Mercurial > repos > rnateam > graphclust_align_cluster

annotate align_cluster.xml @ 0:c05c83b3ef0f draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 4406735e44aba20859c252be39f4e99df28c7a92
author rnateam
date Sat, 27 Oct 2018 13:21:39 -0400
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c05c83b3ef0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 4406735e44aba20859c252be39f4e99df28c7a92
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1 <tool id="graphclust_align_cluster" name="Align GraphClust cluster " version="0.1" >
c05c83b3ef0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 4406735e44aba20859c252be39f4e99df28c7a92
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2 <description>structural alignment and conservation analysis of predicted clusters</description>
c05c83b3ef0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 4406735e44aba20859c252be39f4e99df28c7a92
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3 <requirements>
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4 <requirement type="package" version="0.6.0">graphclust-wrappers</requirement>
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5 <requirement type="package" version='0.5'>perl-array-utils</requirement>
c05c83b3ef0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 4406735e44aba20859c252be39f4e99df28c7a92
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6 <requirement type="package" version='0.18.1'>scikit-learn</requirement>
c05c83b3ef0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 4406735e44aba20859c252be39f4e99df28c7a92
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7 <requirement type="package" version='1.8.10'>locarna</requirement>
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8 <requirement type="package" version='2.1'>rnaz</requirement>
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9 <requirement type="package" version="1.1.2">infernal</requirement>
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10 <requirement type="package" version='2.2.10'>viennarna</requirement>
c05c83b3ef0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 4406735e44aba20859c252be39f4e99df28c7a92
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11 <requirement type="package" version='1.3.30'>graphicsmagick</requirement>
c05c83b3ef0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 4406735e44aba20859c252be39f4e99df28c7a92
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12 <requirement type="package" version='0.6.1'>rscape</requirement>
c05c83b3ef0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 4406735e44aba20859c252be39f4e99df28c7a92
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13 <requirement type="package" version='6.0'>unzip</requirement>
c05c83b3ef0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 4406735e44aba20859c252be39f4e99df28c7a92
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14 <requirement type="package" version='0.1'>evofold2</requirement>
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15 <requirement type="package" version='1.70'>biopython</requirement>
c05c83b3ef0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 4406735e44aba20859c252be39f4e99df28c7a92
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16 <requirement type="package" version='0.23.0'>pandas</requirement>
c05c83b3ef0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 4406735e44aba20859c252be39f4e99df28c7a92
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17 </requirements>
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18 <command detect_errors="aggressive">
c05c83b3ef0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 4406735e44aba20859c252be39f4e99df28c7a92
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19 <![CDATA[
c05c83b3ef0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 4406735e44aba20859c252be39f4e99df28c7a92
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20 #set $alignment_clustal = 'cluster.aln'
c05c83b3ef0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 4406735e44aba20859c252be39f4e99df28c7a92
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21 mkdir ./RESULTS/ &&
c05c83b3ef0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 4406735e44aba20859c252be39f4e99df28c7a92
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22 'gc_align_clusters.pl'
c05c83b3ef0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 4406735e44aba20859c252be39f4e99df28c7a92
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23 '$cluster_all_fa'
c05c83b3ef0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 4406735e44aba20859c252be39f4e99df28c7a92
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24 ./RESULTS/ C1
c05c83b3ef0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 4406735e44aba20859c252be39f4e99df28c7a92
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25 $results_top_num
c05c83b3ef0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 4406735e44aba20859c252be39f4e99df28c7a92
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26
c05c83b3ef0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 4406735e44aba20859c252be39f4e99df28c7a92
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27 "
c05c83b3ef0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 4406735e44aba20859c252be39f4e99df28c7a92
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28 #if str($advanced_opts.advanced_opts_selector) == "show":
c05c83b3ef0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 4406735e44aba20859c252be39f4e99df28c7a92
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29 #if str($advanced_opts.param_type.param_type_selector) == "gclust":
c05c83b3ef0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 4406735e44aba20859c252be39f4e99df28c7a92
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30 $advanced_opts.param_type.p
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31 $advanced_opts.param_type.max_diff_am
c05c83b3ef0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 4406735e44aba20859c252be39f4e99df28c7a92
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32 $advanced_opts.param_type.max_diff
c05c83b3ef0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 4406735e44aba20859c252be39f4e99df28c7a92
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33 $advanced_opts.param_type.tau
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34 $advanced_opts.param_type.struct_weight
c05c83b3ef0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 4406735e44aba20859c252be39f4e99df28c7a92
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35 $advanced_opts.param_type.indel_opening
c05c83b3ef0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 4406735e44aba20859c252be39f4e99df28c7a92
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36 $advanced_opts.param_type.indel
c05c83b3ef0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 4406735e44aba20859c252be39f4e99df28c7a92
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37 $advanced_opts.param_type.alifold_consensus_dp
c05c83b3ef0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 4406735e44aba20859c252be39f4e99df28c7a92
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38 #end if
c05c83b3ef0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 4406735e44aba20859c252be39f4e99df28c7a92
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39 #end if
