Mercurial > repos > rnateam > graphclust_nspdk

annotate NSPDK_candidateClusters.xml @ 5:9b5fb987a484 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 b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
author rnateam
date Fri, 17 Mar 2017 08:28:51 -0400
parents 0625db6b6e45
children 2aaf391798a3
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
1 <tool id="NSPDK_candidateClust" name="NSPDK_candidateClusters" version="9.2">
4
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
2 <requirements>
5
9b5fb987a484 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
rnateam
parents: 4
diff changeset
3 <requirement type="package" version="0.1.11">graphclust-wrappers</requirement>
4
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
4 <requirement type="package" version="0.5">perl-array-utils</requirement>
5
9b5fb987a484 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
rnateam
parents: 4
diff changeset
5 <requirement type="package" version="9.2">nspdk</requirement>
4
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
6 </requirements>
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
7 <stdio>
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
8 <exit_code range="1:" />
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
9 </stdio>
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
10 <command>
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
11 <![CDATA[
0
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
12
4
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
13 mkdir ./SVECTOR &&
0
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
14
4
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
15 #for $ins in $data_svector:
5
9b5fb987a484 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
rnateam
parents: 4
diff changeset
16 ln -f -s '$ins' ./SVECTOR/$ins.element_identifier &&
4
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
17 #end for
0
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
18
4
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
19 NSPDK_candidateClusters.pl
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
20 '$data_fasta'
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
21 '$data_names'
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
22 $noCache
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
23 $ensf
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
24 $oc
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
25 $usn
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
26 $knn
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
27 $nhf
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
28 $nspdk_nhf_max
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
29 $nspdk_nhf_step
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
30 $GLOBAL_num_clusters
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
31 $max_rad
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
32 $max_dist_relations
0
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
33
4
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
34 #if $iteration_num.iteration_num_selector:
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
35 $iteration_num.CI
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
36 '$blacklist'
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
37 '$final_partition_soft'
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
38 '$fast_cluster_last_round'
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
39 $iteration_num.GLOBAL_hit_blacklist_overlap
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
40 #end if
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
41 ]]>
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
42 </command>
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
43 <inputs>
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
44 <param type="data" name="data_svector" multiple="True"/>
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
45 <param type="data" name="data_fasta" format="fasta" />
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
46 <param type="data" name="data_names" format="txt" />
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
47 <conditional name="iteration_num">
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
48 <param name="iteration_num_selector" type="boolean" checked="no" label="Multiple iterations" help="for single iteration- NO, for multiple-YES"/>
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
49 <when value="true">
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
50 <param name="CI" type="integer" value="2" size="5" label="Number of current iteration "/>
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
51 <param type="data" name="blacklist" format="txt" />
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
52 <param type="data" name="final_partition_soft" format="txt" />
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
53 <param type="data" name="fast_cluster_last_round" format="txt" />
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
54 <param name="GLOBAL_hit_blacklist_overlap" type="float" value="0.2" size="5" label="Blacklist hit overlap" />
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
55 </when>
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
56 <when value="false" >
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
57 <param name="CI" type="hidden" value="1" size="5" label="Number of current iteration "></param>
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
58 </when>
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
59 </conditional>
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
60 <param name="max_rad" type="integer" value="3" size="5" label="maximum radius " help="-R"/>
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
61 <param name="max_dist_relations" type="integer" value="3" size="5" label="maximum distance relations" help="-D"/>
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
62 <param name="noCache" truevalue="-no-cache" falsevalue="" checked="True" type="boolean"
0
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
63 label="Deactivate caching of kernel value computation (-no-cache)" help="to minimize memory usage"/>
4
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
64 <param name="ensf" type="integer" value="5" size="5" label="eccess neighbour size factor" help="-ensf"/>
5
9b5fb987a484 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
rnateam
parents: 4
diff changeset
65 <param name="usn" truevalue="-usn" falsevalue="" checked="True" type="boolean"
0
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
66 label="Use shared neighbourhood to weight center density (-usn)" help="by default true"/>
4
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
67 <param name="oc" truevalue="-oc" falsevalue="" checked="True" type="boolean"
0
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
68 label=" flag to output clusters (-oc)" help="by default true"/>
4
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
69 <param name="knn" type="integer" value="20" size="5" label="Number of nearest neighbors" help="-knn num"/>
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
70 <param name="nhf" type="integer" value="500" size="5" label="Number of hash functions " help="-nhf num"/>
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
71 <param name="nspdk_nhf_max" type="integer" value="1000" size="5" label="Maximal number of hash functions " />
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
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."/>
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
73 <param name="GLOBAL_num_clusters" type="integer" value="100" size="5" label="Maxinum number of clusters " />
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
74 </inputs>
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
75 <outputs>
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
76 <data name="fast_cluster" format="txt" from_work_dir="SVECTOR/data.svector.1.fast_cluster" label="fast_cluster.1" >
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
