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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphclust commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9
author bgruening
date Thu, 22 Dec 2016 08:40:17 -0500
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1 <tool id="graphclust" name="graphclust" version="0.1">
2 <description>alignment-free structural clustering of local RNA secondary structures</description>
3 <requirements>
4 <requirement type="package">GraphClust</requirement>
5 <requirement type="package">locarna</requirement>
6 <requirement type="package">RNAShapes</requirement>
7 <requirement type="package">cmfinder</requirement>
8 <requirement type="package">infernal</requirement>
9 <requirement type="package">rnaz</requirement>
10 <requirement type="package">vienna_rna</requirement>
11 </requirements>
12 <command>
13 <![CDATA[
14 MASTER_GraphClust.pl
15 --fasta $input_fasta
16 --config $graphclust_config
17 --root $output.files_path
18 --threads "\${GALAXY_SLOTS:-12}";
19
20 python dir2html.py $output.files_path/RESULTS > $output
21 ]]>
22 </command>
23 <configfiles>
24 <configfile name="graphclust_config">
25 GLOBAL_group_size $GLOBAL_group_size
26 GLOBAL_hit_blacklist_overlap $GLOBAL_hit_blacklist_overlap
27 GLOBAL_iterations $GLOBAL_iterations
28 GLOBAL_num_clusters $GLOBAL_num_clusters
29 GLOBAL_plfold_minlen $GLOBAL_plfold_minlen
30
31 OPTS_RNAfold --noLP
32 OPTS_RNAplfold --noLP -c $RNAplfold_c -L $RNAplfold_L -W $RNAplfold_W
33 OPTS_fasta2shrep_gspan -t "3=0,5=80" -M 5 -c 20 -win 40,150 -shift 30 --cue -u --stack --seq-graph-t --seq-graph-alph
34 OPTS_locarna_maligs -p $locarna_p --max-diff-am $locarna_max_diff_am --tau $locarna_tau --max-diff $locarna_max_diff --alifold-consensus-dp
35 OPTS_locarna_model -p $locarna_p --max-diff-am $locarna_max_diff_am --tau $locarna_tau --max-diff $locarna_max_diff --alifold-consensus-dp
36 OPTS_locarna_p_model -p $locarna_p --max-diff-am $locarna_max_diff_am --tau 100 --max-diff $locarna_max_diff --struct-weight $locarna_struct_weight --plfold-span 150 --plfold-winsize 200 --temperature $locarna_temperature --mea-beta 400 --consistency-transformation
37 OPTS_locarna_paligs -p $locarna_p --max-diff-am $locarna_max_diff_am --tau $locarna_tau --max-diff $locarna_max_diff --indel-open $locarna_indel_open --indel $locarna_indel --struct-weight $locarna_struct_weight
38 OPTS_nspdk -R $nspdk_R -D $nspdk_R -gt $nspdk_gt
39 OPTS_nspdk_centers -ensf 5 -oc -usn
40
41 center_model_type 5
42 center_subtree_max 7
43 center_subtree_min 3
44 center_tree_aligs 2
45 center_tree_type 3
46 cm_bitscore_sig 1
47 cm_calibrate 0
48 cm_max_eval 0.001
49 cm_min_bitscore 15
50 cm_top_only 0
51 evaluate 0
52 evaluate_class0_as_fp 0
53 evaluate_min_overlap 0.51
54 input_add_revcompl 0
55 input_blastclust 1
56 input_blastclust_id 90
57 input_blastclust_len 0.90
58 input_seq_min_length $other_input_seq_min_length
59 input_win_shift $other_input_win_shift
60 input_win_size 0
61 nspdk_fcs 1
62 nspdk_greylist_num 0
63 nspdk_knn_center 10
64 nspdk_nhf 500
65 nspdk_nhf_max 1000
66 nspdk_nhf_step 50
67 results_merge_cluster_ol 0.66
68 results_merge_overlap 0.51
69 results_min_cluster_size $other_results_min_cluster_size
70 results_partition_type soft
71 results_top_num 10
72 </configfile>
73 </configfiles>
74 <inputs>
75
76 <param name="input_fasta" type="data" format="fasta" label="Fasta file containing sequeces you want to cluster" />
