diff create_msp.xml @ 0:4b417094bf71 draft

planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/create_msp.xml	Wed May 02 13:09:23 2018 -0400
@@ -0,0 +1,87 @@
+<tool id="create_msp" name="Create MSP Files from msPurity" version="0.1.1">
+    <description> </description>
+     <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements">
+    </expand>
+
+
+    <command interpreter="Rscript" ><![CDATA[
+	create_msp.R
+	--purity "$purity"
+	--mode "$mode"
+	--ppm "$ppm"
+    ]]></command>
+    <inputs>
+        <param name="purity" type="data" format="rdata" label="msPurity frag4feature dataset" argument="--purity"/>
+        <param name="mode" type="select" label="Spectra use mode (if precursor was fragmented in >1 scans)" help='WARNING: The averaging and max options are still being developed and will likely fail' argument="--mode">
+            <option value="max" >Max Intensity</option>
+            <option value="average">Weighted Average</option>
+            <option value="all" selected="true">All</option>
+        </param>
+        <param name="ppm" optional="true" type="float" label="Allowed mass deviation between fragment MZs for spectra averaging (in ppm)" argument="--ppm"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" label="log" />
+        <data name="msp_out" format="msp" from_work_dir="outfile.msp" label="${purity.name} MSP file"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="mode" value="all"/>
+            <param name="purity" value="lightpurity.RData"/>
+            <output name="msp_out" file="input.msp"/>
+        </test>
+      
+    </tests>
+	<help><![CDATA[
+------------------------------
+Create MSP Files from msPurity
+------------------------------
+
+* TO-DO: Averaging functionality
+* TO-DO: Add citation for MSP
+* TO-DO: Add PRECURSORTYPE if adducts available
+* TO-DO: Create MSP from xcms/mzml files
+
+Description
+-----------
+
+| This tool will extract the MSMS spectra data from an msPurity-frag4feature object into a file with MSP data format.
+| Linking each precursor with its corresponding fragmentation spectra and associating the index within the msPurity object as the name UID.
+| Currently, there are three different methods for extracting the data in case that more than one MSMS scan was acquired for the same precursor m/z. See Parameters.
+
+Parameters
+----------
+
+**\1. msPurity frag4feature dataset** 
+
+Result object from msPurity purityA-frag4feature functions.
+
+**\2. Spectra use mode (if precursor was fragmented in >1 scans)**
+
+* "Max Intensity" will only use the scan where the precursor m/z signal was maximal.
+
+* "Weighted Average" will merge all the scans, group fragment m/z using a PPM deviation (see 3.) and weight the intensities based on the precursor intensity of that scan. 
+
+* "All" will generate a single entry in the MSP file for each MSMS scan independently.  
+
+**\3. PPM deviation for fragmentation spectra averaging**
+
+Set the value only if you selected "Weighted Average" above, the PPM value is used to define the limits for m/z grouping into a single fragment. 
+The weighting is based on the precursor intensity, meaning that the more intense the precursor signal was, the more intensity will its fragments contribute to the averaged spectra.
+
+		
+Developers and contributors
+---------------------------
+
+- **Jordi Capellades ([e-mail]) - Universitat Rovira i Virgili (SP)**
+- **Ralf Weber ([e-mail]) - University of Birmingham (UK)**
+
+	]]></help>
+
+<expand macro="citations" >
+       <citation type="doi">10.1186/s13321-016-0115-9</citation>
+</expand>
+  
+</tool>