77 <filter> iteration_num['iteration_num_selector'] is False</filter>
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
78 </data>
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
79 <data name="fast_cluster_sim" format="txt" from_work_dir="SVECTOR/data.svector.1.fast_cluster_sim" label="fast_cluster_sim.1" >
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
80 <filter> iteration_num['iteration_num_selector'] is False </filter>
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
81 </data>
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
82 <data name="black_list" format="txt" from_work_dir="SVECTOR/data.svector.blacklist.1" label="blacklist.1" >
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
83 <filter> iteration_num['iteration_num_selector'] is False </filter>
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
84 </data>
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
85 <data name="fast_cluster_m" format="txt" from_work_dir="SVECTOR/data.svector.*.fast_cluster" label="fast_cluster.$iteration_num.CI" >
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
86 <filter> iteration_num['iteration_num_selector'] is True</filter>
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
87 </data>
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
88 <data name="fast_cluster_sim_m" format="txt" from_work_dir="SVECTOR/data.svector.*.fast_cluster_sim" label="fast_cluster_sim.$iteration_num.CI" >
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
89 <filter> iteration_num['iteration_num_selector'] is True</filter>
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
90 </data>
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
91 <data name="black_list_m" format="txt" from_work_dir="SVECTOR/data.svector.blacklist.*" label="blacklist.$iteration_num.CI" >
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
92 <filter> iteration_num['iteration_num_selector'] is True</filter>
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
93 </data>
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
94 </outputs>
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
95 <tests>
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
96 <test>
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
97 <param name="data_fasta" value="data.fasta"/>
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
98 <param name="data_names" value="data.names"/>
5
9b5fb987a484 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
rnateam
parents: 4
diff changeset
99 <param name="data_svector" value="1.group.gspan" />
4
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
100 <conditional name="iteration_num">
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
101 <param name="iteration_num_selector" value="false"/>
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
102 </conditional>
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
103 <param name="noCache" value="-no-cache"/>
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
104 <param name="ensf" value="5"/>
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
105 <param name="oc" value="-oc"/>
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
106 <param name="max_rad" value="3"/>
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
107 <param name="max_dist_relations" value="3"/>
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
108 <param name="usn" value="-usn"/>
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
109 <param name="knn" value="20"/>
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
110 <param name="nhf" value="500"/>
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
111 <param name="nspdk_nhf_max" value="1000"/>
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
112 <param name="nspdk_nhf_step" value="25"/>
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
113 <param name="GLOBAL_num_clusters" value="100"/>
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
114 <output name="fast_cluster" file="SVECTOR/data.svector.1.fast_cluster" />
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
115 <output name="fast_cluster_sim" file="SVECTOR/data.svector.1.fast_cluster_sim" />
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
116 <output name="black_list" file="SVECTOR/data.svector.blacklist.1" />
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
117 </test>
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
118 </tests>
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
119 <help>
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
120 <![CDATA[
0
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
121
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
122 **What it does**
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
123
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
124 Copmutes global feature index and returns top dense sets.
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
125 The candidate clusters are chosen as the top ranking neighborhoods provided that the size of their overlap
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
126 is below a specified threshold.
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
127 For more information see *Fast neighborhood subgraph pairwise distance kernel* paper.
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
128
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
129
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
130 **Parameters**
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
131
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
132 + **-knn** : <num nearest neighbors> (default: 10)
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
133
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
134 + **-otknn** : flag to output true (i.e. implies full kernel matrix evaluation) k-nearest neighburs (default: 0)
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
135
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
136 + **-oc** : flag to output clusters (default: 0)
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
137
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
138 + **-nhf** : <num hash functions> for the Locality Sensitive Hashing function (default: 250)
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
139
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
140 + **-ensf** : <eccess neighbour size factor> (default: 10) (0 to avoid trimming)
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
141
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
142 + **-usn** : use shared neighbourhood to weight center density (default: 0)
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
143
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
144
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
145 ]]>
4
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
146 </help>
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
147 <citations>
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
148 <citation type="doi">10.1093/bioinformatics/bts224</citation>
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
149 <citation type="bibtex">@inproceedings{costa2010fast,
0
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
150 title={Fast neighborhood subgraph pairwise distance kernel},
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
151 author={Costa, Fabrizio and De Grave, Kurt},
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
152 booktitle={Proceedings of the 26th International Conference on Machine Learning},
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
153 pages={255--262},
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
154 year={2010},
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
155 organization={Omnipress}
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
156 }
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
157 </citation>
4
0625db6b6e45 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
rnateam
parents: 2
diff changeset
158 </citations>
0
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
159 </tool>