graphclust_postprocessing: glob

annotate glob_report.xml @ 11:e080ebe95476 draft

planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 4dd7269185f6fb9bdc007028007d6540f4cf057d

author	rnateam
date	Sat, 25 Mar 2017 16:50:38 -0400
parents	044bb294db78
children	b5f49453af8c

rev	line source
8 9a69a6098b71 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 5a545fc913b3a07e1452e67f66b2ca593660abdf rnateam parents: 7 diff changeset	1 <tool id="glob_report" name="cluster_collection_report" version="0.1">
5 4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	2 <requirements>
11 e080ebe95476 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 4dd7269185f6fb9bdc007028007d6540f4cf057d rnateam parents: 10 diff changeset	3 <requirement type="package" version="0.1.12">graphclust-wrappers</requirement>
5 4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	4 <requirement type="package" version='0.5'>perl-array-utils</requirement>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	5 <requirement type="package" version='0.18.1'>scikit-learn</requirement>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	6 <requirement type="package" version='1.8.10'>locarna</requirement>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	7 <requirement type="package" version='2.1'>rnaz</requirement>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	8 <requirement type="package" version="1.1">infernal</requirement>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	9 <requirement type="package" version='2.2.10'>viennarna</requirement>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	10 <requirement type="package" version='1.3.23'>graphicsmagick</requirement>
7 870dfc90473f planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit b3fe72d71e27a7b66621ecaae3e2da4bc4ca6986 rnateam parents: 6 diff changeset	11 <requirement type="package" version='0.3.1'>rscape</requirement>
870dfc90473f planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit b3fe72d71e27a7b66621ecaae3e2da4bc4ca6986 rnateam parents: 6 diff changeset	12
5 4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	13 </requirements>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	14 <stdio>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	15 <exit_code range="1:" />
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	16 </stdio>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	17 <command>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	18 <![CDATA[
0 b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	19 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	20
11 e080ebe95476 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 4dd7269185f6fb9bdc007028007d6540f4cf057d rnateam parents: 10 diff changeset	21 mkdir ./CMSEARCH &&
e080ebe95476 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 4dd7269185f6fb9bdc007028007d6540f4cf057d rnateam parents: 10 diff changeset	22 mkdir ./MODEL &&
e080ebe95476 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 4dd7269185f6fb9bdc007028007d6540f4cf057d rnateam parents: 10 diff changeset	23
0 b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	24 #set $inputFiles = ""
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 #for $cms_res in $cmsearch_results:
11 e080ebe95476 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 4dd7269185f6fb9bdc007028007d6540f4cf057d rnateam parents: 10 diff changeset	27 ###set $inputFiles += str($cms_res.element_identifier)+','
e080ebe95476 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 4dd7269185f6fb9bdc007028007d6540f4cf057d rnateam parents: 10 diff changeset	28 ln -f -s '$cms_res' ./CMSEARCH/$cms_res.element_identifier &&
0 b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	29 #end for
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	30 #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	31
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	32 #set $inputFilesTrees = ""
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	33
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	34 #for $mods in $model_tree_files:
11 e080ebe95476 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 4dd7269185f6fb9bdc007028007d6540f4cf057d rnateam parents: 10 diff changeset	35 ###set $inputFilesTrees += str($mods.element_identifier)+','
e080ebe95476 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 4dd7269185f6fb9bdc007028007d6540f4cf057d rnateam parents: 10 diff changeset	36 ln -f -s '$mods' ./MODEL/$mods.element_identifier &&
0 b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	37 #end for
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	38 #set $inputFilesTrees = $inputFilesTrees[:-1]
7 870dfc90473f planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit b3fe72d71e27a7b66621ecaae3e2da4bc4ca6986 rnateam parents: 6 diff changeset	39 'glob_res.pl'
11 e080ebe95476 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 4dd7269185f6fb9bdc007028007d6540f4cf057d rnateam parents: 10 diff changeset	40 ##'$inputFiles'
3 79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c rnateam parents: 2 diff changeset	41 $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	42 $merge_overlap
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c rnateam parents: 2 diff changeset	43 $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	44 $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	45 $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	46 $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	47 $partition_type ''
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c rnateam parents: 2 diff changeset	48 $cut_type
11 e080ebe95476 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 4dd7269185f6fb9bdc007028007d6540f4cf057d rnateam parents: 10 diff changeset	49 ##'$inputFilesTrees'
4 4a9754d476fe planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 287021573c592fdb70fdbbc88943aa16a8740fc0 rnateam parents: 3 diff changeset	50 $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	51 #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	52 $iteration_num.CI
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	53 $final_partition_soft
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	54 $final_partition_used_cmsearch
