graphclust_postprocessing: glob

annotate glob_report.xml @ 2:b8e32e577597 draft

planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 9bc3c9b613d106098a78e16534897c88a3738c07

author	rnateam
date	Sat, 24 Dec 2016 18:08:36 -0500
parents	b797e13169a0
children	79b9117aef01

rev	line source
0 b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	1 <tool id="glob_report" name="Report_Results" version="0.1">
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	2 <requirements>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	3 <requirement type="package" version="0.1">graphclust-wrappers</requirement>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	4 <requirement type="package" version='0.5'>perl-array-utils</requirement>
2 b8e32e577597 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 9bc3c9b613d106098a78e16534897c88a3738c07 rnateam parents: 0 diff changeset	5 <requirement type="package" version='0.18.1'>scikit-learn</requirement>
0 b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	6 </requirements>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	7 <stdio>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	8 <exit_code range="1:" />
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	9 </stdio>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	10 <command>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	11 <![CDATA[
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	12
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	13 unzip $FASTA &> /dev/null &&
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	14
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	15 #set $inputFiles = ""
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	16
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	17 #for $cms_res in $cmsearch_results:
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	18 #set $inputFiles += str($cms_res)+','
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	19 #end for
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	20 #set $inputFiles = $inputFiles[:-1]
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	21
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	22 #set $inputFilesTrees = ""
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	23
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	24 #for $mods in $model_tree_files:
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	25 #set $inputFilesTrees += str($mods)+','
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	26 #end for
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	27 #set $inputFilesTrees = $inputFilesTrees[:-1]
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	28
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	29 'glob_res.pl' '$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 rnateam parents: diff changeset	30 #if $iteration_num.iteration_num_selector:
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	31 $iteration_num.CI
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	32
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	33 $final_partition_soft
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	34 $final_partition_used_cmsearch
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	35 #end if
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	36
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	37 &&
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	38 python '$__tool_directory__/evaluation.py'
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	39 ]]>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	40 </command>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	41 <inputs>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	42 <param type="data" name="FASTA" format="zip" />
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	43 <param type="data" name="cmsearch_results" format="tabular" multiple="True"/>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	44 <param type="data" name="model_tree_files" format="txt" multiple="True"/>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	45 <param name="partition_type" type="boolean" checked="True" truevalue="0" falsevalue="1" label="Hard partition"/>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	46 <param name="cut_type" type="boolean" checked="True" truevalue="0" falsevalue="1" label="Use CM score for cutoff" help="otherwise use E-value"/>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	47 <conditional name="iteration_num">
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	48 <param name="iteration_num_selector" type="boolean" checked="no" label="Multiple iterations" help="for single iteration- NO, for multiple-YES"/>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	49 <when value="true">
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	50 <param name="CI" type="integer" value="2" size="5" label="Number of current iteration "/>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	51 <param type="data" name="final_partition_soft" format="txt" />
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	52 <param type="data" name="final_partition_used_cmsearch" format="txt" />
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	53 </when>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	54 <when value="false" ></when>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	55 </conditional>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	56 <param name="merge_cluster_ol" type="float" value="0.66" size="5" label="merge_cluster_ol" help=""/>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	57 <param name="merge_overlap" type="float" value="0.51" size="5" label="merge_overlap" help=""/>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	58 <param name="min_cluster_size" type="integer" value="3" size="5" label="min_cluster_size" help=""/>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	59 <param name="cm_min_bitscore" type="integer" value="20" size="5" label="cm_min_bitscore" help=""/>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	60 <param name="cm_max_eval" type="float" value="0.001" size="5" label="cm_max_eval" help=""/>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	61 <param name="cm_bitscore_sig" type="integer" value="1" size="5" label="cm_bitscore_sig" help=""/>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	62 </inputs>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	63 <outputs>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	64 <data name="final_stats" format="txt" from_work_dir="RESULTS/cluster.final.stats" label="cluster.final.stats" />
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	65 <data name="tableForEval" format="tabular" from_work_dir="RESULTS/fullTab.tabular" label="tableForEval" />
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	66 <data name="final_soft" format="txt" from_work_dir="RESULTS/partitions/final_partition.soft" label="soft_part" />
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	67 <data name="final_used_cmsearch" format="txt" from_work_dir="RESULTS/partitions/final_partition.used_cmsearch" label="final_partition_used_cmsearch" />
2 b8e32e577597 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 9bc3c9b613d106098a78e16534897c88a3738c07 rnateam parents: 0 diff changeset	68 <data name="evaluation" format="txt" from_work_dir="RESULTS/evaluation.txt" label="evaluation_of_clusters" />
