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annotate graphclust.xml @ 0:a81b012ef352 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphclust commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9
author bgruening
date Thu, 22 Dec 2016 08:40:17 -0500
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a81b012ef352 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphclust commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9
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1 <tool id="graphclust" name="graphclust" version="0.1">
a81b012ef352 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphclust commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9
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2 <description>alignment-free structural clustering of local RNA secondary structures</description>
a81b012ef352 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphclust commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9
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3 <requirements>
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4 <requirement type="package">GraphClust</requirement>
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5 <requirement type="package">locarna</requirement>
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6 <requirement type="package">RNAShapes</requirement>
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7 <requirement type="package">cmfinder</requirement>
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8 <requirement type="package">infernal</requirement>
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9 <requirement type="package">rnaz</requirement>
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10 <requirement type="package">vienna_rna</requirement>
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11 </requirements>
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12 <command>
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13 <![CDATA[
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14 MASTER_GraphClust.pl
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15 --fasta $input_fasta
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16 --config $graphclust_config
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17 --root $output.files_path
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18 --threads "\${GALAXY_SLOTS:-12}";
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19
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20 python dir2html.py $output.files_path/RESULTS > $output
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21 ]]>
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22 </command>
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23 <configfiles>
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24 <configfile name="graphclust_config">
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25 GLOBAL_group_size $GLOBAL_group_size
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26 GLOBAL_hit_blacklist_overlap $GLOBAL_hit_blacklist_overlap
a81b012ef352 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphclust commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9
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27 GLOBAL_iterations $GLOBAL_iterations
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28 GLOBAL_num_clusters $GLOBAL_num_clusters
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29 GLOBAL_plfold_minlen $GLOBAL_plfold_minlen
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30
a81b012ef352 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphclust commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9
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31 OPTS_RNAfold --noLP
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32 OPTS_RNAplfold --noLP -c $RNAplfold_c -L $RNAplfold_L -W $RNAplfold_W
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33 OPTS_fasta2shrep_gspan -t "3=0,5=80" -M 5 -c 20 -win 40,150 -shift 30 --cue -u --stack --seq-graph-t --seq-graph-alph
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34 OPTS_locarna_maligs -p $locarna_p --max-diff-am $locarna_max_diff_am --tau $locarna_tau --max-diff $locarna_max_diff --alifold-consensus-dp
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35 OPTS_locarna_model -p $locarna_p --max-diff-am $locarna_max_diff_am --tau $locarna_tau --max-diff $locarna_max_diff --alifold-consensus-dp
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36 OPTS_locarna_p_model -p $locarna_p --max-diff-am $locarna_max_diff_am --tau 100 --max-diff $locarna_max_diff --struct-weight $locarna_struct_weight --plfold-span 150 --plfold-winsize 200 --temperature $locarna_temperature --mea-beta 400 --consistency-transformation
a81b012ef352 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphclust commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9
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37 OPTS_locarna_paligs -p $locarna_p --max-diff-am $locarna_max_diff_am --tau $locarna_tau --max-diff $locarna_max_diff --indel-open $locarna_indel_open --indel $locarna_indel --struct-weight $locarna_struct_weight
a81b012ef352 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphclust commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9
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38 OPTS_nspdk -R $nspdk_R -D $nspdk_R -gt $nspdk_gt
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39 OPTS_nspdk_centers -ensf 5 -oc -usn
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40
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41 center_model_type 5
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42 center_subtree_max 7
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43 center_subtree_min 3
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44 center_tree_aligs 2
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45 center_tree_type 3
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46 cm_bitscore_sig 1
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47 cm_calibrate 0
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48 cm_max_eval 0.001
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49 cm_min_bitscore 15
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50 cm_top_only 0
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51 evaluate 0
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52 evaluate_class0_as_fp 0
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53 evaluate_min_overlap 0.51
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54 input_add_revcompl 0
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55 input_blastclust 1
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56 input_blastclust_id 90
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57 input_blastclust_len 0.90
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58 input_seq_min_length $other_input_seq_min_length
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59 input_win_shift $other_input_win_shift
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60 input_win_size 0
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61 nspdk_fcs 1
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62 nspdk_greylist_num 0
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63 nspdk_knn_center 10
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64 nspdk_nhf 500
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65 nspdk_nhf_max 1000
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66 nspdk_nhf_step 50
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67 results_merge_cluster_ol 0.66
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68 results_merge_overlap 0.51
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69 results_min_cluster_size $other_results_min_cluster_size
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70 results_partition_type soft
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71 results_top_num 10
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72 </configfile>
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73 </configfiles>
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74 <inputs>
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75
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76 <param name="input_fasta" type="data" format="fasta" label="Fasta file containing sequeces you want to cluster" />
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77
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78 <!--
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79 <conditional name="OPTS_GLOBAL">
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80 <param name="OPTS_GLOBAL_selector" type="select" label="Global advanced options">
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81 <option value="basic" selected="True">Hide Advanced Options</option>
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82 <option value="advanced">Show Advanced Options</option>
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83 </param>
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84 <when value="basic">
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85 </when>
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86 <when value="advanced">
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87 -->
a81b012ef352 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphclust commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9
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88 <param name="GLOBAL_group_size" type="integer" value="50" label="GLOBAL_group_size" />
a81b012ef352 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphclust commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9
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89 <param name="GLOBAL_hit_blacklist_overlap" type="float" value="0.2" label="GLOBAL_hit_blacklist_overlap" />
a81b012ef352 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphclust commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9
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90 <param name="GLOBAL_iterations" type="integer" value="5" label="GLOBAL_iterations" />