77
78 <!--
79 <conditional name="OPTS_GLOBAL">
80 <param name="OPTS_GLOBAL_selector" type="select" label="Global advanced options">
81 <option value="basic" selected="True">Hide Advanced Options</option>
82 <option value="advanced">Show Advanced Options</option>
83 </param>
84 <when value="basic">
85 </when>
86 <when value="advanced">
87 -->
88 <param name="GLOBAL_group_size" type="integer" value="50" label="GLOBAL_group_size" />
89 <param name="GLOBAL_hit_blacklist_overlap" type="float" value="0.2" label="GLOBAL_hit_blacklist_overlap" />
90 <param name="GLOBAL_iterations" type="integer" value="5" label="GLOBAL_iterations" />
91 <param name="GLOBAL_num_clusters" type="integer" value="3" label="GLOBAL_num_clusters" />
92 <param name="GLOBAL_plfold_minlen" type="integer" value="150" label="GLOBAL_plfold_minlen" />
93 <!--
94 </when>
95 </conditional>
96 -->
97
98 ## OPTS_RNAfold --noLP
99 <!--
100 <conditional name="OPTS_RNAplfold">
101 <param name="OPTS_RNAplfold_selector" type="select" label="RNAplfold advanced options">
102 <option value="basic" selected="True">Hide Advanced Options</option>
103 <option value="advanced">Show Advanced Options</option>
104 </param>
105 <when value="basic">
106 </when>
107 <when value="advanced">
108 -->
109 <param name="RNAplfold_c" type="float" value="0.0005" label="Report only base pairs with an average probability greater than this value in the dot plot" />
110 <param name="RNAplfold_L" type="integer" value="200" label="Set the maximum allowed separation of a base pair to span" />
111 <param name="RNAplfold_W" type="integer" value="300" label="Average the pair probabilities over windows of given size" />
112 <!--
113 </when>
114 </conditional>
115 -->
116 ##OPTS_RNAplfold --noLP
117
118 ##OPTS_fasta2shrep_gspan -t "3=0,5=80" -M 5 -c 20 -win 40,150 -shift 30 --cue -u --stack --seq-graph-t --seq-graph-alph
119
120 <!--
121 <conditional name="OPTS_locarna">
122 <param name="OPTS_locarna_selector" type="select" label="LocaRNA advanced options">
123 <option value="basic" selected="True">Hide Advanced Options</option>
124 <option value="advanced">Show Advanced Options</option>
125 </param>
126 <when value="basic">
127 </when>
128 <when value="advanced">
129 -->
130 <param name="locarna_p" type="float" value="0.001" label="Minimal probability" />
131 <param name="locarna_max_diff_am" type="integer" value="50" label="Maximal difference for sizes of matched arcs" />
132 <param name="locarna_tau" type="integer" value="50" label="Tau factor in percent" />
133 <param name="locarna_max_diff" type="integer" value="100" label="Maximal difference for alignment traces" />
134 <param name="locarna_struct_weight" type="integer" value="180" label="Maximal weight of 1/2 arc match" />
135 <param name="locarna_temperature" type="integer" value="180" label="Temperature for PF-computation" />
136 <param name="locarna_indel_open" type="integer" value="-400" label="Indel opening score" />
137 <param name="locarna_indel" type="integer" value="-200" label="Indel score" />
138 <!--
139 </when>
140 </conditional>
141 -->
142 ##OPTS_locarna_maligs -p 0.001 --max-diff-am 50 --tau 50 --max-diff 100 --alifold-consensus-dp
143 ##OPTS_locarna_model -p 0.001 --max-diff-am 50 --tau 50 --max-diff 100 --alifold-consensus-dp
