--- a/tandem.xml	Sun Jan 06 19:14:28 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,128 +0,0 @@
-<tool id="proteomics_search_tandem_1" name="X!Tandem MSMS Search" version="1.0.0">
-	<requirements><requirement type="package">protkgem</requirement></requirements>
-	<description>Run an X!Tandem Search</description>
-
-	<command>
-		#if $database.source_select=="built_in":
-		tandem_search.rb -d $database.dbkey 
-		#else #tandem_search.rb -d $database.fasta_file
-		#end if
-
-		--var-mods='
-		$variable_mods
-		#for $custom_variable_mod in $custom_variable_mods:
-		,${custom_variable_mod.custom_mod}
-		#end for
-		'
-
-		--fix-mods='
-		$fixed_mods
-		#for $custom_fix_mod in $custom_fix_mods:
-		,${custom_fix_mod.custom_mod}
-		#end for
-		'
-
-		$input_file -o $output -r --enzyme=$enzyme --precursor-ion-tol-units=$precursor_tolu -v $missed_cleavages -f $fragment_ion_tol -p $precursor_ion_tol $allow_multi_isotope_search --keep-params-files
-		
-		
-		
-	</command>
-
-	<inputs>	
-		<conditional name="database">
-			<param name="source_select" type="select" label="Database source">
-				<option value="built_in">Built-In</option>
-				<option value="input_ref">Your Upload File</option>
-			</param>
-			<when value="built_in">
-				<param name="dbkey" type="select" format="text" >
-					<label>Database</label>
-					<options from_file="pepxml_databases.loc">
-						<column name="name" index="0" />
-						<column name="value" index="2" />
-					</options>
-				</param>
-			</when>
-			<when value="input_ref">
-				<param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" />
-			</when>
-		</conditional>
-		
-		<param name="input_file" type="data" format="mzml" multiple="false" label="MSMS File" help="An mzML file with MS/MS data"/>
-
-
-		<param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Hold the appropriate key while
-			clicking to select multiple items">
-			<options from_file="tandem_mods.loc">
-				<column name="name" index="0" />
-				<column name="value" index="2" />
-			</options>
-		</param>
-
-		<repeat name="custom_variable_mods" title="Custom Variable Modifications" help="You can specify a modification when present in a motif. For instance, 0.998@N!{P}[ST] is a deamidation modification on N only if it is present in an N[any but P][S or T] motif (N-glycosite).">
-			<param name="custom_mod" type="text">
-			</param>
-		</repeat>
-		
-		
-		<param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Hold the appropriate key while
-			clicking to select multiple items">
-			<options from_file="tandem_mods.loc">
-				<column name="name" index="0" />
-				<column name="value" index="2" />
-			</options>
-		</param>
-
-		<repeat name="custom_fix_mods" title="Custom Fixed Modifications" help="You can specify a modification when present in a motif. For instance, 0.998@N!{P}[ST] is a deamidation modification on N only if it is present in an N[any but P][S or T] motif (N-glycosite).">
-			<param name="custom_mod" type="text">
-			</param>
-		</repeat>
-		
-		
-
-		<param name="missed_cleavages" type="select" format="text" help="Allow peptides to contain up to this many missed enzyme cleavage sites">
-			<label>Missed Cleavages Allowed</label>
-		    <option value="0">0</option>		
-			<option value="1">1</option>
-			<option value="2">2</option>
-		</param>
-		
-		<param name="enzyme" type="select" format="text">
-		    <label>Enzyme</label>
-		    <option value="Trypsin">Trypsin</option>
-		</param>
-		
-		<param name="fragment_ion_tol" help="Fragment Ion Tolerance in Daltons" type="float" value="0.65" min="0" max="10000" label="Fragment ion tolerance"/>
-
-		<param name="precursor_ion_tol" help="Precursor Ion Tolerance (Da or ppm)" type="float" value="100" min="0" max="10000" label="Precursor ion tolerance"/>
-		<param name="precursor_tolu" type="select" format="text">
-		    <label>Precursor Ion Tolerance Units</label>
-		    <option value="ppm">ppm</option>		
-			<option value="Da">Da</option>
-		</param>
-		
-		<param name="allow_multi_isotope_search" type="boolean" label="Allow multi-isotope search" help="This allows peptide candidates in windows around -1 Da and -2 Da from the acquired mass to be considered. Only applicable when the minus/plus window above is set to less than 0.5 Da. Good for accurate-mass instruments for which the reported precursor mass is not corrected to the monoisotopic mass." truevalue="" falsevalue="--strict-monoisotopic-mass"/>
-
-	</inputs>
-
-
-	<outputs>
-		<data format="raw_pepxml" name="output" metadata_source="input_file" label="X!Tandem_vs_${database.dbkey if $database.has_key('dbkey') else $database.fasta_file.display_name}.${input_file.display_name}.${input_file.display_name}.pepXML"/>
-	</outputs>
-
-
-  <help>
-
-**What it does**
-
-Runs an MS/MS database search using the X!Tandem search engine. Output is in the form of a pepXML file containing identified peptides along with their raw search scores.
-
-----
-
-**References**
-
-Please see http://www.thegpm.org/GPM/references.html for details of references describing the X!Tandem search engine.
-
-  </help>
-
-</tool>