Mercurial > repos > rnateam > graphclust_nspdk

annotate NSPDK_sparseVect.xml @ 3:d10410cfd17a 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 5a545fc913b3a07e1452e67f66b2ca593660abdf
author rnateam
date Mon, 27 Feb 2017 12:03:12 -0500
parents ee828c452161
children 0625db6b6e45
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_sparse" name="NSPDK_sparseVect" version="9.2">
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
2 <requirements>
3
d10410cfd17a planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 5a545fc913b3a07e1452e67f66b2ca593660abdf
rnateam
parents: 2
diff changeset
3 <requirement type="package" version="0.1.9">graphclust-wrappers</requirement>
0
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
4 <requirement type="package" version="9.2">nspdk</requirement>
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
5 </requirements>
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
6 <stdio>
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
7 <exit_code range="1:" />
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
8 </stdio>
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
9 <command>
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
10 <![CDATA[
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
11
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
12
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
13 'NSPDK_sparseVect.pl' '$data_fasta' '$gspan_file' $max_rad $max_dist_relations
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
14
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
15 ]]>
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
16 </command>
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
17 <inputs>
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
18 <param type="data" name="gspan_file" format="searchgui_archive" />
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
19 <param type="data" name="data_fasta" format="fasta" />
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
20 <param name="max_rad" type="integer" value="3" size="5" label="maximum radius " help="-R"/>
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
21 <param name="max_dist_relations" type="integer" value="3" size="5" label="maximum distance relations" help="-D"/>
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
22 </inputs>
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
23 <outputs>
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
24 <data name="data_svector" format="zip" from_work_dir="SVECTOR/data.svector" label="data_svector"/>
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
25 </outputs>
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
26 <tests>
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
27 <test>
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
28 <param name="data_fasta" value="data.fasta"/>
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
29 <param name="gspan_file" value="1.group.gspan.bz2" ftype="searchgui_archive"/>
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
30 <param name="max_rad" value="3"/>
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
31 <param name="max_dist_relations" value="3"/>
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
32 <output name="data_svector" file="SVECTOR/data.svector" ftype="zip" />
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
33 </test>
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
34 </tests>
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
35 <help>
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
36 <![CDATA[
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
37
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
38 **What it does**
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
39
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
40 Produces an explicit sparse feature encoding.
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
41 Integer code for the invariant graph encoding is used as a feature indicator. In this way,
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
42 the integer associated to each feature (i.e. each pair or neighborhood subgraphs of radius r whose
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
43 roots are at distance d) can be interpreted as the feature key and the (normalized) count of occurrences as its value.
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
44 This allows to obtain an explicit feature encoding for a given graph G as a sparse vector in ℝ^m (with a very high dimension m).
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
45
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
46 **Parameters**
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
47
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
48 + **-R** <max radius> (default: 1)
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
49 + **-D** <max distance relations> (default: 4)
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
50
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
51
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
52 ]]>
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
53 </help>
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
54 <citations>
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
55 <citation type="doi">10.1093/bioinformatics/bts224</citation>
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
56 <citation type="bibtex">@inproceedings{costa2010fast,
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
57 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
58 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
59 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
60 pages={255--262},
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
61 year={2010},
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
62 organization={Omnipress}
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
63 }
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
64 </citation>
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
65 </citations>
165fe96228be planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
66 </tool>