0 b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	69 <collection name="clusters" type="list" label="CLUSTERS">
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	70 <discover_datasets pattern="(?P<name>^.*\.all$)" directory="RESULTS" />
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	71 </collection>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	72 <collection name="partitions" type="list" label="Partitions">
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	73 <discover_datasets pattern="(?P<name>^.*$)" directory="RESULTS/partitions" />
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	74 </collection>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	75 </outputs>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	76 <tests>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	77 <test>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	78 <param name="FASTA" value="FASTA.zip" ftype="searchgui_archive"/>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	79 <param name="cmsearch_results" value="1.tabular,2.tabular"/>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	80 <param name="model_tree_files" value="1.1.model.tree.fa,1.2.model.tree.fa"/>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	81 <param name="partition_type" value="0"/>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	82 <param name="cut_type" value="0"/>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	83 <conditional name="iteration_num">
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	84 <param name="iteration_num_selector" value="false"/>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	85 </conditional>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	86 <param name="merge_cluster_ol" value="0.66"/>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	87 <param name="merge_overlap" value="0.51"/>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	88 <param name="min_cluster_size" value="3"/>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	89 <param name="cm_min_bitscore" value="20"/>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	90 <param name="cm_max_eval" value="0.001"/>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	91 <param name="cm_bitscore_sig" value="1"/>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	92 <output name="final_stats" file="RESULTS/cluster.final.stats" />
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	93 <output_collection name="clusters" type="list">
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	94 <element name="1.cluster.all" file="RESULTS/1.cluster.all" compare="contains"/>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	95 <element name="2.cluster.all" file="RESULTS/2.cluster.all" compare="contains"/>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	96 </output_collection>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	97 <output_collection name="partitions">
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	98 <element name="final_overlap.map" file="RESULTS/partitions/final_overlap.map" compare="contains">
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	99 <assert_contents>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	100 <has_text text="1.1 1.1" />
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	101 <has_text text="1.2 1.2" />
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	102 </assert_contents>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	103 </element>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	104 <element name="final_overlap.matrix" file="RESULTS/partitions/final_overlap.matrix" compare="contains">
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	105 <assert_contents>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	106 <has_text text="MODEL CLASS 0 0" />
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	107 <has_text text="1.2" />
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	108 <has_text text="1.1" />
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	109 </assert_contents>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	110 </element>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	111 <element name="final_partition.hard.best" file="RESULTS/partitions/final_partition.hard.best" />
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	112 <element name="final_partition.hard.merged" file="RESULTS/partitions/final_partition.hard.merged" />
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	113 <element name="final_partition.soft" file="RESULTS/partitions/final_partition.soft" />
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	114 <element name="final_partition.used_cmsearch" file="RESULTS/partitions/final_partition.used_cmsearch" compare="contains"/>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	115 </output_collection>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	116 </test>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	117 </tests>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	118 <help>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	119 <![CDATA[
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	120
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	121 What it does
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	122
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	123 Post-processing. Redundant clusters are merged and instances that belong to multiple clusters
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	124 are assigned unambiguously. For every pair of clusters, the relative overlap (i.e. the fraction of
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	125 instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%.
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	126 Cluster members are finally ranked by their CM bitscore.
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	127
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	128 ]]>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	129 </help>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	130 <citations>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	131 <citation type="bibtex">@inproceedings{costa2010fast,
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	132 title={Fast neighborhood subgraph pairwise distance kernel},
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	133 author={Costa, Fabrizio and De Grave, Kurt},
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	134 booktitle={Proceedings of the 26th International Conference on Machine Learning},
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	135 pages={255--262},
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	136 year={2010},
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	137 organization={Omnipress}
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	138 }
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	139 </citation>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	140 </citations>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	141 </tool>

Mercurial > repos > rnateam > graphclust_postprocessing

annotate glob_report.xml @ 2:b8e32e577597 draft