10 044bb294db78 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n' rnateam parents: 9 diff changeset	55 '$combined_cm'
044bb294db78 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n' rnateam parents: 9 diff changeset	56
0 b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	57 #end if
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	58
5 4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	59 #if str($advanced_opts.advanced_opts_selector) == "show":
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	60 #if str($advanced_opts.param_type.param_type_selector) == "gclust":
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	61 $advanced_opts.param_type.p
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	62 $advanced_opts.param_type.max_diff_am
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	63 $advanced_opts.param_type.max_diff
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	64 $advanced_opts.param_type.tau
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	65 $advanced_opts.param_type.struct_weight
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	66 $advanced_opts.param_type.indel_opening
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	67 $advanced_opts.param_type.indel
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	68 $advanced_opts.param_type.alifold_consensus_dp
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	69 #end if
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	70 #end if
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	71
0 b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	72 &&
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	73 python '$__tool_directory__/evaluation.py'
5 4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	74 #if $cdhit:
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	75 &&
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	76 python '$__tool_directory__/addCdhitseqs.py' '$cdhit'
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	77 #end if
0 b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	78 ]]>
5 4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	79 </command>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	80 <inputs>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	81 <param type="data" name="FASTA" format="zip" />
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	82 <param type="data" name="cmsearch_results" format="tabular" multiple="True"/>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	83 <param type="data" name="model_tree_files" format="txt" multiple="True"/>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	84 <param name="partition_type" type="boolean" checked="True" truevalue="0" falsevalue="1" label="Hard partition"/>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	85 <param name="cut_type" type="boolean" checked="True" truevalue="0" falsevalue="1" label="Use CM score for cutoff" help="otherwise use E-value"/>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	86 <param type="data" name="cdhit" format="txt" optional="true"/>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	87 <conditional name="iteration_num">
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	88 <param name="iteration_num_selector" type="boolean" checked="no" label="Multiple iterations" help="for single iteration- NO, for multiple-YES"/>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	89 <when value="true">
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	90 <param name="CI" type="integer" value="2" size="5" label="Number of current iteration "/>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	91 <param type="data" name="final_partition_soft" format="txt" />
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	92 <param type="data" name="final_partition_used_cmsearch" format="txt" />
10 044bb294db78 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n' rnateam parents: 9 diff changeset	93 <param type="data" name="combined_cm" format="txt" />
5 4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	94 </when>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	95 <when value="false" ></when>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	96 </conditional>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	97 <param name="merge_cluster_ol" type="float" value="0.66" size="5" label="merge_cluster_ol" help=""/>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	98 <param name="merge_overlap" type="float" value="0.51" size="5" label="merge_overlap" help=""/>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	99 <param name="min_cluster_size" type="integer" value="3" size="5" label="min_cluster_size" help=""/>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	100 <param name="cm_min_bitscore" type="integer" value="20" size="5" label="cm_min_bitscore" help=""/>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	101 <param name="cm_max_eval" type="float" value="0.001" size="5" label="cm_max_eval" help=""/>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	102 <param name="cm_bitscore_sig" type="integer" value="1" size="5" label="cm_bitscore_sig" help=""/>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	103 <param name="results_top_num" type="integer" value="5" size="5" label="results_top_num" help=""/>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	104
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	105 <conditional name="advanced_opts">
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	106 <param name="advanced_opts_selector" type="select" label="Advanced Options">
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	107 <option value="hide" selected="True">Hide</option>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	108 <option value="show">Show</option>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	109 </param>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	110 <when value="hide"></when>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	111 <when value="show">
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	112
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	113 <conditional name="param_type">
