--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/purityX.xml	Wed Nov 27 12:41:53 2019 -0500
@@ -0,0 +1,195 @@
+<tool id="mspurity_purityx" name="msPurity.purityX" version="@TOOL_VERSION@+galaxy@GALAXY_TOOL_VERSION@">
+        <description>Calculate the anticipated precursor ion purity from a LC-MS XCMS dataset.
+    </description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        Rscript '$__tool_directory__/purityX.R'
+            --xset_path='$xset'
+            --out_dir='.'
+            --minOffset=$minoffset
+            --maxOffset=$maxoffset
+            --singleFile=$singleFile
+            --purityType=$purityType
+            --cores=\${GALAXY_SLOTS:-4}
+            #if $xgroups.xgroups == "choose"
+                --xgroups='$xgroups.xgroups_value'
+            #end if
+            --camera_xcms=$camera_xcms
+            #if $camera_xcms == "camera"
+                --rdata_name=xa
+            #else
+                --rdata_name=xset
+            #end if
+            --iwNorm=$iw_norm
+            --ilim=$ilim
+            #if $isotopes.isotopes == "exclude_default"
+                --exclude_isotopes
+            #elif $isotopes.isotopes == "user"
+                --exclude_isotopes
+                --isotope_matrix='$isotopes.im'
+            #end if
+            #if $file_load_conditional.file_load_select == 'yes'
+                --galaxy_files='
+                #for $i in $file_load_conditional.input
+                    $i,
+                #end for
+                '
+            #end if
+            #if $file_load_conditional.file_load_select == 'yes'
+                --files='
+                #for $i in $file_load_conditional.input
+                    $i.name,
+                #end for
+                '
+            #end if
+
+            #if $choose_class_cond.choose_class== 'choose'
+                --choose_class=$choose_class_cond.class
+            #end if
+            #if $ignore_files_cond.ignore_files_choice== 'choose'
+                --ignore_files=$ignore_files_cond.ignore_files
+            #end if
+
+            #if $raw_rt_columns
+                --rtraw_columns
+            #end if
+
+
+    ]]></command>
+    <inputs>
+
+        <param argument="--xset" type="data" format="rdata"
+                help="xcmsSet object saved as an RData file"/>
+        <expand macro="offsets" />
+        <expand macro="general_params" />
+        <param argument="--singleFile" type="integer" label="singleFile" value="0"
+                    help="If just a single file for purity is to be calculated (rather than the grouped XCMS peaks).
+                    Uses the index of the files in xcmsSet object. If zero this is ignored"/>
+
+        <conditional name="choose_class_cond">
+            <param name="choose_class" type="select" label="Choose class of XCMS set object to perform calculation on?" >
+                <option value="choose">Choose class</option>
+                <option value="all" selected="true">calculate average across all classes</option>
+            </param>
+            <when value="all">
+            </when>
+            <when value="choose">
+                <param argument="--class" type="text" label="Choose class"
+                    help="Comma separated string of classes (found in the phenoData slot of xcmsSet object
+                    i.e. xset@phenoData). An average will across all the choosen classes." />
+            </when>
+        </conditional>
+
+        <conditional name="ignore_files_cond">
+            <param name="ignore_files_choice" type="select" label="Ignore files?" >
+                <option value="choose">Choose files to ignore from calculation</option>
+                <option value="none" selected="true" >Include all files of selected classes in calculation</option>
+            </param>
+            <when value="none">
+            </when>
+            <when value="choose">
+               <param argument="--ignore_files" type="text" label="ignore files"
+               help="Comma separated string of filenames to ignore (do not include the directory) eg. blank1.mzML,blank2.mzML,sample4.mzML"  />
+            </when>
+        </conditional>
+
+
+        <conditional name="xgroups">
+            <param name="xgroups" type="select" label="xgroups" >
+                <option value="choose">Choose XCMS grouped features to calculate precursor ion purity</option>
+                <option value="all" selected="true">Calculate precursor ion purity for all XCMS grouped features</option>
+            </param>
+            <when value="choose">
+                <param name="xgroups_value" type="text" label="xgroup ids"
+                    help="Comma separated string of xcms groups to perform prediction on eg. 1,2,3,4"  />
+            </when>
+            <when value="all"/>
+        </conditional>
+
+
+        <param argument="--purityType" type="select" label="Method of averaging purity"
+               help="Area and average used for the purity predictions. FWHM='Full width half maximum', FW='Full width'">
+                <option value="purityFWHMmedian" selected="true" >FWHM median</option>
+                <option value="purityFWHMmean" >FWHM mean</option>
+                <option value="purityFWmedian" >FW median</option>
+                <option value="purityFWmean" >FW mean</option>
+        </param>
+
+        <expand macro="camera_xcms" />
+
+        <param argument="--raw_rt_columns" type="boolean" label="Has the raw retention time been tracked within the peaks?"
