Mercurial > repos > hammock > hammock
comparison hammock.xml @ 1:d90f4809ccc6 draft
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author | hammock |
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date | Fri, 28 Aug 2015 07:38:12 -0400 |
parents | b1ac138f0287 |
children | 4db310b7e37c |
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0:b1ac138f0287 | 1:d90f4809ccc6 |
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1 <tool id="hammock_1.0" name="Hammock - cluster peptides"> | 1 <tool id="hammock_1.0" name="Hammock - cluster peptides" version="1.0.2" hidden="false"> |
2 | 2 |
3 <description>Clusters short peptide sequences</description> | 3 <description>Clusters short peptide sequences</description> |
4 | 4 |
5 <command interpreter="bash"> | 5 <command interpreter="bash"> |
6 wrapper.sh \$HAMMOCK_JAR full --galaxy -t \${GALAXY_SLOTS:-4} -i $input --goc $output_clusters --gos $output_sequences | 6 wrapper.sh \$HAMMOCK_JAR full --galaxy -t \${GALAXY_SLOTS:-4} -i $input --goc $output_clusters --gos $output_sequences |
13 #end if | 13 #end if |
14 | 14 |
15 #if $advanced_greedy_params.set_greedy_params == "set": | 15 #if $advanced_greedy_params.set_greedy_params == "set": |
16 -x $advanced_greedy_params.max_shift | 16 -x $advanced_greedy_params.max_shift |
17 -p $advanced_greedy_params.shift_penalty | 17 -p $advanced_greedy_params.shift_penalty |
18 -R $advanced_greedy_params.set_order.order | |
19 | |
20 #if $advanced_greedy_params.set_order.order == "random": | |
21 -S $advanced_greedy_params.set_order.seed | |
22 #end if | |
23 | |
18 -m \${MATRIX_PATH}${advanced_greedy_params.scoring_matrix}.txt | 24 -m \${MATRIX_PATH}${advanced_greedy_params.scoring_matrix}.txt |
19 #if $advanced_greedy_params.greedy_params.set_greedy == "set": | 25 #if $advanced_greedy_params.greedy_params.set_greedy == "set": |
20 -g $advanced_greedy_params.greedy_params.greedy_threshold | 26 -g $advanced_greedy_params.greedy_params.greedy_threshold |
21 #end if | 27 #end if |
22 #end if | 28 #end if |
100 <when value="set"> | 106 <when value="set"> |
101 | 107 |
102 <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." /> | 108 <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." /> |
103 | 109 |
104 <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."/> | 110 <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."/> |
111 | |
112 <conditional name="set_order"> | |
113 | |
114 <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."> | |
115 <option value="size">Size</option> | |
116 <option value="alphabetic">Alphabetic</option> | |
117 <option value="random">Random</option> | |
118 </param> | |
119 | |
120 <when value="size" /> | |
121 <when value="alphabetic" /> | |
122 <when value="random"> | |
123 <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."/> | |
124 </when> | |
125 | |
126 </conditional> | |
127 | |
128 | |
105 | 129 |
106 <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."> | 130 <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."> |
107 <option value="blosum62">Blosum 62</option> | 131 <option value="blosum62">Blosum 62</option> |
108 <option value="blosum30">Blosum 30</option> | 132 <option value="blosum30">Blosum 30</option> |
109 <option value="blosum35">Blosum 35</option> | 133 <option value="blosum35">Blosum 35</option> |