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	114 <param name="param_type_selector" type="select" label="Choose the type of parameters">
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	115 <option value="locarna">LocARNA defaults</option>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	116 <option value="gclust" selected="True">GrapClust defaults(changeable)</option>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	117 </param>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	118 <when value="gclust">
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	119
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	120 <param name="p" type="float" value="0.001" size="5" label="minimal probability" help="-p"/>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	121 <param name="max_diff_am" type="integer" value="50" size="5" label=" maximal difference for sizes of matched arcs" help="--max-diff-am"/>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	122 <param argument="tau" type="integer" value="50" min="0" max="200" label="Sequence contribution at structure match in percent"/>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	123 <param name="max_diff" type="integer" value="100" size="5" label="maximal difference for alignment traces" help="--max-diff"/>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	124
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	125 <param name="struct_weight" argument="struct-weight"
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	126 label="Structure weight" type="integer"
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	127 value="180" min="0" max="800" />
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	128 <param name="indel_opening" argument="indel-opening"
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	129 label="Indel opening score" type="integer"
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	130 value="-400" max="0" min="-1500" />
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	131 <param argument="indel" label="Indel score" type="integer"
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	132 value="-200" min="-1000" max="0" />
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	133
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	134 <param name="alifold_consensus_dp"
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	135 type="boolean" checked="True"
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	136 truevalue="--alifold-consensus-dp" falsevalue=" "
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	137 label="Compute consensus dot plot by alifold" />
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	138
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	139 </when>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	140 <when value="locarna">
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	141 </when>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	142 </conditional>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	143
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	144 </when>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	145 </conditional>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	146
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	147 </inputs>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	148 <outputs>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	149 <data name="final_stats" format="txt" from_work_dir="RESULTS/cluster.final.stats" label="cluster.final.stats" />
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	150 <data name="tableForEval" format="tabular" from_work_dir="RESULTS/fullTab.tabular" label="tableForEval" />
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	151 <data name="final_soft" format="txt" from_work_dir="RESULTS/partitions/final_partition.soft" label="soft_part" />
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	152 <data name="final_used_cmsearch" format="txt" from_work_dir="RESULTS/partitions/final_partition.used_cmsearch" label="final_partition_used_cmsearch" />
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	153 <data name="evaluation" format="txt" from_work_dir="RESULTS/evaluation.txt" label="evaluation_of_clusters" />
11 e080ebe95476 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 4dd7269185f6fb9bdc007028007d6540f4cf057d rnateam parents: 10 diff changeset	154 <data name="combined_cm_out" format="txt" from_work_dir="combined_cm_out" label="combined_cmsearch_output" />
5 4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	155 <collection name="clusters" type="list" label="CLUSTERS">
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	156 <discover_datasets pattern="(?P<name>^.*\.all$)" directory="RESULTS" />
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	157 </collection>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	158 <collection name="partitions" type="list" label="Partitions">
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	159 <discover_datasets pattern="(?P<name>^.*$)" directory="RESULTS/partitions" />
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	160 </collection>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	161 <collection name="topSecondaryStruct" type="list" label="Top $results_top_num alirna.ps">
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	162 <discover_datasets format="png" pattern="(?P<name>^.*\.alirna.png$)" />
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	163 </collection>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	164 <collection name="topDot" type="list" label="Top $results_top_num aln.ps">
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	165 <discover_datasets format="png" pattern="(?P<name>^.*\.aln.png$)" />
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	166 </collection>
7 870dfc90473f planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit b3fe72d71e27a7b66621ecaae3e2da4bc4ca6986 rnateam parents: 6 diff changeset	167 <collection name="rscapePlot" type="list" label="R-scape Plot">
870dfc90473f planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit b3fe72d71e27a7b66621ecaae3e2da4bc4ca6986 rnateam parents: 6 diff changeset	168 <discover_datasets format="pdf" pattern="(?P<name>^.*\.pdf$)" />
