comparison tandem.xml @ 6:e5b29190a4a0 draft

Uploaded

5:ef9e2ec52236

		#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">

			<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>

6:e5b29190a4a0

		#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

		$cleavage_semi
		
	</command>

	<inputs>	
		<conditional name="database">

			<label>Missed Cleavages Allowed</label>
		    <option value="0">0</option>		
			<option value="1">1</option>
			<option value="2">2</option>
		</param>

		<param name="cleavage_semi" type="boolean" label="Allow semi-cleaved peptides" help="This can increase search time dramatically" truevalue="" falsevalue="--no-cleavage-semi" />
		
		<param name="enzyme" type="select" format="text">
		    <label>Enzyme</label>
		    <option value="Trypsin">Trypsin</option>
		</param>