diff assess_purity_msms.xml @ 0:b6b051e7a5ef draft

planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/assess_purity_msms.xml	Mon Mar 05 10:08:14 2018 -0500
@@ -0,0 +1,152 @@
+<tool id="assess_purity_msms" name="assess_purity_msms" version="0.0.4">
+    <description>
+        Assess the precursor ion purity for fragmentation spectra acquired from either a LC-MS/MS or DI-MS/MS (MSn) experiment
+    </description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+
+    <expand macro="requirements" />
+
+
+ <stdio>
+        <exit_code range="1:" />
+    </stdio>
+    <command interpreter="Rscript"><![CDATA[
+        assess_purity_msms.R
+            --out_dir=.
+            #if $mzML_data.format == "mzML_files"
+                --mzML_files='
+                #for $i in $mzML_data.source
+                    $i,
+                #end for
+                '
+                --galaxy_names='
+                #for $i in $mzML_data.source
+                    $i.name,
+                #end for
+                '
+            #elif $mzML_data.format == "library"
+                --mzML_files $__app__.config.user_library_import_dir/$__user_email__/$mzML_data.source
+            #end if
+                    #if $offsets.offsets == 'user'
+                --minOffset=$minoffset
+                --maxOffset=$maxoffset
+            #end if
+
+            --iwNorm=$iw_norm
+            --ilim=$ilim
+
+            --cores=\${GALAXY_SLOTS:-4}
+
+            #if $nearest
+                --nearest
+            #end if
+
+            #if $mostIntense
+                --mostIntense
+            #end if
+
+            #if $isotopes.isotopes == "exclude_default"
+                --exclude_isotopes
+            #elif $isotopes.isotopes == "user"
+                --exclude_isotopes
+                --isotope_matrix=$isotopes.im
+            #end if
+
+    ]]></command>
+    <inputs>
+
+        <conditional name="mzML_data">
+            <param name="format" type="select" label="Choose the source for the dataset" >
+                <option value="mzML_files" selected="true">.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>
+            </param>
+            <when value="mzML_files">
+                <param name="source" type="data_collection" format="mzml" label="*.mzML files" >
+                    <validator type="empty_field" />
+                </param>
+            </when>
+            <when value="library">
+                <param name="source" type="text"
+                       size="40" label="Library directory containing *.mzml files
+                                                                 or path to an individual *.mzML">
+                    <validator type="empty_field" />
+                </param>
+            </when>
+        </conditional>
+
+         <param name="mostIntense" type="boolean" checked="true" label="Use most intense peak within isolation window for precursor?"
+               help="If yes, this will ignore the recorded precursor within the mzML file and use
+               use the most intense peak within the isolation window to calculate the precursor ion purity"/>
+
+        <param name="nearest" type="boolean" checked="true" label="Use nearest full scan to determine precursor?"
+               help="If yes, this will use the neareset full scan to the fragmentation scan to determine what the m/z value
+                     is of the precursor"/>
+
+
+        <conditional name="offsets">
+            <param name="offsets" type="select" label="offsets" >
+                <option value="auto" selected="true">Uses offsets determined in the mzML file</option>
+                <option value="user">User supplied offset values</option>
+            </param>
+            <when value="user">
+                <expand macro="offsets" />
+            </when>
+	        <when value="auto">
+            </when>
+
+        </conditional>
+
+        <expand macro="general_params" />
+
+
+    </inputs>
+    <outputs>
+	    <data name="assess_purity_msms" format="tsv" label="${tool.name} on ${on_string}: tsv"
+              from_work_dir="purity_msms.tsv" />
+        <data name="assess_purity_msms_rdata" format="rdata" label="${tool.name} on ${on_string}: RData"
+              from_work_dir="purity_msms.RData" />
+    </outputs>
+    <tests>
+       <test>
+        <conditional name="mzML_data">
+           <param name="format" value="mzML_files"/>
+           <param name="source" >
+                <collection type="list">
+                    <element name="LCMSMS_1.mzML" value="LCMSMS_1.mzML"/>
+                </collection>
+            </param>
+        </conditional>
+        <output name="assess_purity_msms" value="assess_purity_msms_output_LCMSMS1.tsv" />
+        </test>
+    </tests>
+    <expand macro="citations" />
+    <help><![CDATA[
+=============================================================
+Assess precursor ion purity of MS/MS files
+=============================================================
+-----------
+Description
+-----------
+
+Tool to assess precursor ion purity of MS/MS files
+
+Data input of mzML files either from:
+
+* A data collection of the mzML files containing MS/MS scans
+* A path to a folder that has mzML files containing MS/MS scans
+
+See Bioconductor documentation for more details about the function used, msPurity::purityA().
+
+-----------
+Outputs
+-----------
+
+* purity_msms: A tsv file of all the precursor ion purity score (and other metrics) of each fragmentation spectra
+* purity_msms_rdata: The purityA object saved as an rdata file
+
+
+    ]]></help>
+</tool>