Mercurial > repos > rnateam > graphclust_nspdk

comparison NSPDK_candidateClusters.xml @ 3:2a7f99a14b5f draft

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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 08:24:36 -0400
parents 062be03c293f
children a0bfb7782af1
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2:062be03c293f 3:2a7f99a14b5f
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="0.1.10">graphclust-wrappers</requirement> 3 <requirement type="package" version="0.1.11">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 ./SVECTOR && 13 mkdir ./SVECTOR &&
14 14
15 #for $ins in $data_svector: 15 #for $ins in $data_svector:
16 ln -f -s '$ins' ./SVECTOR/ && 16 ln -f -s '$ins' ./SVECTOR/$ins.element_identifier &&
17 #end for 17 #end for
18 18
19 NSPDK_candidateClusters.pl 19 NSPDK_candidateClusters.pl
20 '$data_fasta' 20 '$data_fasta'
21 '$data_names' 21 '$data_names'
60 <param name="max_rad" type="integer" value="3" size="5" label="maximum radius " help="-R"/> 60 <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"/> 61 <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" 62 <param name="noCache" truevalue="-no-cache" falsevalue="" checked="True" type="boolean"
63 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"/>
64 <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"/>
65 <param name="usn" truevalue="-usn" falsevalue="" checked="True" type="boolean" 65 <param name="usn" truevalue="-usn" falsevalue="" checked="True" type="boolean"
66 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"/>
67 <param name="oc" truevalue="-oc" falsevalue="" checked="True" type="boolean" 67 <param name="oc" truevalue="-oc" falsevalue="" checked="True" type="boolean"
68 label=" flag to output clusters (-oc)" help="by default true"/> 68 label=" flag to output clusters (-oc)" help="by default true"/>
69 <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"/>
70 <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"/>
94 </outputs> 94 </outputs>
95 <tests> 95 <tests>
96 <test> 96 <test>
97 <param name="data_fasta" value="data.fasta"/> 97 <param name="data_fasta" value="data.fasta"/>
98 <param name="data_names" value="data.names"/> 98 <param name="data_names" value="data.names"/>
99 <param name="data_svector" value="data.svector.1" ftype="zip" /> 99 <param name="data_svector" value="1.group.gspan" />
100 <conditional name="iteration_num"> 100 <conditional name="iteration_num">
101 <param name="iteration_num_selector" value="false"/> 101 <param name="iteration_num_selector" value="false"/>
102 </conditional> 102 </conditional>
103 <param name="noCache" value="-no-cache"/> 103 <param name="noCache" value="-no-cache"/>
104 <param name="ensf" value="5"/> 104 <param name="ensf" value="5"/>