Mercurial > repos > rnateam > graphclust_nspdk

comparison NSPDK_candidateClusters.xml @ 4:0625db6b6e45 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
author rnateam
date Mon, 13 Mar 2017 18:05:04 -0400
parents ee828c452161
children 9b5fb987a484
comparison
equal deleted inserted replaced
3:d10410cfd17a 4:0625db6b6e45
1 <tool id="NSPDK_candidateClust" name="NSPDK_candidateClusters" version="9.2"> 1 <tool id="NSPDK_candidateClust" name="NSPDK_candidateClusters" version="9.2">
2 <requirements> 2 <requirements>
3 <requirement type="package" version="0.1.8">graphclust-wrappers</requirement> 3 <requirement type="package" version="0.1.10">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="9.2">nspdk</requirement> 5 <requirement type="package" version="9.2">nspdk</requirement>
6 </requirements> 6 </requirements>
7 <stdio> 7 <stdio>
8 <exit_code range="1:" /> 8 <exit_code range="1:" />
9 </stdio> 9 </stdio>
10 <command> 10 <command>
11 <![CDATA[ 11 <![CDATA[
12 12
13 mkdir -p SVECTOR && 13 mkdir ./SVECTOR &&
14 14
15 cp $data_svector SVECTOR/data.svector && 15 #for $ins in $data_svector:
16 ln -f -s '$ins' ./SVECTOR/ &&
17 #end for
16 18
17 'NSPDK_candidateClusters.pl' '$data_fasta' '$data_names' $noCache $ensf $oc $usn $knn $nhf $nspdk_nhf_max $nspdk_nhf_step $GLOBAL_num_clusters $max_rad $max_dist_relations 19 NSPDK_candidateClusters.pl
20 '$data_fasta'
21 '$data_names'
22 $noCache
23 $ensf
24 $oc
25 $usn
26 $knn
27 $nhf
28 $nspdk_nhf_max
29 $nspdk_nhf_step
30 $GLOBAL_num_clusters
31 $max_rad
32 $max_dist_relations
18 33
19 #if $iteration_num.iteration_num_selector: 34 #if $iteration_num.iteration_num_selector:
20 $iteration_num.CI 35 $iteration_num.CI
21 '$blacklist' 36 '$blacklist'
22 '$final_partition_soft' 37 '$final_partition_soft'
23 '$fast_cluster_last_round' 38 '$fast_cluster_last_round'
24 $iteration_num.GLOBAL_hit_blacklist_overlap 39 $iteration_num.GLOBAL_hit_blacklist_overlap
25
26 #else:
27 1
28
29 #end if 40 #end if
30 41 ]]>
31 ]]> 42 </command>
32 </command> 43 <inputs>
33 <inputs> 44 <param type="data" name="data_svector" multiple="True"/>
34 <param type="data" name="data_svector" format="zip" /> 45 <param type="data" name="data_fasta" format="fasta" />
35 <param type="data" name="data_fasta" format="fasta" /> 46 <param type="data" name="data_names" format="txt" />
36 <param type="data" name="data_names" format="txt" /> 47 <conditional name="iteration_num">
37 <conditional name="iteration_num"> 48 <param name="iteration_num_selector" type="boolean" checked="no" label="Multiple iterations" help="for single iteration- NO, for multiple-YES"/>
38 <param name="iteration_num_selector" type="boolean" checked="no" label="Multiple iterations" help="for single iteration- NO, for multiple-YES"/> 49 <when value="true">
39 <when value="true"> 50 <param name="CI" type="integer" value="2" size="5" label="Number of current iteration "/>
40 <param name="CI" type="integer" value="2" size="5" label="Number of current iteration "/> 51 <param type="data" name="blacklist" format="txt" />
41 <param type="data" name="blacklist" format="txt" /> 52 <param type="data" name="final_partition_soft" format="txt" />
42 <param type="data" name="final_partition_soft" format="txt" /> 53 <param type="data" name="fast_cluster_last_round" format="txt" />
43 <param type="data" name="fast_cluster_last_round" format="txt" /> 54 <param name="GLOBAL_hit_blacklist_overlap" type="float" value="0.2" size="5" label="Blacklist hit overlap" />
44 <param name="GLOBAL_hit_blacklist_overlap" type="float" value="0.2" size="5" label="Blacklist hit overlap" /> 55 </when>
45 </when> 56 <when value="false" >
46 <when value="false" > 57 <param name="CI" type="hidden" value="1" size="5" label="Number of current iteration "></param>
47 <param name="CI" type="hidden" value="1" size="5" label="Number of current iteration "></param> 58 </when>
48 </when> 59 </conditional>
49 </conditional> 60 <param name="max_rad" type="integer" value="3" size="5" label="maximum radius " help="-R"/>
50 <param name="max_rad" type="integer" value="3" size="5" label="maximum radius " help="-R"/> 61 <param name="max_dist_relations" type="integer" value="3" size="5" label="maximum distance relations" help="-D"/>
51 <param name="max_dist_relations" type="integer" value="3" size="5" label="maximum distance relations" help="-D"/> 62 <param name="noCache" truevalue="-no-cache" falsevalue="" checked="True" type="boolean"
