Mercurial > repos > rnateam > graphclust_nspdk

annotate NSPDK_candidateClusters.xml @ 2:ee828c452161 draft

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author rnateam
date Wed, 22 Feb 2017 16:53:08 -0500
parents 90a4a2e7d876
children 0625db6b6e45
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1 <tool id="NSPDK_candidateClust" name="NSPDK_candidateClusters" version="9.2">
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2 <requirements>
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3 <requirement type="package" version="0.1.8">graphclust-wrappers</requirement>
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4 <requirement type="package" version="0.5">perl-array-utils</requirement>
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5 <requirement type="package" version="9.2">nspdk</requirement>
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6 </requirements>
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7 <stdio>
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8 <exit_code range="1:" />
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9 </stdio>
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10 <command>
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11 <![CDATA[
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13 mkdir -p SVECTOR &&
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15 cp $data_svector SVECTOR/data.svector &&
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17 'NSPDK_candidateClusters.pl' '$data_fasta' '$data_names' $noCache $ensf $oc $usn $knn $nhf $nspdk_nhf_max $nspdk_nhf_step $GLOBAL_num_clusters $max_rad $max_dist_relations
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19 #if $iteration_num.iteration_num_selector:
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20 $iteration_num.CI
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21 '$blacklist'
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22 '$final_partition_soft'
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23 '$fast_cluster_last_round'
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24 $iteration_num.GLOBAL_hit_blacklist_overlap
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26 #else:
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27 1
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29 #end if
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31 ]]>
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32 </command>
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33 <inputs>
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34 <param type="data" name="data_svector" format="zip" />
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35 <param type="data" name="data_fasta" format="fasta" />
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36 <param type="data" name="data_names" format="txt" />
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37 <conditional name="iteration_num">
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38 <param name="iteration_num_selector" type="boolean" checked="no" label="Multiple iterations" help="for single iteration- NO, for multiple-YES"/>
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39 <when value="true">
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40 <param name="CI" type="integer" value="2" size="5" label="Number of current iteration "/>
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41 <param type="data" name="blacklist" format="txt" />
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42 <param type="data" name="final_partition_soft" format="txt" />
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43 <param type="data" name="fast_cluster_last_round" format="txt" />
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44 <param name="GLOBAL_hit_blacklist_overlap" type="float" value="0.2" size="5" label="Blacklist hit overlap" />
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45 </when>
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46 <when value="false" >
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47 <param name="CI" type="hidden" value="1" size="5" label="Number of current iteration "></param>
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48 </when>
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49 </conditional>
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50 <param name="max_rad" type="integer" value="3" size="5" label="maximum radius " help="-R"/>
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51 <param name="max_dist_relations" type="integer" value="3" size="5" label="maximum distance relations" help="-D"/>
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52 <param name="noCache" truevalue="-no-cache" falsevalue="" checked="True" type="boolean"
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53 label="Deactivate caching of kernel value computation (-no-cache)" help="to minimize memory usage"/>
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54 <param name="ensf" type="integer" value="5" size="5" label="eccess neighbour size factor" help="-ensf"/>
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55 <param name="usn" truevalue="-usn" falsevalue="" checked="True" type="boolean"
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56 label="Use shared neighbourhood to weight center density (-usn)" help="by default true"/>
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57 <param name="oc" truevalue="-oc" falsevalue="" checked="True" type="boolean"
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58 label=" flag to output clusters (-oc)" help="by default true"/>
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59 <param name="knn" type="integer" value="20" size="5" label="Number of nearest neighbors" help="-knn num"/>
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60 <param name="nhf" type="integer" value="500" size="5" label="Number of hash functions " help="-nhf num"/>
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61 <param name="nspdk_nhf_max" type="integer" value="1000" size="5" label="Maximal number of hash functions " />
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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."/>
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63 <param name="GLOBAL_num_clusters" type="integer" value="100" size="5" label="Maxinum number of clusters " />
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64 </inputs>
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65 <outputs>
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66 <data name="fast_cluster" format="txt" from_work_dir="SVECTOR/data.svector.1.fast_cluster" label="fast_cluster.1" >
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67 <filter> iteration_num['iteration_num_selector'] is False</filter>
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68 </data>
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69 <data name="fast_cluster_sim" format="txt" from_work_dir="SVECTOR/data.svector.1.fast_cluster_sim" label="fast_cluster_sim.1" >
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70 <filter> iteration_num['iteration_num_selector'] is False </filter>
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71 </data>
