source" value="dimsPredictPuritySingle_full_scan.mzML" />
+            <param name="remove_NAs" value="True" />
+            <param name="dimspy_usage|usage" value="dimspy" />
+            <param name="dimspy_usage|file_num_dimspy" value="1" />
+            <param name="peaks_file" value="dimsPredictPuritySingle_input_dimspy_peakmatrix.tsv" />
+            <output name="dimsPredictPuritySingle_output" value="dimsPredictPuritySingle_output.tsv" />
+        </test>
+    </tests>
+
+
+
+    <help><![CDATA[
+
+=============================================================
+Calculate anticipated precursor ion purity from DI-MS dataset
+=============================================================
+-----------
+Description
+-----------
+
+Tool to calculate the anticipated precursor ion purity of selected precursor based on a prior DI-MS dataset. The dataset
+can either be in the form of multiple 'full scans' or a SIM-Stitch dataset. See the Bioconductor documentation for more
+details, function msPurity::dimsPredictPurity()
+
+--------------
+Output example
+--------------
+Output consists of the mz column (along with any other columns that were in the original mz file). The median and
+mean calculated purity. The standard deviation (sdPurity), coefficient of variation (relative standard deviation)
+cvPurity, the standard error of the purity (sdePurity) and the median number of peaks within the isolation window
+(medianPeakNum)
+
+============= ============= ============= ================ ================ ================ ================
+mz            medianPurity  meanPurity    sdPurity         cvPurity	        sdePurity        medianPeakNum
+============= ============= ============= ================ ================ ================ ================
+50.20428      0.39          0.39          0.0007           0.19             0.0005           3
+------------- ------------- ------------- ---------------- ---------------- ---------------- ----------------
+56.91206      0.01          0.01          0.0002           4.53             0.0001           12
+------------- ------------- ------------- ---------------- ---------------- ---------------- ----------------
+62.02906      0.14          0.13          0.0014           22.63            0.0009           7
+------------- ------------- ------------- ---------------- ---------------- ---------------- ----------------
+75.07431      0.93          0.94          0.019            37.87            0.0134           3
+============= ============= ============= ================ ================ ================ ================
+
+    ]]></help>
+    <expand macro="citations" />
+</tool>