diff create_sqlite_db.xml @ 0:fe7d7cc95ca5 draft

planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/create_sqlite_db.xml	Tue Mar 27 06:03:50 2018 -0400
@@ -0,0 +1,118 @@
+<tool id="create_sqlite_db" name="create_sqlite_db" version="0.0.1">
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+
+    <expand macro="requirements">
+        <!-- would ideally have xcms 3.0.0 but not available in bioconda at the point of tool creation-->
+    </expand>
+
+    <description>
+        Create SQLite database of an XCMS-CAMERA dataset
+    </description>
+ <stdio>
+        <exit_code range="1:" />
+    </stdio>
+    <command interpreter="Rscript"><![CDATA[
+        create_sqlite_db.R
+            --out_dir=.
+            --xset_xa=$xset_xa
+	    --pa=$pa
+            --xcms_camera_option=$camera_xcms
+            --cores=\${GALAXY_SLOTS:-4}
+            #if $file_load_conditional.file_load_select=="yes"
+                --mzML_files='
+                #for $i in $file_load_conditional.input
+                    $i,
+                #end for
+                '
+                --galaxy_names='
+                #for $i in $file_load_conditional.input
+                    $i.name,
+                #end for
+                '
+            #end if
+
+            #if $eic
+                --eic
+            #end if
+            #if $raw_rt_columns
+                --raw_rt_columns
+            #end if
+            #if $grp_peaklist_opt.grp_peaklist_opt=="yes"
+                --grp_peaklist=$grp_peaklist
+            #end if
+
+    ]]></command>
+    <inputs>
+
+
+        <param type="data" name="xset_xa" label="xcmsSet or CAMERA object"
+               help="Either xcmsSet object saved as 'xset' or CAMERA 'xa' object in an RData file. Please
+                     specify which to use below" format="rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata.xcms.fillpeaks,rdata.camera.quick,rdata.camera.positive,rdata.camera.negative,rdata"/>
+        <expand macro="camera_xcms" />
+
+        <param type="data" name="pa" label="purityA object" format="rdata"
+               help="purityA object saved as 'pa' in a RData file (output from assess_purity_msms)"/>
+
+	<param name="eic" type="boolean" label="Include EIC data?"
+               help="The Extracted Ion Chromatogram can be calculated for each peak and stored in
+                     the database. Note, this will take considerable time for large datasets and
+                     the resulting SQLite database can be large"/>
+	
+	<param name="raw_rt_columns" type="boolean" label="Use user defined Raw RT columns?"
+               help="Only use if the track_rt_raw tool has been used"/>
+
+
+        <expand macro="grp_peaklist" />
+
+
+        <expand macro="fileload" />
+
+    </inputs>
+    <outputs>
+        <data name="lcms_data_sqlite" format="sqlite" label="${tool.name} on ${on_string}: LC-MS(/MS) data SQLite db"
+              from_work_dir="lcms_data.sqlite" visible="true"/>
+        <data name="cpeakgroup_msms" format="sqlite" label="${tool.name} on ${on_string}: c-peak-group-msms"
+              from_work_dir="cpeakgroup_msms.tsv" visible="true"/>
+
+    </outputs>
+    <tests>
+        <test>
+            <conditional name="file_load_conditional">
+                <param name="file_load_select" value="yes"/>
+                <param name="input" >
+                    <collection type="list">
+                        <element name="LCMS_1.mzML" value="LCMS_1.mzML"/>
+                        <element name="LCMS_2.mzML" value="LCMS_2.mzML"/>
+                        <element name="LCMSMS_1.mzML" value="LCMSMS_1.mzML"/>
+                        <element name="LCMSMS_2.mzML" value="LCMSMS_2.mzML"/>
+                    </collection>
+                </param>
+            </conditional>
+	    <param name="camera_xcms" value="xcms"/>
+            <param name="xset_xa" value="LCMS_1_LCMS_2_LCMSMS_1_LCMSMS_2.xset.group.rdata"/>
+            <param name="pa" value="frag4feature.rdata"/>
+            <output name="cpeakgroup_msms" value="cpeakgroup_msms.tsv" >
+            </output>
+        </test>
+    </tests>
+    <expand macro="citations" />
+    <help><![CDATA[
+=============================================================
+Create SQLite database for LC-MS(/MS) dataset
+=============================================================
+Create an SQLite database for the msPurity and XCMS (CAMERA) outputs. The SQLite database created can 
+be used as input to the spectral_matching tool. 
+
+Please note that getting the extracted ion chromatograms can take a long time if the dataset has a large number of files and peaks.
+
+-----------
+Output
+-----------
+* lcms_sqlite: An SQLite database of the LC-MS(/MS) data (including fragmentation scans)
+* cpeakgroup_msms: A csv file for all grouped features that have associated fragmentation spectra
+
+    ]]></help>
+
+</tool>