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72 <data name="black_list" format="txt" from_work_dir="SVECTOR/data.svector.blacklist.1" label="blacklist.1" >
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73 <filter> iteration_num['iteration_num_selector'] is False </filter>
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74 </data>
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75 <data name="fast_cluster_m" format="txt" from_work_dir="SVECTOR/data.svector.*.fast_cluster" label="fast_cluster.$iteration_num.CI" >
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76 <filter> iteration_num['iteration_num_selector'] is True</filter>
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77 </data>
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78 <data name="fast_cluster_sim_m" format="txt" from_work_dir="SVECTOR/data.svector.*.fast_cluster_sim" label="fast_cluster_sim.$iteration_num.CI" >
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79 <filter> iteration_num['iteration_num_selector'] is True</filter>
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80 </data>
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81 <data name="black_list_m" format="txt" from_work_dir="SVECTOR/data.svector.blacklist.*" label="blacklist.$iteration_num.CI" >
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82 <filter> iteration_num['iteration_num_selector'] is True</filter>
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83 </data>
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84 </outputs>
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85 <tests>
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86 <test>
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87 <param name="data_fasta" value="data.fasta"/>
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88 <param name="data_names" value="data.names"/>
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89 <param name="data_svector" value="data.svector.1" ftype="zip" />
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90 <conditional name="iteration_num">
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91 <param name="iteration_num_selector" value="false"/>
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92 </conditional>
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93 <param name="noCache" value="-no-cache"/>
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94 <param name="ensf" value="5"/>
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95 <param name="oc" value="-oc"/>
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96 <param name="max_rad" value="3"/>
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97 <param name="max_dist_relations" value="3"/>
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98 <param name="usn" value="-usn"/>
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99 <param name="knn" value="20"/>
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100 <param name="nhf" value="500"/>
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101 <param name="nspdk_nhf_max" value="1000"/>
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102 <param name="nspdk_nhf_step" value="25"/>
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103 <param name="GLOBAL_num_clusters" value="100"/>
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104 <output name="fast_cluster" file="SVECTOR/data.svector.1.fast_cluster" />
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105 <output name="fast_cluster_sim" file="SVECTOR/data.svector.1.fast_cluster_sim" />
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106 <output name="black_list" file="SVECTOR/data.svector.blacklist.1" />
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107 </test>
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108 </tests>
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109 <help>
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110 <![CDATA[
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111
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112 **What it does**
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113
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114 Copmutes global feature index and returns top dense sets.
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115 The candidate clusters are chosen as the top ranking neighborhoods provided that the size of their overlap
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116 is below a specified threshold.
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117 For more information see *Fast neighborhood subgraph pairwise distance kernel* paper.
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118
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119
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120 **Parameters**
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121
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122 + **-knn** : <num nearest neighbors> (default: 10)
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123
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124 + **-otknn** : flag to output true (i.e. implies full kernel matrix evaluation) k-nearest neighburs (default: 0)
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125
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126 + **-oc** : flag to output clusters (default: 0)
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127
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128 + **-nhf** : <num hash functions> for the Locality Sensitive Hashing function (default: 250)
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129
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130 + **-ensf** : <eccess neighbour size factor> (default: 10) (0 to avoid trimming)
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131
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132 + **-usn** : use shared neighbourhood to weight center density (default: 0)
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133
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134
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135 ]]>
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136 </help>
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137 <citations>
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138 <citation type="doi">10.1093/bioinformatics/bts224</citation>
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139 <citation type="bibtex">@inproceedings{costa2010fast,
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140 title={Fast neighborhood subgraph pairwise distance kernel},
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141 author={Costa, Fabrizio and De Grave, Kurt},
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142 booktitle={Proceedings of the 26th International Conference on Machine Learning},
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143 pages={255--262},
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144 year={2010},
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145 organization={Omnipress}
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146 }
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147 </citation>
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148 </citations>
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149 </tool>