Feature/add met frag

tools/metfrag/.shed.yml

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+categories: 
+  - Metabolomics
+description: MetFrag performs annotation of tandem mass spectra of metabolites. Candidate molecules of different databases are fragmented in silico and matched against mass MS/MS spectra.
+homepage_url: http://c-ruttkies.github.io/MetFrag/
+name: metfrag
+owner: iuc
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/metfrag/

tools/metfrag/metfrag-cli-batch.xml

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+<?xml version='1.0' encoding='UTF-8'?>
+<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/).-->
+<!--Proposed Tool Section: [PhenoMeNal]-->
+<tool id="metfrag-cli-batch" name="metfrag-cli-batch" version="0.4">
+    <description>Run MetFrag with a given parameter set.</description>
+    <requirements>
+	<requirement type="package" version="2.4.5">metfrag</requirement>
+    </requirements> 
+    <!--
+	#if $additionalparameters != "None"
+        -a "$additionalparameters"
+	#end if
+	#if $additional_metfrag_scores != "None"
+        -s "$additional_metfrag_scores"
+	#end if
+    -->
+    <command detect_errors="aggressive"><![CDATA[
+    metfrag ParameterFile='$metfrag_cli_batch_input_1' ResultsFile='$metfrag_cli_batch_output_1'     
+    #if $metfrag_cli_batch_database_file != "None"
+    LocalDatabasePath="$metfrag_cli_batch_database_file"
+    #end if
+    ]]>
+    </command>
+    <inputs>
+	<param name="metfrag_cli_batch_input_1" type="data" format="txt" optional="False" label="File with MetFrag parameters" help="File containing MetFrag parameters which is generated by msms2metfrag" />
+	<param name="additionalparameters" type="text" value="" optional="True" label="Additional Parameters" help="Additional parameters that can be passed to MetFrag. This can include e.g. access information for a local MetChem database instance" />
+	<param name="metfrag_cli_batch_database_file" type="data" format="csv" optional="True" label="Database File" help="File containing candidates used as database" />
+	<param name="additional_metfrag_scores" type="select" display="checkboxes" multiple="true" label="Additional MetFrag scores" help="Add additional MetFrag scores used to score candidates">
+	    <option value="OfflineMetFusionScore">Spectral Similarity (MoNA)</option>
+	</param>
+    </inputs>
+    <outputs>
+	<data name="metfrag_cli_batch_output_1" format="csv" label="MetFrag result file" />
+    </outputs>
+    <tests>
+	<test>
+	    <param name="metfrag_cli_batch_input_1" value="1_746.022_716.5434_1569591.66000003_PE_PG_AutoMS_2-B_3_03_18583.mzML.txt" />
+	    <param name="metfrag_cli_batch_database_file" value="candidates.csv" />
+	    <output name="metfrag_cli_batch_output_1" file="1_746.022_716.5434_1569591.66000003_PE_PG_AutoMS_2-B_3_03_18583.mzML.csv" ftype="csv"/>
+	</test>
+    </tests>
+    <help>
+
+	.. class:: infomark
+
+	| **Tool update: See the 'NEWS' section at the bottom of the page**
+
+	---------------------------------------------------
+
+	.. class:: infomark
+
+	**Authors**
+
+	| **Payam Emami ([email protected])** and **Christoph Ruttkies ([email protected])** wrote and maintain this wrapper for MetFrag batch mode processing.
+
+	---------------------------------------------------
+
+	.. class:: infomark
+
+	**Please cite**
+
+	Ruttkies, C., Schymanski, E. L., Wolf, S., Hollender, J. and Neumann, S. MetFrag relaunched: incorporating strategies beyond in silico fragmentation. J Cheminform 8:3, (2016) DOI: 10.1186/s13321-016-0115-9
+
+	---------------------------------------------------
+
+	=====================
+	MetFrag CLI Batch
+	=====================
+
+	-----------
+	Description
+	-----------
+
+	| This module is used to run MetFrag on annotated MS/MS spectra for compound annotation. The parameters are set by **msms2metfrag**.
+
+
+	-----------
+	Input files
+	-----------
+
+	+------------------------------+------------+
+	| File                         |   Format   |
+	+==============================+============+
+	| 1)  File with MetFrag        |    txt     |
+	|     parameters               |            |
+	+------------------------------+------------+
+	| 2)  Database File (optional) |    csv     |
+	+------------------------------+------------+
+
+	----------
+	Parameters
+	----------
+
+	File with MetFrag parameters
+        | File containing MetFrag parameters which is generated by **msms2metfrag**
+        |
+
+	Additional Parameters
+        | Additional parameters that can be passed to MetFrag. This can include e.g. access information for a local MetChem database instance
+        |
+
+	Database File
+	| File containing candidates used as database
+	| 
+
+	Additional MetFrag scores
+	| Add additional MetFrag scores used to score candidates
+	|
+
+	------------
+	Output files
+	------------
+
+	metfrag_cli_batch_output_1.csv
+        | A csv output file with scored candidates and properties
+        |
+
+	---------------------------------------------------
+
+	----
+	NEWS
+	----
+
+	CHANGES IN VERSION 0.3
+	========================
+
+	- added support for additional MetFrag scores
+
+	CHANGES IN VERSION 0.2
+	========================
+
+	- added support for a local file database
+
+
+	CHANGES IN VERSION 0.1
+	========================
+
+	First version
+
+    </help>
+    <citations>
+	<citation type="doi">10.1186/s13321-016-0115-9</citation>
+    </citations>    
+</tool>
+
+<!-- Local Variables: -->
+<!-- nxml-child-indent: 4 -->
+<!-- nxml-attribute-indent: 4 -->
+<!-- End: -->