annotate glob_report.xml @ 1:ed8c7191b322 draft

planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9
author rnateam
date Thu, 22 Dec 2016 09:06:48 -0500
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1 <tool id="glob_report" name="Report_Results" version="0.1">
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2 <requirements>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
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3 <requirement type="package" version="0.1">graphclust-wrappers</requirement>
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4 <requirement type="package" version='0.5'>perl-array-utils</requirement>
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5 </requirements>
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6 <stdio>
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7 <exit_code range="1:" />
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8 </stdio>
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9 <command>
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10 <![CDATA[
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11
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
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12 unzip $FASTA &> /dev/null &&
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
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13
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
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14 #set $inputFiles = ""
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15
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16 #for $cms_res in $cmsearch_results:
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17 #set $inputFiles += str($cms_res)+','
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18 #end for
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19 #set $inputFiles = $inputFiles[:-1]
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21 #set $inputFilesTrees = ""
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23 #for $mods in $model_tree_files:
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
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24 #set $inputFilesTrees += str($mods)+','
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25 #end for
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26 #set $inputFilesTrees = $inputFilesTrees[:-1]
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27
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28 'glob_res.pl' '$inputFiles' $merge_cluster_ol $merge_overlap $min_cluster_size $cm_min_bitscore $cm_max_eval $cm_bitscore_sig $partition_type '' $cut_type '$inputFilesTrees'
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
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29 #if $iteration_num.iteration_num_selector:
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30 $iteration_num.CI
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31
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32 $final_partition_soft
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33 $final_partition_used_cmsearch
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34 #end if
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35
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36 &&
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
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37 python '$__tool_directory__/evaluation.py'
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38 ]]>
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39 </command>
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40 <inputs>
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41 <param type="data" name="FASTA" format="zip" />
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42 <param type="data" name="cmsearch_results" format="tabular" multiple="True"/>
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43 <param type="data" name="model_tree_files" format="txt" multiple="True"/>
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44 <param name="partition_type" type="boolean" checked="True" truevalue="0" falsevalue="1" label="Hard partition"/>
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45 <param name="cut_type" type="boolean" checked="True" truevalue="0" falsevalue="1" label="Use CM score for cutoff" help="otherwise use E-value"/>
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46 <conditional name="iteration_num">
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47 <param name="iteration_num_selector" type="boolean" checked="no" label="Multiple iterations" help="for single iteration- NO, for multiple-YES"/>
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48 <when value="true">
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49 <param name="CI" type="integer" value="2" size="5" label="Number of current iteration "/>
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50 <param type="data" name="final_partition_soft" format="txt" />
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51 <param type="data" name="final_partition_used_cmsearch" format="txt" />
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52 </when>
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53 <when value="false" ></when>
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54 </conditional>
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55 <param name="merge_cluster_ol" type="float" value="0.66" size="5" label="merge_cluster_ol" help=""/>
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56 <param name="merge_overlap" type="float" value="0.51" size="5" label="merge_overlap" help=""/>
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57 <param name="min_cluster_size" type="integer" value="3" size="5" label="min_cluster_size" help=""/>
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58 <param name="cm_min_bitscore" type="integer" value="20" size="5" label="cm_min_bitscore" help=""/>
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59 <param name="cm_max_eval" type="float" value="0.001" size="5" label="cm_max_eval" help=""/>
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60 <param name="cm_bitscore_sig" type="integer" value="1" size="5" label="cm_bitscore_sig" help=""/>
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61 </inputs>
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62 <outputs>
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63 <data name="final_stats" format="txt" from_work_dir="RESULTS/cluster.final.stats" label="cluster.final.stats" />
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64 <data name="tableForEval" format="tabular" from_work_dir="RESULTS/fullTab.tabular" label="tableForEval" />
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65 <data name="final_soft" format="txt" from_work_dir="RESULTS/partitions/final_partition.soft" label="soft_part" />
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66 <data name="final_used_cmsearch" format="txt" from_work_dir="RESULTS/partitions/final_partition.used_cmsearch" label="final_partition_used_cmsearch" />
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67 <collection name="clusters" type="list" label="CLUSTERS">
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68 <discover_datasets pattern="(?P&lt;name&gt;^.*\.all$)" directory="RESULTS" />
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69 </collection>
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70 <collection name="partitions" type="list" label="Partitions">
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71 <discover_datasets pattern="(?P&lt;name&gt;^.*$)" directory="RESULTS/partitions" />
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72 </collection>
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73 </outputs>
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74 <tests>
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75 <test>
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76 <param name="FASTA" value="FASTA.zip" ftype="searchgui_archive"/>
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77 <param name="cmsearch_results" value="1.tabular,2.tabular"/>
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78 <param name="model_tree_files" value="1.1.model.tree.fa,1.2.model.tree.fa"/>
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79 <param name="partition_type" value="0"/>
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80 <param name="cut_type" value="0"/>
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81 <conditional name="iteration_num">
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82 <param name="iteration_num_selector" value="false"/>
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83 </conditional>
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84 <param name="merge_cluster_ol" value="0.66"/>
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85 <param name="merge_overlap" value="0.51"/>
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86 <param name="min_cluster_size" value="3"/>
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87 <param name="cm_min_bitscore" value="20"/>
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88 <param name="cm_max_eval" value="0.001"/>
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89 <param name="cm_bitscore_sig" value="1"/>
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90 <output name="final_stats" file="RESULTS/cluster.final.stats" />
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91 <output_collection name="clusters" type="list">
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92 <element name="1.cluster.all" file="RESULTS/1.cluster.all" compare="contains"/>
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93 <element name="2.cluster.all" file="RESULTS/2.cluster.all" compare="contains"/>
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94 </output_collection>
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95 <output_collection name="partitions">
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96 <element name="final_overlap.map" file="RESULTS/partitions/final_overlap.map" compare="contains">
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97 <assert_contents>
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98 <has_text text="1.1 1.1" />
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99 <has_text text="1.2 1.2" />
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100 </assert_contents>
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101 </element>
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102 <element name="final_overlap.matrix" file="RESULTS/partitions/final_overlap.matrix" compare="contains">
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103 <assert_contents>
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104 <has_text text="MODEL CLASS 0 0" />
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105 <has_text text="1.2" />
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106 <has_text text="1.1" />
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107 </assert_contents>
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108 </element>
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109 <element name="final_partition.hard.best" file="RESULTS/partitions/final_partition.hard.best" />
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110 <element name="final_partition.hard.merged" file="RESULTS/partitions/final_partition.hard.merged" />
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111 <element name="final_partition.soft" file="RESULTS/partitions/final_partition.soft" />
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112 <element name="final_partition.used_cmsearch" file="RESULTS/partitions/final_partition.used_cmsearch" compare="contains"/>
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113 </output_collection>
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114 </test>
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115 </tests>
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116 <help>
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117 <![CDATA[
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118
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119 **What it does**
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120
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121 Post-processing. Redundant clusters are merged and instances that belong to multiple clusters
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122 are assigned unambiguously. For every pair of clusters, the relative overlap (i.e. the fraction of
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123 instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%.
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124 Cluster members are finally ranked by their CM bitscore.
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125
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126 ]]>
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127 </help>
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128 <citations>
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129 <citation type="bibtex">@inproceedings{costa2010fast,
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130 title={Fast neighborhood subgraph pairwise distance kernel},
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131 author={Costa, Fabrizio and De Grave, Kurt},
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132 booktitle={Proceedings of the 26th International Conference on Machine Learning},
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133 pages={255--262},
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134 year={2010},
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135 organization={Omnipress}
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136 }
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137 </citation>
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138 </citations>
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139 </tool>