Mercurial > repos > rnateam > graphclust_postprocessing
comparison glob_report.xml @ 5:4310ac018d05 draft
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
author | rnateam |
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date | Sat, 21 Jan 2017 17:39:21 -0500 |
parents | 4a9754d476fe |
children | 869a6e807d76 |
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4:4a9754d476fe | 5:4310ac018d05 |
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1 <tool id="glob_report" name="Report_Results" version="0.1"> | 1 <tool id="glob_report" name="Report_Results" version="0.1"> |
2 <requirements> | 2 <requirements> |
3 <requirement type="package" version="0.1">graphclust-wrappers</requirement> | 3 <requirement type="package" version="0.1.7">graphclust-wrappers</requirement> |
4 <requirement type="package" version='0.5'>perl-array-utils</requirement> | 4 <requirement type="package" version='0.5'>perl-array-utils</requirement> |
5 <requirement type="package" version='0.18.1'>scikit-learn</requirement> | 5 <requirement type="package" version='0.18.1'>scikit-learn</requirement> |
6 <requirement type="package" version='1.8.10'>locarna</requirement> | 6 <requirement type="package" version='1.8.10'>locarna</requirement> |
7 <requirement type="package" version='2.1'>rnaz</requirement> | 7 <requirement type="package" version='2.1'>rnaz</requirement> |
8 <requirement type="package" version="1.1">infernal</requirement> | 8 <requirement type="package" version="1.1">infernal</requirement> |
9 <requirement type="package" version='2.2.10'>viennarna</requirement> | 9 <requirement type="package" version='2.2.10'>viennarna</requirement> |
10 <requirement type="package" version='1.3.23'>graphicsmagick</requirement> | 10 <requirement type="package" version='1.3.23'>graphicsmagick</requirement> |
11 </requirements> | 11 </requirements> |
12 <stdio> | 12 <stdio> |
13 <exit_code range="1:" /> | 13 <exit_code range="1:" /> |
14 </stdio> | 14 </stdio> |
15 <command> | 15 <command> |
16 <![CDATA[ | 16 <![CDATA[ |
17 unzip $FASTA &> /dev/null && | 17 unzip $FASTA &> /dev/null && |
18 | 18 |
19 #set $inputFiles = "" | 19 #set $inputFiles = "" |
20 | 20 |
21 #for $cms_res in $cmsearch_results: | 21 #for $cms_res in $cmsearch_results: |
27 | 27 |
28 #for $mods in $model_tree_files: | 28 #for $mods in $model_tree_files: |
29 #set $inputFilesTrees += str($mods)+',' | 29 #set $inputFilesTrees += str($mods)+',' |
30 #end for | 30 #end for |
31 #set $inputFilesTrees = $inputFilesTrees[:-1] | 31 #set $inputFilesTrees = $inputFilesTrees[:-1] |
32 glob_res.pl | 32 'glob_res.pl' |
33 '$inputFiles' | 33 '$inputFiles' |
34 $merge_cluster_ol | 34 $merge_cluster_ol |
35 $merge_overlap | 35 $merge_overlap |
36 $min_cluster_size | 36 $min_cluster_size |
37 $cm_min_bitscore | 37 $cm_min_bitscore |
45 $iteration_num.CI | 45 $iteration_num.CI |
46 $final_partition_soft | 46 $final_partition_soft |
47 $final_partition_used_cmsearch | 47 $final_partition_used_cmsearch |
48 #end if | 48 #end if |
49 | 49 |
50 #if str($advanced_opts.advanced_opts_selector) == "show": | |
51 #if str($advanced_opts.param_type.param_type_selector) == "gclust": | |
52 $advanced_opts.param_type.p | |
53 $advanced_opts.param_type.max_diff_am | |
54 $advanced_opts.param_type.max_diff | |
55 $advanced_opts.param_type.tau | |
56 $advanced_opts.param_type.struct_weight | |
57 $advanced_opts.param_type.indel_opening | |
58 $advanced_opts.param_type.indel | |
59 $advanced_opts.param_type.alifold_consensus_dp | |
60 #end if | |
61 #end if | |
62 | |
50 && | 63 && |
51 python '$__tool_directory__/evaluation.py' | 64 python '$__tool_directory__/evaluation.py' |
52 #if $cdhit: | 65 #if $cdhit: |
53 && | 66 && |
54 python '$__tool_directory__/addCdhitseqs.py' '$cdhit' | 67 python '$__tool_directory__/addCdhitseqs.py' '$cdhit' |
55 #end if | 68 #end if |
56 ]]> | 69 ]]> |
57 </command> | 70 </command> |