c05c83b3ef0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 4406735e44aba20859c252be39f4e99df28c7a92
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40 "
c05c83b3ef0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 4406735e44aba20859c252be39f4e99df28c7a92
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41 &&
c05c83b3ef0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 4406735e44aba20859c252be39f4e99df28c7a92
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42 R-scape --outdir ./RESULTS/ result.aln.sth &&
c05c83b3ef0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 4406735e44aba20859c252be39f4e99df28c7a92
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43 RNAz --locarnate '$alignment_clustal' > alignment.rnaz.out &&
c05c83b3ef0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 4406735e44aba20859c252be39f4e99df28c7a92
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44 #if str($genomic_cons_opts.genomic_cons_opts_selector) != "no":
c05c83b3ef0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 4406735e44aba20859c252be39f4e99df28c7a92
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45 clustal_to_alma.py '$alignment_clustal' $cluster_all &&
c05c83b3ef0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 4406735e44aba20859c252be39f4e99df28c7a92
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46 EvoFoldV2.sh -o alignment.evofold.out '${alignment_clustal}.ama'
c05c83b3ef0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 4406735e44aba20859c252be39f4e99df28c7a92
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47 #if str($genomic_cons_opts.genomic_cons_opts_selector) == "hg38_100way":
c05c83b3ef0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 4406735e44aba20859c252be39f4e99df28c7a92
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48 '$__tool_directory__/hg38.100way.nh'
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49 #elif str($genomic_cons_opts.genomic_cons_opts_selector) == "hg38_20way":
c05c83b3ef0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 4406735e44aba20859c252be39f4e99df28c7a92
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50 '$__tool_directory__/hg38.20way.nh'
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51 #else
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52 '$alignment_clustal'.ama '$genomic_cons_opts.phylo_tree'
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53 #end if
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54 &&
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55 #else
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56 touch alignment.evofold.out &&
c05c83b3ef0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 4406735e44aba20859c252be39f4e99df28c7a92
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57 #end if
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58
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59 extract_conservation_metrics.py
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60 '$alignment_clustal' alignment.rnaz.out RESULTS/result.aln.sum alignment.evofold.out
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61 '$cluster_all'
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62 #if str($bed_opts.bed_opts_selector) == "yes":
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63 '$bed_opts.transcript_loci_fasta'
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64 '$bed_opts.transcript_loci_bed'
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65 '$bed_opts.genome_version'
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66 #else
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67 '' '' ''
c05c83b3ef0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 4406735e44aba20859c252be39f4e99df28c7a92
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68 #end if
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69 conservation_metrics.tsv
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70
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71 ]]>
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72 </command>
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73 <inputs>
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74 <param type="data" name="cluster_all_fa" label="cluster-sequences-sorted" format="fasta"
c05c83b3ef0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 4406735e44aba20859c252be39f4e99df28c7a92
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75 help="Cluster sequences from the collect-result step"/>
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76 <param type="data" name="cluster_all" label="cmsearch-results" format="txt"
c05c83b3ef0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 4406735e44aba20859c252be39f4e99df28c7a92
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77 help="Tabular cmsearch results of the cluster-collection step (CLUSTERS-cmsearch)"/>
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78 <param name="results_top_num" type="integer" value="5" size="5" label="results_top_num"
c05c83b3ef0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 4406735e44aba20859c252be39f4e99df28c7a92
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79 help="Top number of cmsearch hit sequences are used for structural alignment and metrics"/>
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80
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81 <conditional name="genomic_cons_opts">
c05c83b3ef0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 4406735e44aba20859c252be39f4e99df28c7a92
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82 <param type="select" name="genomic_cons_opts_selector" label="Phylo tree for evofold"
c05c83b3ef0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 4406735e44aba20859c252be39f4e99df28c7a92
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83 help="For MAF genomic alignments as input data, corresponding phylo tree is required to perform Evofold2 structural conservation predcition. For other genomic alignemnts, please upload the tree file.">
c05c83b3ef0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 4406735e44aba20859c252be39f4e99df28c7a92
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84 <option value="no">No</option>
c05c83b3ef0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 4406735e44aba20859c252be39f4e99df28c7a92
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85 <option value="hg38_100way">hg38-100way</option>
c05c83b3ef0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 4406735e44aba20859c252be39f4e99df28c7a92
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86 <option value="hg38_20way">hg38-20way</option>
c05c83b3ef0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 4406735e44aba20859c252be39f4e99df28c7a92
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87 <option value="user_phylo_tree">from history</option>
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88 </param>
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89 <when value="no" />
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90 <when value="hg38_100way" />
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91 <when value="hg38_20way" />
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92 <when value="user_phylo_tree">
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93 <param format="newick" name="phylo_tree" type="data" label="Newick phylo-tree" />
