graphclust_postprocessing: glob

annotate glob_report.xml @ 4:4a9754d476fe draft

planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 287021573c592fdb70fdbbc88943aa16a8740fc0

author	rnateam
date	Fri, 13 Jan 2017 16:59:29 -0500
parents	79b9117aef01
children	4310ac018d05

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>
4 4a9754d476fe planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 287021573c592fdb70fdbbc88943aa16a8740fc0 rnateam parents: 3 diff changeset	6 <requirement type="package" version='1.8.10'>locarna</requirement>
4a9754d476fe planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 287021573c592fdb70fdbbc88943aa16a8740fc0 rnateam parents: 3 diff changeset	7 <requirement type="package" version='2.1'>rnaz</requirement>
4a9754d476fe planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 287021573c592fdb70fdbbc88943aa16a8740fc0 rnateam parents: 3 diff changeset	8 <requirement type="package" version="1.1">infernal</requirement>
4a9754d476fe planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 287021573c592fdb70fdbbc88943aa16a8740fc0 rnateam parents: 3 diff changeset	9 <requirement type="package" version='2.2.10'>viennarna</requirement>
4a9754d476fe planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 287021573c592fdb70fdbbc88943aa16a8740fc0 rnateam parents: 3 diff changeset	10 <requirement type="package" version='1.3.23'>graphicsmagick</requirement>
0 b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	11 </requirements>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	12 <stdio>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	13 <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	14 </stdio>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	15 <command>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	16 <![CDATA[
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	17 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	18
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	19 #set $inputFiles = ""
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	20
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	21 #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	22 #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	23 #end for
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	24 #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	25
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	26 #set $inputFilesTrees = ""
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	27
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	28 #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	29 #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	30 #end for
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	31 #set $inputFilesTrees = $inputFilesTrees[:-1]
4 4a9754d476fe planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 287021573c592fdb70fdbbc88943aa16a8740fc0 rnateam parents: 3 diff changeset	32 glob_res.pl
3 79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c rnateam parents: 2 diff changeset	33 '$inputFiles'
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c rnateam parents: 2 diff changeset	34 $merge_cluster_ol
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c rnateam parents: 2 diff changeset	35 $merge_overlap
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c rnateam parents: 2 diff changeset	36 $min_cluster_size
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c rnateam parents: 2 diff changeset	37 $cm_min_bitscore
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c rnateam parents: 2 diff changeset	38 $cm_max_eval
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c rnateam parents: 2 diff changeset	39 $cm_bitscore_sig
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c rnateam parents: 2 diff changeset	40 $partition_type ''
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c rnateam parents: 2 diff changeset	41 $cut_type
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c rnateam parents: 2 diff changeset	42 '$inputFilesTrees'
4 4a9754d476fe planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 287021573c592fdb70fdbbc88943aa16a8740fc0 rnateam parents: 3 diff changeset	43 $results_top_num
0 b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	44 #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	45 $iteration_num.CI
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	46 $final_partition_soft
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	47 $final_partition_used_cmsearch
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	48 #end if
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	49
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	50 &&
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	51 python '$__tool_directory__/evaluation.py'
3 79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c rnateam parents: 2 diff changeset	52 #if $cdhit:
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c rnateam parents: 2 diff changeset	53 &&
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c rnateam parents: 2 diff changeset	54 python '$__tool_directory__/addCdhitseqs.py' '$cdhit'
4 4a9754d476fe planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 287021573c592fdb70fdbbc88943aa16a8740fc0 rnateam parents: 3 diff changeset	55 #end if
0 b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	56 ]]>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	57 </command>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	58 <inputs>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	59 <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	60 <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	61 <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	62 <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	63 <param name="cut_type" type="boolean" checked="True" truevalue="0" falsevalue="1" label="Use CM score for cutoff" help="otherwise use E-value"/>
3 79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c rnateam parents: 2 diff changeset	64 <param type="data" name="cdhit" format="txt" optional="true"/>
0 b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	65 <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	66 <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	67 <when value="true">
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	68 <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	69 <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	70 <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	71 </when>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	72 <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	73 </conditional>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	74 <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	75 <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	76 <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	77 <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	78 <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	79 <param name="cm_bitscore_sig" type="integer" value="1" size="5" label="cm_bitscore_sig" help=""/>
4 4a9754d476fe planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 287021573c592fdb70fdbbc88943aa16a8740fc0 rnateam parents: 3 diff changeset	80 <param name="results_top_num" type="integer" value="5" size="5" label="results_top_num" help=""/>
0 b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	81 </inputs>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	82 <outputs>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	83 <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	84 <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	85 <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	86 <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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b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	90 </collection>
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b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	93 </collection>
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4a9754d476fe planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 287021573c592fdb70fdbbc88943aa16a8740fc0 rnateam parents: 3 diff changeset	96 </collection>
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0 b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	100 </outputs>
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b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	105 <param name="model_tree_files" value="1.1.model.tree.fa,1.2.model.tree.fa"/>
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b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	110 </conditional>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	111 <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	112 <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	113 <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	114 <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	115 <param name="cm_max_eval" value="0.001"/>
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b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	117 <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	118 <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	119 <element name="1.cluster.all" file="RESULTS/1.cluster.all" compare="contains"/>
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b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	123 <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	124 <assert_contents>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	125 <has_text text="1.1 1.1" />
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b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	127 </assert_contents>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	128 </element>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	129 <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	130 <assert_contents>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	131 <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	132 <has_text text="1.2" />
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b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	134 </assert_contents>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	135 </element>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	136 <element name="final_partition.hard.best" file="RESULTS/partitions/final_partition.hard.best" />
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b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	138 <element name="final_partition.soft" file="RESULTS/partitions/final_partition.soft" />
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4a9754d476fe planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 287021573c592fdb70fdbbc88943aa16a8740fc0 rnateam parents: 3 diff changeset	146 <output_collection name="topDot" type="list">
4a9754d476fe planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 287021573c592fdb70fdbbc88943aa16a8740fc0 rnateam parents: 3 diff changeset	147 <element name="1.cluster.top5.aln.png" file="1.cluster.top5.aln.png" ftype="png" compare="sim_size"/>
4a9754d476fe planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 287021573c592fdb70fdbbc88943aa16a8740fc0 rnateam parents: 3 diff changeset	148 <element name="2.cluster.top5.aln.png" file="2.cluster.top5.aln.png" ftype="png" compare="sim_size"/>
4a9754d476fe planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 287021573c592fdb70fdbbc88943aa16a8740fc0 rnateam parents: 3 diff changeset	149 </output_collection>
0 b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	150 </test>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	151 </tests>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	152 <help>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	153 <![CDATA[
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	154
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	155 What it does
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	156
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	157 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	158 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	159 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	160 Cluster members are finally ranked by their CM bitscore.
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b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	163 </help>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	164 <citations>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	165 <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	166 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	167 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	168 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	169 pages={255--262},
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	170 year={2010},
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	171 organization={Omnipress}
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	172 }
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	173 </citation>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	174 </citations>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	175 </tool>

Mercurial > repos > rnateam > graphclust_postprocessing

annotate glob_report.xml @ 4:4a9754d476fe draft