a81b012ef352 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphclust commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9
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91 <param name="GLOBAL_num_clusters" type="integer" value="3" label="GLOBAL_num_clusters" />
a81b012ef352 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphclust commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9
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92 <param name="GLOBAL_plfold_minlen" type="integer" value="150" label="GLOBAL_plfold_minlen" />
a81b012ef352 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphclust commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9
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93 <!--
a81b012ef352 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphclust commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9
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94 </when>
a81b012ef352 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphclust commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9
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95 </conditional>
a81b012ef352 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphclust commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9
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96 -->
a81b012ef352 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphclust commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9
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97
a81b012ef352 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphclust commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9
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98 ## OPTS_RNAfold --noLP
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99 <!--
a81b012ef352 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphclust commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9
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100 <conditional name="OPTS_RNAplfold">
a81b012ef352 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphclust commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9
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101 <param name="OPTS_RNAplfold_selector" type="select" label="RNAplfold advanced options">
a81b012ef352 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphclust commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9
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102 <option value="basic" selected="True">Hide Advanced Options</option>
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103 <option value="advanced">Show Advanced Options</option>
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104 </param>
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105 <when value="basic">
a81b012ef352 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphclust commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9
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106 </when>
a81b012ef352 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphclust commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9
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107 <when value="advanced">
a81b012ef352 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphclust commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9
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108 -->
a81b012ef352 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphclust commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9
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109 <param name="RNAplfold_c" type="float" value="0.0005" label="Report only base pairs with an average probability greater than this value in the dot plot" />
a81b012ef352 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphclust commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9
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110 <param name="RNAplfold_L" type="integer" value="200" label="Set the maximum allowed separation of a base pair to span" />
a81b012ef352 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphclust commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9
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111 <param name="RNAplfold_W" type="integer" value="300" label="Average the pair probabilities over windows of given size" />
a81b012ef352 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphclust commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9
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112 <!--
a81b012ef352 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphclust commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9
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113 </when>
a81b012ef352 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphclust commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9
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114 </conditional>
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115 -->
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116 ##OPTS_RNAplfold --noLP
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117
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118 ##OPTS_fasta2shrep_gspan -t "3=0,5=80" -M 5 -c 20 -win 40,150 -shift 30 --cue -u --stack --seq-graph-t --seq-graph-alph
a81b012ef352 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphclust commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9
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119
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120 <!--
a81b012ef352 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphclust commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9
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121 <conditional name="OPTS_locarna">
a81b012ef352 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphclust commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9
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122 <param name="OPTS_locarna_selector" type="select" label="LocaRNA advanced options">
a81b012ef352 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphclust commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9
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123 <option value="basic" selected="True">Hide Advanced Options</option>
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124 <option value="advanced">Show Advanced Options</option>
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125 </param>
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126 <when value="basic">
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127 </when>
a81b012ef352 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphclust commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9
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128 <when value="advanced">
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129 -->
a81b012ef352 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphclust commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9
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130 <param name="locarna_p" type="float" value="0.001" label="Minimal probability" />
a81b012ef352 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphclust commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9
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131 <param name="locarna_max_diff_am" type="integer" value="50" label="Maximal difference for sizes of matched arcs" />
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132 <param name="locarna_tau" type="integer" value="50" label="Tau factor in percent" />
a81b012ef352 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphclust commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9
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133 <param name="locarna_max_diff" type="integer" value="100" label="Maximal difference for alignment traces" />
a81b012ef352 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphclust commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9
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134 <param name="locarna_struct_weight" type="integer" value="180" label="Maximal weight of 1/2 arc match" />
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135 <param name="locarna_temperature" type="integer" value="180" label="Temperature for PF-computation" />
a81b012ef352 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphclust commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9
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136 <param name="locarna_indel_open" type="integer" value="-400" label="Indel opening score" />
a81b012ef352 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphclust commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9
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137 <param name="locarna_indel" type="integer" value="-200" label="Indel score" />
a81b012ef352 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphclust commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9
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138 <!--
a81b012ef352 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphclust commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9
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139 </when>
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140 </conditional>
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141 -->
a81b012ef352 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphclust commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9
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142 ##OPTS_locarna_maligs -p 0.001 --max-diff-am 50 --tau 50 --max-diff 100 --alifold-consensus-dp
a81b012ef352 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphclust commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9
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143 ##OPTS_locarna_model -p 0.001 --max-diff-am 50 --tau 50 --max-diff 100 --alifold-consensus-dp
a81b012ef352 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphclust commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9
