--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/maxquant_phosphopeptide_intensity.xml	Thu Nov 04 18:35:10 2021 +0000
@@ -0,0 +1,63 @@
+<tool id="maxquant_phosphopeptide_intensity" name="MaxQuant Phosphopeptide Intensity" version="0.1.0" python_template_version="3.5">
+    <description>for each sample</description>
+    <requirements>
+        <requirement type="package" version="1.14.2">r-data.table</requirement>
+        <requirement type="package" version="1.7.1">r-optparse</requirement>
+        <requirement type="package" version="1.4.0">r-stringr</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+Rscript '$__tool_directory__/MaxQuantProcessingScript.R' 
+-i '$phospho_sites' 
+--enriched $enriched
+--phosphoCol $phosphoCol
+--numSamples $numSamples
+--startCol $startCol 
+--intervalCol $intervalCol
+--localProbCutoff $localProbCutoff
+--collapse_func $collapse_func
+-o phosphopeptide_intensities.tsv
+&& head phosphopeptide_intensities.tsv
+
+    ]]></command>
+    <inputs>
+        <param name="phospho_sites" type="data" format="tabular" label="MaxQuant Phospho (STY)Sites.txt"/>
+        <param name="phosphoCol" type="data_column" numerical="false" data_ref="phospho_sites" label="Column: Number of Phospho (STY)" />
+        <param name="numSamples" type="integer" value="1" min="1" label="Number of samples or runs"/>
+        <param name="startCol" type="data_column" numerical="false" data_ref="phospho_sites" label="Column: Intensity of the first sample" />
+        <param name="intervalCol" type="integer" value="1" min="1" label="Interval between the intensity column of samples" help="eg, 1 if subsequent column; 2 if every other column"/>
+        <param name="enriched" type="select" label="Phospho enrichemnt type">
+            <option value="ST">ST</option>
+            <option value="Y">Y</option>
+        </param>
+        <param name="collapse_func" type="select" label="Intensity merge function">
+            <option value="sum">sum</option>
+            <option value="averge">averge</option>
+        </param>
+        <param name="localProbCutoff" type="float" value="0.75" min="0" max="1.0" label="Localization Probability Cutoff"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="tabular" from_work_dir="phosphopeptide_intensities.tsv"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="phospho_sites" ftype="tabular" value="Phospho (ST)Sites_NancyDu.txt"/>
+            <param name="phosphoCol" value="37"/>
+            <param name="numSamples" value="6"/>
+            <param name="startCol" value="58"/>
+            <param name="intervalCol" value="1"/>
+            <param name="enriched" value="ST"/>
+            <param name="collapse_func" value="sum"/>
+            <param name="localProbCutoff" value="0.75"/>
+            <output name="output">
+                <assert_contents>
+                    <has_text text="Phosphopeptide" />
+                    <has_text text="AAAAAAAGDpSDpSWDADAFSVEDPVRK" />
+                    <has_text text="997800000" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+        TODO: Fill in help.
+    ]]></help>
+</tool>