c05c83b3ef0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 4406735e44aba20859c252be39f4e99df28c7a92
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94 </when>
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95 </conditional>
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96 <conditional name="bed_opts">
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97 <param type="select" name="bed_opts_selector" label="Extract genomic coordinates of the clusters" >
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98 <option value="no">No</option>
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99 <option value="yes">Yes</option>
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100 </param>
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101 <when value="no" />
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102 <when value="yes" >
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103 <param format="fasta" name="transcript_loci_fasta" type="data" label="Loci reference sequence"
c05c83b3ef0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 4406735e44aba20859c252be39f4e99df28c7a92
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104 help="Sequence of reference species (human) for the genomic loci (precursor mRNA/lncRNA) to locate the clusters" />
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105 <param name='transcript_loci_bed' type="text" value="chr1 0 100000 gene 0 +"
c05c83b3ef0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 4406735e44aba20859c252be39f4e99df28c7a92
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106 help="bed entry string of the reference transcript loci for bed/ucsc-track output. 'chrom start end name score strand' white-space separated.">
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107 <validator type="regex" message="one-line bed string must have at least 6 entries as BED6 format (chrom start end name 0 strand)
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108 (space and tab allowed)">^\S+\s+[0-9]+\s+[0-9]+\s+\S+\s+\S+\s+[-+]\s*$</validator>
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109 </param>
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110 <param name='genome_version' value="hg38" type="text" label="reference genome assembly"
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111 help="ucsc reference genome assembly version used in the input MAF alignments (e.g. hg38, hg19, mm10). To identify the reference in clusters">
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112 <validator type="regex" message="ucsc genome assembly version has an alphabet prefix and a number suffix">^[a-zA-Z]+[0-9]+$</validator>
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113 </param>
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114 </when>
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115 </conditional>
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116 <conditional name="advanced_opts">
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117 <param name="advanced_opts_selector" type="select" label="Locarna alignment options">
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118 <option value="hide" selected="True">Hide</option>
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119 <option value="show">Show</option>
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120 </param>
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121 <when value="hide"></when>
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122 <when value="show">
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123 <conditional name="param_type">
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124 <param name="param_type_selector" type="select" label="Choose the type of parameters">
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125 <option value="locarna">LocARNA defaults</option>
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126 <option value="gclust" selected="True">GrapClust defaults(changeable)</option>
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127 </param>
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128 <when value="gclust">
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129 <param name="p" type="float" value="0.001" size="5" label="minimal probability" help="-p"/>
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130 <param name="max_diff_am" type="integer" value="50" size="5" label=" maximal difference for sizes of matched arcs" help="--max-diff-am"/>
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131 <param argument="tau" type="integer" value="50" min="0" max="200" label="Sequence contribution at structure match in percent"/>
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132 <param name="max_diff" type="integer" value="100" size="5" label="maximal difference for alignment traces" help="--max-diff"/>
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133 <param name="struct_weight" argument="struct-weight"
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134 label="Structure weight" type="integer"
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135 value="180" min="0" max="800" />
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136 <param name="indel_opening" argument="indel-opening"
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137 label="Indel opening score" type="integer"
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138 value="-400" max="0" min="-1500" />
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139 <param argument="indel" label="Indel score" type="integer"
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140 value="-200" min="-1000" max="0" />
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141 <param name="alifold_consensus_dp"
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142 type="boolean" checked="True"
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143 truevalue="--alifold-consensus-dp" falsevalue=" "
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144 label="Compute consensus dot plot by alifold" />
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145 </when>
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146 <when value="locarna">
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147 </when>
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148 </conditional>
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149 </when>
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150 </conditional>
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151 </inputs>
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152 <outputs>
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153 <data name="alignment_ps" format="data" from_work_dir="cluster.aln.ps" label="alignment.ps" />
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154 <data name="alignment_png" format="png" from_work_dir="cluster.aln.png" label="alignment.png" />
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155 <data name="structure_ps" format="data" from_work_dir="cluster.alirna.ps" label="structure.ps" />
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156 <data name="structure_png" format="png" from_work_dir="cluster.alirna.png" label="structure.png" />
