diff createMSP.xml @ 0:35898942bfbb draft

"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/createMSP.xml	Wed Nov 27 14:20:07 2019 -0500
@@ -0,0 +1,156 @@
+<tool id="mspurity_createmsp" name="msPurity.createMSP" version="@TOOL_VERSION@+galaxy@GALAXY_TOOL_VERSION@">
+    <description>Create MSP files from msPurity processed data</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements">
+    </expand>
+    <command detect_errors="exit_code"><![CDATA[
+    Rscript '$__tool_directory__/createMSP.R'
+    --rdata_input '$rdata_input'
+    --method '$method'
+
+    #if $metadata_cond.metadata_select == "true"
+        --metadata '$metadata_cond.metadata'
+        --metadata_cols '$metadata_cond.metadata_cols'
+        --metadata_cols_filter '$metadata_cond.metadata_cols_filter'
+
+    #end if
+
+    #if $xcms_group_cond.xcms_group_select == "true"
+        --xcms_groupids '$xcms_group_cond.xcms_groupids'
+    #end if
+
+    $filter
+    $adduct_split
+
+    --msp_schema $msp_schema
+    --intensity_ra $intensity_ra
+    --include_adducts $include_adducts
+
+    --out_dir '.'
+    ]]></command>
+    <inputs>
+        <param argument="--rdata_input" type="data" format="rdata" label="msPurity purityA dataset"
+        help="RData file containing the purityA object following frag4feature and/or averageFragmentation"/>
+        <param argument="--method" type="select" label="How to choose fragmentation spectra (if precursor was fragmented in >1 scans per XCMS group feature)"
+        help="'Average all' will use the averaged MS/MS spectra of the XCMS grouped feature, ignoring inter and intra file relationships,
+             'Average' (intra)' will use the intra file (within file) averaged MS/MS spectra of the XCMS grouped feature,
+             'Average (inter)' will use the inter file (across file) MS/MS averaged spectra,
+             'All scans' will export all matching MS/MS spectra to XCMS grouped features,
+             'Max intensity' will choose the most MS/MS spectra with the most intense precursor ion for each XCMS grouped feature"
+             >
+            <option value="av_all" selected="true">Average (all)</option>
+            <option value="av_intra">Average (intra)</option>
+            <option value="av_inter">Average (inter)</option>
+            <option value="all">All scans</option>
+            <option value="max" >Max intensity</option>
+        </param>
+
+        <conditional name="metadata_cond">
+            <param name="metadata_select" type="boolean" label="Use additional metadata?" />
+	    <when value="true">
+                <param argument="--metadata" type="data" label="Metadata for each feature" format="tsv,tabular"
+                help="Metadata for each grouped XCMS feature, e.g. could be the adduct calculated from CAMERA "/>
+
+                <param argument="--metadata_cols_filter" type="text" label="Metadata columns to use" value=""
+                help="Comma separated string of column names where the corresponding values in the metadata will be used"/>
+
+                <param argument="--metadata_cols" type="text" label="Metadata columns for MSP spectra name" value=""
+                help="Comma separated string of column names where the corresponding values in the metadata will be used
+                      for MSP spectra name"/>
+
+                </when>
+            <when value="false">
+            </when>
+        </conditional>
+
+        <conditional name="xcms_group_cond">
+            <param name="xcms_group_select" type="boolean" label="Select XCMS groups?" help="if set to no, all XCMS group features will be used" />
+            <when value="true">
+                <param argument="--xcms_groupids" type="text" label="XCMS peak group ids" value=""
+                help="Comma separated string of XCMS group ids to export MSP spectra for. If blank all XCMS peak groups will be used"/>
+            </when>
+            <when value="false">
+            </when>
+        </conditional>
+
+        <param argument="--intensity_ra" type="select" label="Include intensity, relative abundanace or both in the MSP file">
+            <option value="intensity_ra" selected="true">Both intensity and relative abundance</option>
+            <option value="intensity">Intensity only</option>
+            <option value="ra">Relative abundance only</option>
+        </param>
+
+        <param argument="--msp_schema" type="select" label="MSP schema to use for files">
+            <option value="massbank" selected="true">MassBank (Europe)</option>
+            <option value="mona">MoNA</option>
+
+        </param>
+
+        <param argument="--filter" type="boolean" checked="true" truevalue="--filter" falsevalue=""
+        label="Filter peaks that have been flagged in prior processing steps"   help="" />
+
+
+       <param argument="--include_adducts" type="select" label="Always include the following adduct descriptions in the MSP file"
+        help="Additional adducts to include, can be useful for downstream processing" multiple="true">
+            <option value="[M+H]+">[M+H]+</option>
+            <option value="[M+Na]+">[M+Na]+</option>
+            <option value="[M+NH4]+">[M+NH4]+</option>
+            <option value="[M+K]+" >[M+K]+</option>
+            <option value="[M+CH3OH+H]+">[M+CH3OH+H]+</option>
+            <option value="[M+ACN+H]+">[M+ACN+H]+</option>
+            <option value="[M+ACN+Na]+">[M+ACN+Na]+</option>
+            <option value="[M+2ACN+H]+">[M+2ACN+H]+</option>
+            <option value="[M-H]-">[M-H]-</option>
+            <option value="[M+HCOO]-" >[M+HCOO]-</option>
+            <option value="[M+CH3COO]-" >[M+CH3COO]-</option>
+            <option value="[M-H+CH3COOH]-" >[M-H+CH3COOH]-</option>
+        </param>
+        <param argument="--adduct_split" type="boolean" checked="true" label="Create MSP spectra for each adduct?"
+        help="Useful if the MSP file will be used for further annotation" truevalue="--adduct_split" falsevalue=""  />
+
+    </inputs>
+    <outputs>
+        <data name="createMSP_output" format="msp" from_work_dir="lcmsms_spectra.msp" label="${tool.name} on ${on_string}: msp"/>
+    </outputs>
+    <tests>
+
+        <test>
+            <!-- 3) Test all average with metadata -->
+            <param name="method" value="av_all"/>
+            <param name="rdata_input" value="averageFragSpectra_output_all.RData"/>
+            <param name="metadata_cond|metadata_select" value="true"/>
+            <param name="metadata_cond|metadata" value="createMSP_input_metadata.tsv"/>
+            <param name="xcms_group_cond|xcms_group_select" value="true"/>
+            <param name="xcms_group_cond|xcms_groupids" value="8,12"/>
+            <param name="metadata_cond|adduct_split" value="true"/>
+            <output name="createMSP_output" file="createMSP_output_av_all_metadata.msp"/>
+        </test>
+
+    </tests>
+	<help><![CDATA[
+------------------------------
+Create MSP Files from msPurity
+------------------------------
+
+Description
+-----------
+
+| This tool will extract the MSMS spectra data from an msPurity-frag4feature object into a file with MSP data format.
+
+
+
+
+Developers and contributors
+---------------------------
+
+- **Jordi Capellades ([e-mail]) - Universitat Rovira i Virgili (SP)**
+- **Andris Jankevics ([e-mail]) - University of Birmingham (UK)**
+- **Thomas N. Lawson ([e-mail]) - University of Birmingham (UK)**
+- **Ralf Weber ([e-mail]) - University of Birmingham (UK)**
+
+	]]></help>
+
+<expand macro="citations" />
+
+</tool>