58 <inputs> | 71 <inputs> |
59 <param type="data" name="FASTA" format="zip" /> | 72 <param type="data" name="FASTA" format="zip" /> |
60 <param type="data" name="cmsearch_results" format="tabular" multiple="True"/> | 73 <param type="data" name="cmsearch_results" format="tabular" multiple="True"/> |
61 <param type="data" name="model_tree_files" format="txt" multiple="True"/> | 74 <param type="data" name="model_tree_files" format="txt" multiple="True"/> |
62 <param name="partition_type" type="boolean" checked="True" truevalue="0" falsevalue="1" label="Hard partition"/> | 75 <param name="partition_type" type="boolean" checked="True" truevalue="0" falsevalue="1" label="Hard partition"/> |
63 <param name="cut_type" type="boolean" checked="True" truevalue="0" falsevalue="1" label="Use CM score for cutoff" help="otherwise use E-value"/> | 76 <param name="cut_type" type="boolean" checked="True" truevalue="0" falsevalue="1" label="Use CM score for cutoff" help="otherwise use E-value"/> |
64 <param type="data" name="cdhit" format="txt" optional="true"/> | 77 <param type="data" name="cdhit" format="txt" optional="true"/> |
65 <conditional name="iteration_num"> | 78 <conditional name="iteration_num"> |
66 <param name="iteration_num_selector" type="boolean" checked="no" label="Multiple iterations" help="for single iteration- NO, for multiple-YES"/> | 79 <param name="iteration_num_selector" type="boolean" checked="no" label="Multiple iterations" help="for single iteration- NO, for multiple-YES"/> |
67 <when value="true"> | 80 <when value="true"> |
68 <param name="CI" type="integer" value="2" size="5" label="Number of current iteration "/> | 81 <param name="CI" type="integer" value="2" size="5" label="Number of current iteration "/> |
69 <param type="data" name="final_partition_soft" format="txt" /> | 82 <param type="data" name="final_partition_soft" format="txt" /> |
70 <param type="data" name="final_partition_used_cmsearch" format="txt" /> | 83 <param type="data" name="final_partition_used_cmsearch" format="txt" /> |
71 </when> | 84 </when> |
72 <when value="false" ></when> | 85 <when value="false" ></when> |
73 </conditional> | 86 </conditional> |
74 <param name="merge_cluster_ol" type="float" value="0.66" size="5" label="merge_cluster_ol" help=""/> | 87 <param name="merge_cluster_ol" type="float" value="0.66" size="5" label="merge_cluster_ol" help=""/> |
75 <param name="merge_overlap" type="float" value="0.51" size="5" label="merge_overlap" help=""/> | 88 <param name="merge_overlap" type="float" value="0.51" size="5" label="merge_overlap" help=""/> |
76 <param name="min_cluster_size" type="integer" value="3" size="5" label="min_cluster_size" help=""/> | 89 <param name="min_cluster_size" type="integer" value="3" size="5" label="min_cluster_size" help=""/> |
77 <param name="cm_min_bitscore" type="integer" value="20" size="5" label="cm_min_bitscore" help=""/> | 90 <param name="cm_min_bitscore" type="integer" value="20" size="5" label="cm_min_bitscore" help=""/> |
78 <param name="cm_max_eval" type="float" value="0.001" size="5" label="cm_max_eval" help=""/> | 91 <param name="cm_max_eval" type="float" value="0.001" size="5" label="cm_max_eval" help=""/> |
79 <param name="cm_bitscore_sig" type="integer" value="1" size="5" label="cm_bitscore_sig" help=""/> | 92 <param name="cm_bitscore_sig" type="integer" value="1" size="5" label="cm_bitscore_sig" help=""/> |
80 <param name="results_top_num" type="integer" value="5" size="5" label="results_top_num" help=""/> | 93 <param name="results_top_num" type="integer" value="5" size="5" label="results_top_num" help=""/> |
81 </inputs> | 94 |
82 <outputs> | 95 <conditional name="advanced_opts"> |
83 <data name="final_stats" format="txt" from_work_dir="RESULTS/cluster.final.stats" label="cluster.final.stats" /> | 96 <param name="advanced_opts_selector" type="select" label="Advanced Options"> |