+               help="Only applicable when using retention time correction with obiwarp. When obiwarp is used
+                     the retention time correction tracking is slightly different to the other correction methods. To ensure
+                     correct tracking with obiwarp an additional tool (track_rt_raw) should be performed prior to
+                     any retention time correction."/>
+
+        <expand macro="fileload" />
+
+    </inputs>
+    <outputs>
+	    <data name="purityX_tsv" format="tsv" label="${tool.name} on ${on_string}: tsv"
+              from_work_dir="purityX.tsv" />
+        <data name="purityX_rdata" format="rdata" label="${tool.name} on ${on_string}: RData"
+              from_work_dir="purityX.rdata" />
+    </outputs>
+    <tests>
+        <test>
+            <conditional name="file_load_conditional">
+                <param name="file_load_select" value="yes"/>
+                <param name="input" >
+                    <collection type="list">
+                        <element name="LCMSMS_2.mzML" value="LCMSMS_2.mzML"/>
+                        <element name="LCMSMS_1.mzML" value="LCMSMS_1.mzML"/>
+                        <element name="LCMS_2.mzML" value="LCMS_2.mzML"/>
+                        <element name="LCMS_1.mzML" value="LCMS_1.mzML"/>
+                    </collection>
+                </param>
+            </conditional>
+            <conditional name="xgroups">
+                <param name="xgroups" value="choose"/>
+                <param name="xgroups_value" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15"/>
+            </conditional>
+            <param name="iw_norm" value="QE5" />
+            <param name="xset" value="xset_group_LCMS_1_LCMS_2_LCMSMS_1_LCMSMS_2.RData"/>
+            <output name="purityX_tsv" value="purityX_output.tsv" />
+            <output name="purityX_rdata" value="purityX_output.Rdata" ftype="rdata" compare="sim_size"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+===================================================================
+Calculate anticipated precursor ion purity from LC-MS XCMS dataset
+===================================================================
+-----------
+Description
+-----------
+
+Tool to calculate the anticipated precursor ion purity of selected precursor based on a prior LC-MS dataset. Based on
+XCMS determined features
+
+--------------
+Output example
+--------------
+Output consists of the mz and intensity of the XCMS features (id based on the XCMS group id) and various
+metrics regarding the anticipated precursor ion purity.
+
+============= ============= ============= ================ ================ ================ ================ ================ ================
+grpid         mean          median        sd               stde	            RSD              pknm             i                mz
+============= ============= ============= ================ ================ ================ ================ ================ ================
+1             1.00          1.00          0.0000           0.0000           0.0000           1                5404920          100.0758
+------------- ------------- ------------- ---------------- ---------------- ---------------- ---------------- ---------------- ----------------
+2             0.59          0.57          0.3016           0.1508           50.570           3                8793845          101.0084
+------------- ------------- ------------- ---------------- ---------------- ---------------- ---------------- ---------------- ----------------
+3             0.08          0.07          0.0784           0.0164           29.643           4                1526502          100.9781
+------------- ------------- ------------- ---------------- ---------------- ---------------- ---------------- ---------------- ----------------
+4             1.00          1.00          0.0000           0.0000           0.0000           1                42513139         102.0914
+============= ============= ============= ================ ================ ================ ================ ================ ================
+
+
+
+    ]]></help>
+    <expand macro="citations" />
+</tool>