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157 <data name="alignment_sth" format="stockholm" from_work_dir="result.aln.sth" label="alignment.sth" />
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158 <data name="alignment_clustal_out" format="clustal" from_work_dir="cluster.aln" label="alignment.clustal" />
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159 <data name="Rscape_R2R" format="pdf" from_work_dir="RESULTS/result.aln_1.R2R.sto.pdf" label="Rscape-R2R" />
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160 <data name="rnaz_out" format="txt" from_work_dir="alignment.rnaz.out" label="rnaz.out" />
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161 <data name="rscape_out" format="txt" from_work_dir="alignment.sum" label="Rscape.summary" />
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162 <data name="evofold_out" format="txt" from_work_dir="alignment.evofold.out" label="evofold.out" />
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163 <data name="cons_tsv" format="tabular" from_work_dir="conservation_metrics.tsv" label="conservation_metrics.tsv" />
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164 </outputs>
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165 <tests>
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166 <test>
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167 <param name="cluster_all_fa" value="cluster1.all.fa"/>
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168 <param name="cluster_all" value="cluster1.all"/>
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169 <output name="alignment_ps" file="alignment1.ps" compare="sim_size" />
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170 <output name="alignment_png" file="alignment1.png" compare="sim_size" />
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171 <output name="structure_ps" file="structure1.ps" compare="sim_size" />
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172 <output name="structure_png" file="structure1.png" compare="sim_size" />
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173 <output name="alignment_sth" file="alignment1.sth" compare="sim_size" delta="100" />
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174 <output name="alignment_clustal_out" file="alignment1.clustal" />
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175 <output name="Rscape_R2R" file="alignment1_R2R.sto.pdf" compare="sim_size" />
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176 <output name="rnaz_out" file="alignment1.rnaz.out" compare="sim_size" delta="10"/>
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177 <output name="evofold_out" file="alignment1.evofold.out" />
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178 <output name="cons_tsv" file="alignment1.cons.tsv" compare="sim_size" delta="0"/>
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179 <conditional name="genomic_cons_opts">
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180 <param name="genomic_cons_opts_selector" value="no"/>
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181 </conditional>
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182 <param name="results_top_num" value="5"/>
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183
c05c83b3ef0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 4406735e44aba20859c252be39f4e99df28c7a92
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184 </test>
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185
c05c83b3ef0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 4406735e44aba20859c252be39f4e99df28c7a92
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186 <test>
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187 <param name="cluster_all_fa" value="cluster2.all.fa"/>
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188 <param name="cluster_all" value="cluster2.all"/>
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189 <output name="alignment_png" file="alignment2.png" compare="sim_size" />
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190 <output name="structure_png" file="structure2.png" compare="sim_size" />
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191 <output name="alignment_sth" file="alignment2.sth" compare="sim_size" delta="100" />
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192 <output name="alignment_clustal_out" file="alignment2.clustal" />
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193 <output name="rnaz_out" file="alignment2.rnaz.out" />
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194 <output name="evofold_out" file="alignment2.evofold.out" />
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195 <output name="cons_tsv" file="alignment2.cons.tsv" />
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196 <conditional name="genomic_cons_opts">
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197 <param name="genomic_cons_opts_selector" value="hg38_20way"/>
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198 </conditional>
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199 </test>
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200
c05c83b3ef0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 4406735e44aba20859c252be39f4e99df28c7a92
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201 <test>
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202 <param name="cluster_all_fa" value="cluster2.all.fa"/>
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203 <param name="cluster_all" value="cluster2.all"/>
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204 <output name="cons_tsv" file="alignment2b.cons.tsv" />
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205 <conditional name="genomic_cons_opts">
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206 <param name="genomic_cons_opts_selector" value="hg38_20way"/>
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207 </conditional>
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208 <conditional name="bed_opts">
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209 <param name="bed_opts_selector" value="yes"/>
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210 <param name="transcript_loci_fasta" value="alignment2b-transcript.fa"/>
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211 <param name="transcript_loci_bed" value="chr7 27162434 27166719 Hoxa9-Xtend5UTR 2 -"/>
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212 </conditional>
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213 </test>
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214 </tests>
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215 <help>
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216 <![CDATA[
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217 Align predicted clusters of glob_report_no_align step with locarna and conservation analysis and visualizations.
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218
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219 ]]>
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220 </help>
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221 <citations>
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222 <citation type="doi">10.5281/zenodo.597695</citation>
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223 </citations>
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224 </tool>