144 ##OPTS_locarna_p_model -p 0.001 --max-diff-am 50 --tau 100 --max-diff 100 --struct-weight 180 --plfold-span 150 --plfold-winsize 200 --temperature 180 --mea-beta 400 --consistency-transformation
145 ##OPTS_locarna_paligs -p 0.001 --max-diff-am 50 --tau 50 --max-diff 100 --indel-open -400 --indel -200 --struct-weight 180
146
147 <!--
148 <conditional name="OPTS_nspdk">
149 <param name="OPTS_nspdk_selector" type="select" label="NSPDK advanced options">
150 <option value="basic" selected="True">Hide Advanced Options</option>
151 <option value="advanced">Show Advanced Options</option>
152 </param>
153 <when value="basic">
154 </when>
155 <when value="advanced">
156 -->
157 <param name="nspdk_R" type="integer" value="3" label="Radius" />
158 <param name="nspdk_D" type="integer" value="3" label="Distance" />
159 <param name="nspdk_gt" type="select" label="graph type" >
160 <option value="DIRECTED" selected="True">DIRECTED</option>
161 <option value="UNDIRECTED">UNDIRECTED</option>
162 </param>
163 <param name="nspdk_ensf" type="integer" value="5" label="eccess neighbour size factor" />
164 <param name="nspdk_knn_center" type="integer" value="10" label="number of nearest neighbors" />
165 <param name="nspdk_ensf" type="integer" value="5" label="eccess neighbour size factor" />
166 <param name="nspdk_ensf" type="integer" value="5" label="eccess neighbour size factor" />
167 <param name="nspdk_ensf" type="integer" value="5" label="eccess neighbour size factor" />
168 <!--
169 </when>
170 </conditional>
171 -->
172 #OPTS_nspdk -R 3 -D 3 -gt DIRECTED
173 #OPTS_nspdk_centers -ensf 5 -oc -usn
174
175 <!--
176 <conditional name="OPTS_other">
177 <param name="OPTS_other_selector" type="select" label="Other advanced options">
178 <option value="basic" selected="True">Hide Advanced Options</option>
179 <option value="advanced">Show Advanced Options</option>
180 </param>
181 <when value="basic">
182 </when>
183 <when value="advanced">
184 -->
185 <param name="other_input_seq_min_length" type="integer" value="50" label="input_seq_min_length" />
186 <param name="other_input_win_shift" type="integer" value="33" label="input_win_shift" />
187 <param name="other_results_min_cluster_size" type="integer" value="5" label="results_min_cluster_size" />
188 <!--
189 </when>
190 </conditional>
191 -->
192 ##center_model_type 5
193 ##center_subtree_max 7
194 ##center_subtree_min 3
195 ##center_tree_aligs 2
196 ##center_tree_type 3
197 ##cm_bitscore_sig 1
198 ##cm_calibrate 0
199 ##cm_max_eval 0.001
200 ##cm_min_bitscore 15
201 ##cm_top_only 0
202 ##evaluate 0
203 ##evaluate_class0_as_fp 0
204 ##evaluate_min_overlap 0.51
205 ##input_add_revcompl 0
206 ##input_blastclust 1
207 ##input_blastclust_id 90
208 ##input_blastclust_len 0.90
209 ##input_seq_min_length 50
210 ##input_win_shift 33
211 ##input_win_size 0
212 ##nspdk_fcs 1
213 ##nspdk_greylist_num 0
214 ##nspdk_knn_center 10
215 ##nspdk_nhf 500
216 ##nspdk_nhf_max 1000
217 ##nspdk_nhf_step 50
218 ##results_merge_cluster_ol 0.66
219 ##results_merge_overlap 0.51
220 ##results_min_cluster_size 5
221 ##results_partition_type soft
222 ##results_top_num 10
223
224 </inputs>
225 <outputs>
226 <data name="output" format="html" label="GraphClust on ${on_string}"/>
227 </outputs>
228 <help>
229 <![CDATA[
230
231 .. class:: infomark
232
233 **What it does**
234
235 GraphClust
236
237 TODO
238
239 ]]>
240 </help>
241 <citations>
242 <citation type="doi">10.1093/bioinformatics/bts224</citation>
243 </citations>
244 </tool>