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144 ##OPTS_locarna_p_model -p 0.001 --max-diff-am 50 --tau 100 --max-diff 100 --struct-weight 180 --plfold-span 150 --plfold-winsize 200 --temperature 180 --mea-beta 400 --consistency-transformation
a81b012ef352 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphclust commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9
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145 ##OPTS_locarna_paligs -p 0.001 --max-diff-am 50 --tau 50 --max-diff 100 --indel-open -400 --indel -200 --struct-weight 180
a81b012ef352 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphclust commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9
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146
a81b012ef352 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphclust commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9
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147 <!--
a81b012ef352 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphclust commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9
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148 <conditional name="OPTS_nspdk">
a81b012ef352 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphclust commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9
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149 <param name="OPTS_nspdk_selector" type="select" label="NSPDK advanced options">
a81b012ef352 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphclust commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9
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150 <option value="basic" selected="True">Hide Advanced Options</option>
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151 <option value="advanced">Show Advanced Options</option>
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152 </param>
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153 <when value="basic">
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154 </when>
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155 <when value="advanced">
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156 -->
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157 <param name="nspdk_R" type="integer" value="3" label="Radius" />
a81b012ef352 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphclust commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9
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158 <param name="nspdk_D" type="integer" value="3" label="Distance" />
a81b012ef352 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphclust commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9
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159 <param name="nspdk_gt" type="select" label="graph type" >
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160 <option value="DIRECTED" selected="True">DIRECTED</option>
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161 <option value="UNDIRECTED">UNDIRECTED</option>
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162 </param>
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163 <param name="nspdk_ensf" type="integer" value="5" label="eccess neighbour size factor" />
a81b012ef352 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphclust commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9
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164 <param name="nspdk_knn_center" type="integer" value="10" label="number of nearest neighbors" />
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165 <param name="nspdk_ensf" type="integer" value="5" label="eccess neighbour size factor" />
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166 <param name="nspdk_ensf" type="integer" value="5" label="eccess neighbour size factor" />
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167 <param name="nspdk_ensf" type="integer" value="5" label="eccess neighbour size factor" />
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168 <!--
a81b012ef352 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphclust commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9
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169 </when>
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170 </conditional>
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171 -->
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172 #OPTS_nspdk -R 3 -D 3 -gt DIRECTED
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173 #OPTS_nspdk_centers -ensf 5 -oc -usn
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174
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175 <!--
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176 <conditional name="OPTS_other">
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177 <param name="OPTS_other_selector" type="select" label="Other advanced options">
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178 <option value="basic" selected="True">Hide Advanced Options</option>
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179 <option value="advanced">Show Advanced Options</option>
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180 </param>
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181 <when value="basic">
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182 </when>
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183 <when value="advanced">
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184 -->
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185 <param name="other_input_seq_min_length" type="integer" value="50" label="input_seq_min_length" />
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186 <param name="other_input_win_shift" type="integer" value="33" label="input_win_shift" />
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187 <param name="other_results_min_cluster_size" type="integer" value="5" label="results_min_cluster_size" />
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188 <!--
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189 </when>
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190 </conditional>
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191 -->
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192 ##center_model_type 5
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193 ##center_subtree_max 7
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194 ##center_subtree_min 3
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195 ##center_tree_aligs 2
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196 ##center_tree_type 3
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197 ##cm_bitscore_sig 1
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198 ##cm_calibrate 0
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199 ##cm_max_eval 0.001
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200 ##cm_min_bitscore 15
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201 ##cm_top_only 0
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202 ##evaluate 0
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203 ##evaluate_class0_as_fp 0
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204 ##evaluate_min_overlap 0.51
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205 ##input_add_revcompl 0
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206 ##input_blastclust 1
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207 ##input_blastclust_id 90
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208 ##input_blastclust_len 0.90
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209 ##input_seq_min_length 50
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210 ##input_win_shift 33
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211 ##input_win_size 0
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212 ##nspdk_fcs 1
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213 ##nspdk_greylist_num 0
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214 ##nspdk_knn_center 10
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215 ##nspdk_nhf 500
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216 ##nspdk_nhf_max 1000
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217 ##nspdk_nhf_step 50
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218 ##results_merge_cluster_ol 0.66
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219 ##results_merge_overlap 0.51
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220 ##results_min_cluster_size 5
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221 ##results_partition_type soft
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222 ##results_top_num 10
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223
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224 </inputs>
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225 <outputs>
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226 <data name="output" format="html" label="GraphClust on ${on_string}"/>
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227 </outputs>
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228 <help>
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229 <![CDATA[
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230
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231 .. class:: infomark
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232
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233 **What it does**
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234
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235 GraphClust
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236
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237 TODO
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238
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239 ]]>
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240 </help>
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241 <citations>
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242 <citation type="doi">10.1093/bioinformatics/bts224</citation>
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243 </citations>
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244 </tool>