84 <data name="tableForEval" format="tabular" from_work_dir="RESULTS/fullTab.tabular" label="tableForEval" /> | 97 <option value="hide" selected="True">Hide</option> |
85 <data name="final_soft" format="txt" from_work_dir="RESULTS/partitions/final_partition.soft" label="soft_part" /> | 98 <option value="show">Show</option> |
86 <data name="final_used_cmsearch" format="txt" from_work_dir="RESULTS/partitions/final_partition.used_cmsearch" label="final_partition_used_cmsearch" /> | 99 </param> |
87 <data name="evaluation" format="txt" from_work_dir="RESULTS/evaluation.txt" label="evaluation_of_clusters" /> | 100 <when value="hide"></when> |
88 <collection name="clusters" type="list" label="CLUSTERS"> | 101 <when value="show"> |
89 <discover_datasets pattern="(?P<name>^.*\.all$)" directory="RESULTS" /> | 102 |
90 </collection> | 103 <conditional name="param_type"> |
91 <collection name="partitions" type="list" label="Partitions"> | 104 <param name="param_type_selector" type="select" label="Choose the type of parameters"> |
92 <discover_datasets pattern="(?P<name>^.*$)" directory="RESULTS/partitions" /> | 105 <option value="locarna">LocARNA defaults</option> |
93 </collection> | 106 <option value="gclust" selected="True">GrapClust defaults(changeable)</option> |
94 <collection name="topSecondaryStruct" type="list" label="Top $results_top_num alirna.ps"> | 107 </param> |
95 <discover_datasets format="png" pattern="(?P<name>^.*\.alirna.png$)" /> | 108 <when value="gclust"> |
96 </collection> | 109 |
97 <collection name="topDot" type="list" label="Top $results_top_num aln.ps"> | 110 <param name="p" type="float" value="0.001" size="5" label="minimal probability" help="-p"/> |
98 <discover_datasets format="png" pattern="(?P<name>^.*\.aln.png$)" /> | 111 <param name="max_diff_am" type="integer" value="50" size="5" label=" maximal difference for sizes of matched arcs" help="--max-diff-am"/> |
99 </collection> | 112 <param argument="tau" type="integer" value="50" min="0" max="200" label="Sequence contribution at structure match in percent"/> |
100 </outputs> | 113 <param name="max_diff" type="integer" value="100" size="5" label="maximal difference for alignment traces" help="--max-diff"/> |
101 <tests> | 114 |
102 <test> | 115 <param name="struct_weight" argument="struct-weight" |
103 <param name="FASTA" value="FASTA.zip" ftype="searchgui_archive"/> | 116 label="Structure weight" type="integer" |
104 <param name="cmsearch_results" value="1.tabular,2.tabular"/> | 117 value="180" min="0" max="800" /> |
105 <param name="model_tree_files" value="1.1.model.tree.fa,1.2.model.tree.fa"/> | 118 <param name="indel_opening" argument="indel-opening" |
106 <param name="partition_type" value="0"/> | 119 label="Indel opening score" type="integer" |
107 <param name="cut_type" value="0"/> | 120 value="-400" max="0" min="-1500" /> |
108 <conditional name="iteration_num"> | 121 <param argument="indel" label="Indel score" type="integer" |
109 <param name="iteration_num_selector" value="false"/> | 122 value="-200" min="-1000" max="0" /> |
110 </conditional> | 123 |
111 <param name="merge_cluster_ol" value="0.66"/> | 124 <param name="alifold_consensus_dp" |
112 <param name="merge_overlap" value="0.51"/> | 125 type="boolean" checked="True" |
113 <param name="min_cluster_size" value="3"/> | 126 truevalue="--alifold-consensus-dp" falsevalue=" " |
114 <param name="cm_min_bitscore" value="20"/> | 127 label="Compute consensus dot plot by alifold" /> |
115 <param name="cm_max_eval" value="0.001"/> | 128 |
116 <param name="cm_bitscore_sig" value="1"/> | 129 </when> |
117 <output name="final_stats" file="RESULTS/cluster.final.stats" /> | 130 <when value="locarna"> |
118 <output_collection name="clusters" type="list"> | 131 </when> |
119 <element name="1.cluster.all" file="RESULTS/1.cluster.all" compare="contains"/> | 132 </conditional> |