52 <param name="noCache" truevalue="-no-cache" falsevalue="" checked="True" type="boolean"
53 label="Deactivate caching of kernel value computation (-no-cache)" help="to minimize memory usage"/> 63 label="Deactivate caching of kernel value computation (-no-cache)" help="to minimize memory usage"/>
54 <param name="ensf" type="integer" value="5" size="5" label="eccess neighbour size factor" help="-ensf"/> 64 <param name="ensf" type="integer" value="5" size="5" label="eccess neighbour size factor" help="-ensf"/>
55 <param name="usn" truevalue="-usn" falsevalue="" checked="True" type="boolean" 65 <param name="usn" truevalue="-usn" falsevalue="" checked="True" type="boolean"
56 label="Use shared neighbourhood to weight center density (-usn)" help="by default true"/> 66 label="Use shared neighbourhood to weight center density (-usn)" help="by default true"/>
57 <param name="oc" truevalue="-oc" falsevalue="" checked="True" type="boolean" 67 <param name="oc" truevalue="-oc" falsevalue="" checked="True" type="boolean"
58 label=" flag to output clusters (-oc)" help="by default true"/> 68 label=" flag to output clusters (-oc)" help="by default true"/>
59 <param name="knn" type="integer" value="20" size="5" label="Number of nearest neighbors" help="-knn num"/> 69 <param name="knn" type="integer" value="20" size="5" label="Number of nearest neighbors" help="-knn num"/>
60 <param name="nhf" type="integer" value="500" size="5" label="Number of hash functions " help="-nhf num"/> 70 <param name="nhf" type="integer" value="500" size="5" label="Number of hash functions " help="-nhf num"/>
61 <param name="nspdk_nhf_max" type="integer" value="1000" size="5" label="Maximal number of hash functions " /> 71 <param name="nspdk_nhf_max" type="integer" value="1000" size="5" label="Maximal number of hash functions " />
62 <param name="nspdk_nhf_step" type="integer" value="25" size="5" label="Size of step for increasing hash functions " help="The number of hash functions is increased by this value after each iteration."/> 72 <param name="nspdk_nhf_step" type="integer" value="25" size="5" label="Size of step for increasing hash functions " help="The number of hash functions is increased by this value after each iteration."/>
63 <param name="GLOBAL_num_clusters" type="integer" value="100" size="5" label="Maxinum number of clusters " /> 73 <param name="GLOBAL_num_clusters" type="integer" value="100" size="5" label="Maxinum number of clusters " />
64 </inputs> 74 </inputs>
65 <outputs> 75 <outputs>
66 <data name="fast_cluster" format="txt" from_work_dir="SVECTOR/data.svector.1.fast_cluster" label="fast_cluster.1" > 76 <data name="fast_cluster" format="txt" from_work_dir="SVECTOR/data.svector.1.fast_cluster" label="fast_cluster.1" >
67 <filter> iteration_num['iteration_num_selector'] is False</filter> 77 <filter> iteration_num['iteration_num_selector'] is False</filter>
68 </data> 78 </data>
69 <data name="fast_cluster_sim" format="txt" from_work_dir="SVECTOR/data.svector.1.fast_cluster_sim" label="fast_cluster_sim.1" > 79 <data name="fast_cluster_sim" format="txt" from_work_dir="SVECTOR/data.svector.1.fast_cluster_sim" label="fast_cluster_sim.1" >
70 <filter> iteration_num['iteration_num_selector'] is False </filter> 80 <filter> iteration_num['iteration_num_selector'] is False </filter>
71 </data> 81 </data>
72 <data name="black_list" format="txt" from_work_dir="SVECTOR/data.svector.blacklist.1" label="blacklist.1" > 82 <data name="black_list" format="txt" from_work_dir="SVECTOR/data.svector.blacklist.1" label="blacklist.1" >
73 <filter> iteration_num['iteration_num_selector'] is False </filter> 83 <filter> iteration_num['iteration_num_selector'] is False </filter>
74 </data> 84 </data>
75 <data name="fast_cluster_m" format="txt" from_work_dir="SVECTOR/data.svector.*.fast_cluster" label="fast_cluster.$iteration_num.CI" > 85 <data name="fast_cluster_m" format="txt" from_work_dir="SVECTOR/data.svector.*.fast_cluster" label="fast_cluster.$iteration_num.CI" >
76 <filter> iteration_num['iteration_num_selector'] is True</filter> 86 <filter> iteration_num['iteration_num_selector'] is True</filter>
77 </data> 87 </data>
78 <data name="fast_cluster_sim_m" format="txt" from_work_dir="SVECTOR/data.svector.*.fast_cluster_sim" label="fast_cluster_sim.$iteration_num.CI" > 88 <data name="fast_cluster_sim_m" format="txt" from_work_dir="SVECTOR/data.svector.*.fast_cluster_sim" label="fast_cluster_sim.$iteration_num.CI" >