870dfc90473f planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit b3fe72d71e27a7b66621ecaae3e2da4bc4ca6986 rnateam parents: 6 diff changeset	169 </collection>
5 4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	170 <data name="RESULTS_zip" format="zip" from_work_dir="RESULTS.zip" label="RESULTS.zip" />
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	171 </outputs>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	172 <tests>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	173 <test>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	174 <param name="FASTA" value="FASTA.zip" ftype="searchgui_archive"/>
6 869a6e807d76 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 057c2fd398055dc86eb2c00d8a74f301d5c231d9-dirty rnateam parents: 5 diff changeset	175 <param name="cmsearch_results" value="1.tabular,2.tabular,3.tabular,4.tabular,5.tabular"/>
869a6e807d76 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 057c2fd398055dc86eb2c00d8a74f301d5c231d9-dirty rnateam parents: 5 diff changeset	176 <param name="model_tree_files" value="1.1.model.tree.fa,1.2.model.tree.fa,1.3.model.tree.fa,1.4.model.tree.fa,1.5.model.tree.fa"/>
5 4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	177 <param name="partition_type" value="0"/>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	178 <param name="cut_type" value="0"/>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	179 <conditional name="iteration_num">
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	180 <param name="iteration_num_selector" value="false"/>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	181 </conditional>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	182 <param name="merge_cluster_ol" value="0.66"/>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	183 <param name="merge_overlap" value="0.51"/>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	184 <param name="min_cluster_size" value="3"/>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	185 <param name="cm_min_bitscore" value="20"/>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	186 <param name="cm_max_eval" value="0.001"/>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	187 <param name="cm_bitscore_sig" value="1"/>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	188 <output name="final_stats" file="RESULTS/cluster.final.stats" />
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	189 <output_collection name="clusters" type="list">
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	190 <element name="1.cluster.all" file="RESULTS/1.cluster.all" compare="contains"/>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	191 <element name="2.cluster.all" file="RESULTS/2.cluster.all" compare="contains"/>
6 869a6e807d76 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 057c2fd398055dc86eb2c00d8a74f301d5c231d9-dirty rnateam parents: 5 diff changeset	192 <element name="3.cluster.all" file="RESULTS/3.cluster.all" compare="contains"/>
869a6e807d76 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 057c2fd398055dc86eb2c00d8a74f301d5c231d9-dirty rnateam parents: 5 diff changeset	193 <element name="4.cluster.all" file="RESULTS/4.cluster.all" compare="contains"/>
5 4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	194 </output_collection>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	195 <output_collection name="partitions">
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	196 <element name="final_overlap.map" file="RESULTS/partitions/final_overlap.map" compare="contains">
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	197 <assert_contents>
6 869a6e807d76 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 057c2fd398055dc86eb2c00d8a74f301d5c231d9-dirty rnateam parents: 5 diff changeset	198 <has_text text="1.1 1.1 1.2" />
869a6e807d76 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 057c2fd398055dc86eb2c00d8a74f301d5c231d9-dirty rnateam parents: 5 diff changeset	199 <has_text text="1.3 1.3" />
869a6e807d76 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 057c2fd398055dc86eb2c00d8a74f301d5c231d9-dirty rnateam parents: 5 diff changeset	200 <has_text text="1.4 1.4" />
869a6e807d76 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 057c2fd398055dc86eb2c00d8a74f301d5c231d9-dirty rnateam parents: 5 diff changeset	201 <has_text text="1.5 1.5 " />
5 4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	202 </assert_contents>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	203 </element>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	204 <element name="final_overlap.matrix" file="RESULTS/partitions/final_overlap.matrix" compare="contains">
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	205 <assert_contents>
6 869a6e807d76 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 057c2fd398055dc86eb2c00d8a74f301d5c231d9-dirty rnateam parents: 5 diff changeset	206 <has_text text="MODEL CLASS 0 0 0 0 0" />
869a6e807d76 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 057c2fd398055dc86eb2c00d8a74f301d5c231d9-dirty rnateam parents: 5 diff changeset	207 <!--has_text text="1.2" />
869a6e807d76 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 057c2fd398055dc86eb2c00d8a74f301d5c231d9-dirty rnateam parents: 5 diff changeset	208 <has_text text="1.1" /-->
5 4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	209 </assert_contents>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	210 </element>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	211 <element name="final_partition.hard.best" file="RESULTS/partitions/final_partition.hard.best" />
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	212 <element name="final_partition.hard.merged" file="RESULTS/partitions/final_partition.hard.merged" />
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	213 <element name="final_partition.soft" file="RESULTS/partitions/final_partition.soft" />