120 <element name="2.cluster.all" file="RESULTS/2.cluster.all" compare="contains"/> | 133 |
121 </output_collection> | 134 </when> |
122 <output_collection name="partitions"> | 135 </conditional> |
123 <element name="final_overlap.map" file="RESULTS/partitions/final_overlap.map" compare="contains"> | 136 |
124 <assert_contents> | 137 </inputs> |
125 <has_text text="1.1 1.1" /> | 138 <outputs> |
126 <has_text text="1.2 1.2" /> | 139 <data name="final_stats" format="txt" from_work_dir="RESULTS/cluster.final.stats" label="cluster.final.stats" /> |
127 </assert_contents> | 140 <data name="tableForEval" format="tabular" from_work_dir="RESULTS/fullTab.tabular" label="tableForEval" /> |
128 </element> | 141 <data name="final_soft" format="txt" from_work_dir="RESULTS/partitions/final_partition.soft" label="soft_part" /> |
129 <element name="final_overlap.matrix" file="RESULTS/partitions/final_overlap.matrix" compare="contains"> | 142 <data name="final_used_cmsearch" format="txt" from_work_dir="RESULTS/partitions/final_partition.used_cmsearch" label="final_partition_used_cmsearch" /> |
130 <assert_contents> | 143 <data name="evaluation" format="txt" from_work_dir="RESULTS/evaluation.txt" label="evaluation_of_clusters" /> |
131 <has_text text="MODEL CLASS 0 0" /> | 144 <collection name="clusters" type="list" label="CLUSTERS"> |
132 <has_text text="1.2" /> | 145 <discover_datasets pattern="(?P<name>^.*\.all$)" directory="RESULTS" /> |
133 <has_text text="1.1" /> | 146 </collection> |
134 </assert_contents> | 147 <collection name="partitions" type="list" label="Partitions"> |
135 </element> | 148 <discover_datasets pattern="(?P<name>^.*$)" directory="RESULTS/partitions" /> |
136 <element name="final_partition.hard.best" file="RESULTS/partitions/final_partition.hard.best" /> | 149 </collection> |
137 <element name="final_partition.hard.merged" file="RESULTS/partitions/final_partition.hard.merged" /> | 150 <collection name="topSecondaryStruct" type="list" label="Top $results_top_num alirna.ps"> |
138 <element name="final_partition.soft" file="RESULTS/partitions/final_partition.soft" /> | 151 <discover_datasets format="png" pattern="(?P<name>^.*\.alirna.png$)" /> |
139 <element name="final_partition.used_cmsearch" file="RESULTS/partitions/final_partition.used_cmsearch" compare="contains"/> | 152 </collection> |
140 </output_collection> | 153 <collection name="topDot" type="list" label="Top $results_top_num aln.ps"> |
141 <param name="results_top_num" value="5"/> | 154 <discover_datasets format="png" pattern="(?P<name>^.*\.aln.png$)" /> |
142 <output_collection name="topSecondaryStruct" type="list"> | 155 </collection> |
143 <element name="1.cluster.top5.alirna.png" file="1.cluster.top5.alirna.png" ftype="png" compare="sim_size" /> | 156 <data name="RESULTS_zip" format="zip" from_work_dir="RESULTS.zip" label="RESULTS.zip" /> |
144 <element name="2.cluster.top5.alirna.png" file="2.cluster.top5.alirna.png" ftype="png" compare="sim_size" /> | 157 </outputs> |
145 </output_collection> | 158 <tests> |
146 <output_collection name="topDot" type="list"> | 159 <test> |
147 <element name="1.cluster.top5.aln.png" file="1.cluster.top5.aln.png" ftype="png" compare="sim_size"/> | 160 <param name="FASTA" value="FASTA.zip" ftype="searchgui_archive"/> |
148 <element name="2.cluster.top5.aln.png" file="2.cluster.top5.aln.png" ftype="png" compare="sim_size"/> | 161 <param name="cmsearch_results" value="1.tabular,2.tabular"/> |
149 </output_collection> | 162 <param name="model_tree_files" value="1.1.model.tree.fa,1.2.model.tree.fa"/> |
150 </test> | 163 <param name="partition_type" value="0"/> |
151 </tests> | 164 <param name="cut_type" value="0"/> |
152 <help> | 165 <conditional name="iteration_num"> |
153 <![CDATA[ | 166 <param name="iteration_num_selector" value="false"/> |
167 </conditional> | |
168 <param name="merge_cluster_ol" value="0.66"/> | |