79 <filter> iteration_num['iteration_num_selector'] is True</filter> 89 <filter> iteration_num['iteration_num_selector'] is True</filter>
80 </data> 90 </data>
81 <data name="black_list_m" format="txt" from_work_dir="SVECTOR/data.svector.blacklist.*" label="blacklist.$iteration_num.CI" > 91 <data name="black_list_m" format="txt" from_work_dir="SVECTOR/data.svector.blacklist.*" label="blacklist.$iteration_num.CI" >
82 <filter> iteration_num['iteration_num_selector'] is True</filter> 92 <filter> iteration_num['iteration_num_selector'] is True</filter>
83 </data> 93 </data>
84 </outputs> 94 </outputs>
85 <tests> 95 <tests>
86 <test> 96 <test>
87 <param name="data_fasta" value="data.fasta"/> 97 <param name="data_fasta" value="data.fasta"/>
88 <param name="data_names" value="data.names"/> 98 <param name="data_names" value="data.names"/>
89 <param name="data_svector" value="data.svector.1" ftype="zip" /> 99 <param name="data_svector" value="data.svector.1" ftype="zip" />
90 <conditional name="iteration_num"> 100 <conditional name="iteration_num">
91 <param name="iteration_num_selector" value="false"/> 101 <param name="iteration_num_selector" value="false"/>
92 </conditional> 102 </conditional>
93 <param name="noCache" value="-no-cache"/> 103 <param name="noCache" value="-no-cache"/>
94 <param name="ensf" value="5"/> 104 <param name="ensf" value="5"/>
95 <param name="oc" value="-oc"/> 105 <param name="oc" value="-oc"/>
96 <param name="max_rad" value="3"/> 106 <param name="max_rad" value="3"/>
97 <param name="max_dist_relations" value="3"/> 107 <param name="max_dist_relations" value="3"/>
98 <param name="usn" value="-usn"/> 108 <param name="usn" value="-usn"/>
99 <param name="knn" value="20"/> 109 <param name="knn" value="20"/>
100 <param name="nhf" value="500"/> 110 <param name="nhf" value="500"/>
101 <param name="nspdk_nhf_max" value="1000"/> 111 <param name="nspdk_nhf_max" value="1000"/>
102 <param name="nspdk_nhf_step" value="25"/> 112 <param name="nspdk_nhf_step" value="25"/>
103 <param name="GLOBAL_num_clusters" value="100"/> 113 <param name="GLOBAL_num_clusters" value="100"/>
104 <output name="fast_cluster" file="SVECTOR/data.svector.1.fast_cluster" /> 114 <output name="fast_cluster" file="SVECTOR/data.svector.1.fast_cluster" />
105 <output name="fast_cluster_sim" file="SVECTOR/data.svector.1.fast_cluster_sim" /> 115 <output name="fast_cluster_sim" file="SVECTOR/data.svector.1.fast_cluster_sim" />
106 <output name="black_list" file="SVECTOR/data.svector.blacklist.1" /> 116 <output name="black_list" file="SVECTOR/data.svector.blacklist.1" />
107 </test> 117 </test>
108 </tests> 118 </tests>
109 <help> 119 <help>
110 <![CDATA[ 120 <![CDATA[
111 121
112 **What it does** 122 **What it does**
113 123
114 Copmutes global feature index and returns top dense sets. 124 Copmutes global feature index and returns top dense sets.
115 The candidate clusters are chosen as the top ranking neighborhoods provided that the size of their overlap 125 The candidate clusters are chosen as the top ranking neighborhoods provided that the size of their overlap
131 141
132 + **-usn** : use shared neighbourhood to weight center density (default: 0) 142 + **-usn** : use shared neighbourhood to weight center density (default: 0)
133 143
134 144
135 ]]> 145 ]]>
136 </help> 146 </help>
137 <citations> 147 <citations>
138 <citation type="doi">10.1093/bioinformatics/bts224</citation> 148 <citation type="doi">10.1093/bioinformatics/bts224</citation>
139 <citation type="bibtex">@inproceedings{costa2010fast, 149 <citation type="bibtex">@inproceedings{costa2010fast,
140 title={Fast neighborhood subgraph pairwise distance kernel}, 150 title={Fast neighborhood subgraph pairwise distance kernel},
141 author={Costa, Fabrizio and De Grave, Kurt}, 151 author={Costa, Fabrizio and De Grave, Kurt},
142 booktitle={Proceedings of the 26th International Conference on Machine Learning}, 152 booktitle={Proceedings of the 26th International Conference on Machine Learning},
143 pages={255--262}, 153 pages={255--262},
144 year={2010}, 154 year={2010},
145 organization={Omnipress} 155 organization={Omnipress}
146 } 156 }
147 </citation> 157 </citation>
148 </citations> 158 </citations>
149 </tool> 159 </tool>