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	214 <element name="final_partition.used_cmsearch" file="RESULTS/partitions/final_partition.used_cmsearch" compare="contains"/>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	215 </output_collection>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	216 <param name="results_top_num" value="5"/>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	217 <output_collection name="topSecondaryStruct" type="list">
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	218 <element name="1.cluster.top5.alirna.png" file="1.cluster.top5.alirna.png" ftype="png" compare="sim_size" />
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	219 <element name="2.cluster.top5.alirna.png" file="2.cluster.top5.alirna.png" ftype="png" compare="sim_size" />
6 869a6e807d76 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 057c2fd398055dc86eb2c00d8a74f301d5c231d9-dirty rnateam parents: 5 diff changeset	220 <element name="3.cluster.top5.alirna.png" file="3.cluster.top5.alirna.png" ftype="png" compare="sim_size" />
869a6e807d76 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 057c2fd398055dc86eb2c00d8a74f301d5c231d9-dirty rnateam parents: 5 diff changeset	221 <element name="4.cluster.top5.alirna.png" file="4.cluster.top5.alirna.png" ftype="png" compare="sim_size" />
5 4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	222 </output_collection>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	223 <output_collection name="topDot" type="list">
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	224 <element name="1.cluster.top5.aln.png" file="1.cluster.top5.aln.png" ftype="png" compare="sim_size" />
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	225 <element name="2.cluster.top5.aln.png" file="2.cluster.top5.aln.png" ftype="png" compare="sim_size" />
6 869a6e807d76 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 057c2fd398055dc86eb2c00d8a74f301d5c231d9-dirty rnateam parents: 5 diff changeset	226 <element name="3.cluster.top5.aln.png" file="3.cluster.top5.aln.png" ftype="png" compare="sim_size" />
869a6e807d76 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 057c2fd398055dc86eb2c00d8a74f301d5c231d9-dirty rnateam parents: 5 diff changeset	227 <element name="4.cluster.top5.aln.png" file="4.cluster.top5.aln.png" ftype="png" compare="sim_size" />
5 4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	228 </output_collection>
7 870dfc90473f planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit b3fe72d71e27a7b66621ecaae3e2da4bc4ca6986 rnateam parents: 6 diff changeset	229
870dfc90473f planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit b3fe72d71e27a7b66621ecaae3e2da4bc4ca6986 rnateam parents: 6 diff changeset	230 <output_collection name="rscapePlot" type="list">
870dfc90473f planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit b3fe72d71e27a7b66621ecaae3e2da4bc4ca6986 rnateam parents: 6 diff changeset	231 <element name="1.cluster.top5.result.aln_1.R2R.sto.pdf" file="1.cluster.top5.result.aln_1.R2R.sto.pdf" ftype="pdf" compare="sim_size" />
870dfc90473f planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit b3fe72d71e27a7b66621ecaae3e2da4bc4ca6986 rnateam parents: 6 diff changeset	232 <element name="2.cluster.top5.result.aln_1.R2R.sto.pdf" file="2.cluster.top5.result.aln_1.R2R.sto.pdf" ftype="pdf" compare="sim_size" />
870dfc90473f planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit b3fe72d71e27a7b66621ecaae3e2da4bc4ca6986 rnateam parents: 6 diff changeset	233 <element name="3.cluster.top5.result.aln_1.R2R.sto.pdf" file="3.cluster.top5.result.aln_1.R2R.sto.pdf" ftype="pdf" compare="sim_size" />
870dfc90473f planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit b3fe72d71e27a7b66621ecaae3e2da4bc4ca6986 rnateam parents: 6 diff changeset	234 <element name="4.cluster.top5.result.aln_1.R2R.sto.pdf" file="4.cluster.top5.result.aln_1.R2R.sto.pdf" ftype="pdf" compare="sim_size" />
870dfc90473f planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit b3fe72d71e27a7b66621ecaae3e2da4bc4ca6986 rnateam parents: 6 diff changeset	235 </output_collection>
870dfc90473f planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit b3fe72d71e27a7b66621ecaae3e2da4bc4ca6986 rnateam parents: 6 diff changeset	236
870dfc90473f planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit b3fe72d71e27a7b66621ecaae3e2da4bc4ca6986 rnateam parents: 6 diff changeset	237 <output name="RESULTS_zip" file="RESULTS.zip" ftype="zip" compare="sim_size" delta="20000"/>
5 4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	238
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	239 </test>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	240 </tests>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	241 <help>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	242 <![CDATA[
0 b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	243
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	244 What it does
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	245
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	246 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	247 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	248 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	249 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	250
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	251 ]]>
5 4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	252 </help>
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 rnateam parents: 4 diff changeset	253 <citations>
0 b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	254 <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	255 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	256 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	257 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	258 pages={255--262},
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	259 year={2010},
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	260 organization={Omnipress}
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	261 }
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	262 </citation>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	263 </citations>
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 rnateam parents: diff changeset	264 </tool>

Mercurial > repos > rnateam > graphclust_postprocessing

annotate glob_report.xml @ 11:e080ebe95476 draft