169 <param name="merge_overlap" value="0.51"/> | |
170 <param name="min_cluster_size" value="3"/> | |
171 <param name="cm_min_bitscore" value="20"/> | |
172 <param name="cm_max_eval" value="0.001"/> | |
173 <param name="cm_bitscore_sig" value="1"/> | |
174 <output name="final_stats" file="RESULTS/cluster.final.stats" /> | |
175 <output_collection name="clusters" type="list"> | |
176 <element name="1.cluster.all" file="RESULTS/1.cluster.all" compare="contains"/> | |
177 <element name="2.cluster.all" file="RESULTS/2.cluster.all" compare="contains"/> | |
178 </output_collection> | |
179 <output_collection name="partitions"> | |
180 <element name="final_overlap.map" file="RESULTS/partitions/final_overlap.map" compare="contains"> | |
181 <assert_contents> | |
182 <has_text text="1.1 1.1" /> | |
183 <has_text text="1.2 1.2" /> | |
184 </assert_contents> | |
185 </element> | |
186 <element name="final_overlap.matrix" file="RESULTS/partitions/final_overlap.matrix" compare="contains"> | |
187 <assert_contents> | |
188 <has_text text="MODEL CLASS 0 0" /> | |
189 <has_text text="1.2" /> | |
190 <has_text text="1.1" /> | |
191 </assert_contents> | |
192 </element> | |
193 <element name="final_partition.hard.best" file="RESULTS/partitions/final_partition.hard.best" /> | |
194 <element name="final_partition.hard.merged" file="RESULTS/partitions/final_partition.hard.merged" /> | |
195 <element name="final_partition.soft" file="RESULTS/partitions/final_partition.soft" /> | |
196 <element name="final_partition.used_cmsearch" file="RESULTS/partitions/final_partition.used_cmsearch" compare="contains"/> | |
197 </output_collection> | |
198 <param name="results_top_num" value="5"/> | |
199 <output_collection name="topSecondaryStruct" type="list"> | |
200 <element name="1.cluster.top5.alirna.png" file="1.cluster.top5.alirna.png" ftype="png" compare="sim_size" /> | |
201 <element name="2.cluster.top5.alirna.png" file="2.cluster.top5.alirna.png" ftype="png" compare="sim_size" /> | |
202 </output_collection> | |
203 <output_collection name="topDot" type="list"> | |
204 <element name="1.cluster.top5.aln.png" file="1.cluster.top5.aln.png" ftype="png" compare="sim_size" /> | |
205 <element name="2.cluster.top5.aln.png" file="2.cluster.top5.aln.png" ftype="png" compare="sim_size" /> | |
206 </output_collection> | |
207 <output name="RESULTS_zip" file="RESULTS.zip" ftype="zip" compare="sim_size" /> | |
208 | |
209 </test> | |
210 </tests> | |
211 <help> | |
212 <![CDATA[ | |
154 | 213 |
155 **What it does** | 214 **What it does** |
156 | 215 |
157 Post-processing. Redundant clusters are merged and instances that belong to multiple clusters | 216 Post-processing. Redundant clusters are merged and instances that belong to multiple clusters |
158 are assigned unambiguously. For every pair of clusters, the relative overlap (i.e. the fraction of | 217 are assigned unambiguously. For every pair of clusters, the relative overlap (i.e. the fraction of |
159 instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. | 218 instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. |
160 Cluster members are finally ranked by their CM bitscore. | 219 Cluster members are finally ranked by their CM bitscore. |
161 | 220 |
162 ]]> | 221 ]]> |
163 </help> | 222 </help> |
164 <citations> | 223 <citations> |
165 <citation type="bibtex">@inproceedings{costa2010fast, | 224 <citation type="bibtex">@inproceedings{costa2010fast, |
166 title={Fast neighborhood subgraph pairwise distance kernel}, | 225 title={Fast neighborhood subgraph pairwise distance kernel}, |
167 author={Costa, Fabrizio and De Grave, Kurt}, | 226 author={Costa, Fabrizio and De Grave, Kurt}, |
168 booktitle={Proceedings of the 26th International Conference on Machine Learning}, | 227 booktitle={Proceedings of the 26th International Conference on Machine Learning}, |
169 pages={255--262}, | 228 pages={255--262}, |