comparison hammock.xml @ 1:d90f4809ccc6 draft

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0:b1ac138f0287

<tool id="hammock_1.0" name="Hammock - cluster peptides">

    <description>Clusters short peptide sequences</description>

    <command interpreter="bash">
wrapper.sh \$HAMMOCK_JAR full --galaxy -t \${GALAXY_SLOTS:-4} -i $input --goc $output_clusters --gos $output_sequences

	    #end if

	    #if $advanced_greedy_params.set_greedy_params == "set":
		-x $advanced_greedy_params.max_shift
		-p $advanced_greedy_params.shift_penalty
		-m \${MATRIX_PATH}${advanced_greedy_params.scoring_matrix}.txt
            	#if $advanced_greedy_params.greedy_params.set_greedy == "set":
                	-g $advanced_greedy_params.greedy_params.greedy_threshold
            	#end if
            #end if

	    <when value="set">

         	<param name="max_shift" type="integer" value="3" min="0" label="Maximal sequence shift" help="Maximal number of positions sequences are allowed to shift for during greedy clustering. See -x, --max shift in manual for details." />

         	<param name="shift_penalty" type="integer" value="0" label="Sequence shift penalty" help="Score penalty added to to each alignment score during greedy clustering. This penalty is added for every amino acid aligned towards a (trailing) gap. This value should typically be non-positive (With a positive value, sequences benefit from containing more gaps). See -p, --gap penalty in manual for details."/>

              <param name="scoring_matrix" type="select" label="Substitiution matrix schema." help="Select a substitution matrix to be used to score alignments during glreedy clustering. See -m, --matrix in manual for details.">
                  <option value="blosum62">Blosum 62</option>
                  <option value="blosum30">Blosum 30</option>
                  <option value="blosum35">Blosum 35</option>

1:d90f4809ccc6

<tool id="hammock_1.0" name="Hammock - cluster peptides" version="1.0.2" hidden="false">

    <description>Clusters short peptide sequences</description>

    <command interpreter="bash">
wrapper.sh \$HAMMOCK_JAR full --galaxy -t \${GALAXY_SLOTS:-4} -i $input --goc $output_clusters --gos $output_sequences

	    #end if

	    #if $advanced_greedy_params.set_greedy_params == "set":
		-x $advanced_greedy_params.max_shift
		-p $advanced_greedy_params.shift_penalty
		-R $advanced_greedy_params.set_order.order

		#if $advanced_greedy_params.set_order.order == "random":
			-S $advanced_greedy_params.set_order.seed
		#end if
	
		-m \${MATRIX_PATH}${advanced_greedy_params.scoring_matrix}.txt
            	#if $advanced_greedy_params.greedy_params.set_greedy == "set":
                	-g $advanced_greedy_params.greedy_params.greedy_threshold
            	#end if
            #end if

	    <when value="set">

         	<param name="max_shift" type="integer" value="3" min="0" label="Maximal sequence shift" help="Maximal number of positions sequences are allowed to shift for during greedy clustering. See -x, --max shift in manual for details." />

         	<param name="shift_penalty" type="integer" value="0" label="Sequence shift penalty" help="Score penalty added to to each alignment score during greedy clustering. This penalty is added for every amino acid aligned towards a (trailing) gap. This value should typically be non-positive (With a positive value, sequences benefit from containing more gaps). See -p, --gap penalty in manual for details."/>

	      <conditional name="set_order">

              		<param name="order" type="select" label="Greedy clustering order" help="Select the order of sequences during the greedy clustering. See -R, --order in manual for details.">
                  		<option value="size">Size</option>
                  		<option value="alphabetic">Alphabetic</option>
                  		<option value="random">Random</option>
              		</param>

			<when value="size" />
			<when value="alphabetic" />
            		<when value="random">
         			<param name="seed" type="integer" value="42" label="Seed for random number generation" help="Set a seed value for the pseudorandom sequence order. See -S, --seed in manual for details."/>
			</when>

		</conditional>

		

              <param name="scoring_matrix" type="select" label="Substitiution matrix schema." help="Select a substitution matrix to be used to score alignments during glreedy clustering. See -m, --matrix in manual for details.">
                  <option value="blosum62">Blosum 62</option>
                  <option value="blosum30">Blosum 30</option>
                  <option value="blosum35">Blosum 35</option>