Mercurial > repos > rnateam > graphclust_postprocessing

annotate glob_report.xml.orig @ 17:f93c868203cc draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults commit 4406735e44aba20859c252be39f4e99df28c7a92
author rnateam
date Sat, 27 Oct 2018 13:23:06 -0400
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17
f93c868203cc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults commit 4406735e44aba20859c252be39f4e99df28c7a92
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1 <<<<<<< HEAD
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2 <tool id="glob_report" name="cluster_collection_report" version="0.4" >
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3 =======
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4 <tool id="glob_report" name="cluster_collection_report" version="0.3" >
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5 >>>>>>> edc317491e1fdf1233bd9b45376dc05abf6eabd5
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6 <requirements>
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7 <requirement type="package" version="0.5.2">graphclust-wrappers</requirement>
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8 <requirement type="package" version='0.5'>perl-array-utils</requirement>
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9 <requirement type="package" version='0.18.1'>scikit-learn</requirement>
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10 <requirement type="package" version='1.8.10'>locarna</requirement>
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11 <requirement type="package" version='2.1'>rnaz</requirement>
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12 <requirement type="package" version="1.1.2">infernal</requirement>
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13 <requirement type="package" version='2.2.10'>viennarna</requirement>
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14 <requirement type="package" version='1.3.26'>graphicsmagick</requirement>
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15 <requirement type="package" version='0.6.1'>rscape</requirement>
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16 <requirement type="package" version='6.0'>unzip</requirement>
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17
f93c868203cc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults commit 4406735e44aba20859c252be39f4e99df28c7a92
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18 </requirements>
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19 <stdio>
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20 <exit_code range="1:" />
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21 </stdio>
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22 <command>
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23 <![CDATA[
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24 unzip $FASTA &> /dev/null &&
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25
f93c868203cc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults commit 4406735e44aba20859c252be39f4e99df28c7a92
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26 mkdir ./CMSEARCH &&
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27 mkdir ./MODEL &&
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28
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29 #set $inputFiles = ""
f93c868203cc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults commit 4406735e44aba20859c252be39f4e99df28c7a92
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30
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31 #for $cms_res in $cmsearch_results:
f93c868203cc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults commit 4406735e44aba20859c252be39f4e99df28c7a92
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32 ###set $inputFiles += str($cms_res.element_identifier)+','
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33 ln -f -s '$cms_res' ./CMSEARCH/$cms_res.element_identifier &&
f93c868203cc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults commit 4406735e44aba20859c252be39f4e99df28c7a92
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34 #end for
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35 #set $inputFiles = $inputFiles[:-1]
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36
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37 #set $inputFilesTrees = ""
f93c868203cc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults commit 4406735e44aba20859c252be39f4e99df28c7a92
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38
f93c868203cc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults commit 4406735e44aba20859c252be39f4e99df28c7a92
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39 #for $mods in $model_tree_files:
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40 ###set $inputFilesTrees += str($mods.element_identifier)+','
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41 ln -f -s '$mods' ./MODEL/$mods.element_identifier &&
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42 #end for
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43 #set $inputFilesTrees = $inputFilesTrees[:-1]
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44
f93c868203cc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults commit 4406735e44aba20859c252be39f4e99df28c7a92
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45
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46 'glob_res.pl'
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47 ##'$inputFiles'
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48 $merge_cluster_ol
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49 $merge_overlap
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50 $min_cluster_size
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51 $cm_min_bitscore
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52 $cm_max_eval
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53 $cm_bitscore_sig
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54 $partition_type ''
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55 $cut_type
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56 ##'$inputFilesTrees'
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57 $results_top_num
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58 #if $iteration_num.iteration_num_selector:
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59 $iteration_num.CI
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60 $final_partition_soft
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61 $final_partition_used_cmsearch
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62 '$combined_cm'
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63
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64 #end if
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65
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66 #if str($advanced_opts.advanced_opts_selector) == "show":
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67 #if str($advanced_opts.param_type.param_type_selector) == "gclust":
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68 $advanced_opts.param_type.p
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69 $advanced_opts.param_type.max_diff_am
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70 $advanced_opts.param_type.max_diff
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71 $advanced_opts.param_type.tau
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72 $advanced_opts.param_type.struct_weight
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73 $advanced_opts.param_type.indel_opening
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74 $advanced_opts.param_type.indel
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75 $advanced_opts.param_type.alifold_consensus_dp
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76 #end if
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77 #end if
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78
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79 &&
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80 <<<<<<< HEAD
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81 python '$__tool_directory__/evaluation.py' FASTA/ RESULTS/
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82 =======
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83 python '$__tool_directory__/evaluation.py'
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84 >>>>>>> edc317491e1fdf1233bd9b45376dc05abf6eabd5
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85
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86 #if $cdhit:
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87 &&
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88 python '$__tool_directory__/addCdhitseqs.py' '$cdhit'
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89 #end if
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90 ]]>
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91 </command>
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92 <inputs>
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93 <param type="data" name="FASTA" format="zip" />
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94 <param type="data" name="cmsearch_results" format="tabular" multiple="True"/>
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95 <param type="data" name="model_tree_files" format="txt" multiple="True"/>
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96 <param name="partition_type" type="boolean" checked="True" truevalue="0" falsevalue="1" label="Hard partition"/>
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97 <param name="cut_type" type="boolean" checked="True" truevalue="0" falsevalue="1" label="Use CM score for cutoff" help="otherwise use E-value"/>
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98 <param type="data" name="cdhit" format="txt" optional="true"/>
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99 <conditional name="iteration_num">
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100 <param name="iteration_num_selector" type="boolean" checked="no" label="Multiple iterations" help="for single iteration- NO, for multiple-YES"/>
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101 <when value="true">
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102 <param name="CI" type="integer" value="2" size="5" label="Number of current iteration "/>
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103 <param type="data" name="final_partition_soft" format="txt" />
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104 <param type="data" name="final_partition_used_cmsearch" format="txt" />
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105 <param type="data" name="combined_cm" format="txt" />
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106 </when>
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107 <when value="false" ></when>
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108 </conditional>
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109 <param name="merge_cluster_ol" type="float" value="0.66" size="5" label="merge_cluster_ol" help=""/>
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110 <param name="merge_overlap" type="float" value="0.51" size="5" label="merge_overlap" help=""/>
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111 <param name="min_cluster_size" type="integer" value="3" size="5" label="min_cluster_size" help=""/>
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112 <param name="cm_min_bitscore" type="integer" value="20" size="5" label="cm_min_bitscore" help=""/>
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113 <param name="cm_max_eval" type="float" value="0.001" size="5" label="cm_max_eval" help=""/>
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114 <param name="cm_bitscore_sig" type="integer" value="1" size="5" label="cm_bitscore_sig" help=""/>
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115 <param name="results_top_num" type="integer" value="5" size="5" label="results_top_num" help=""/>
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116
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117 <conditional name="advanced_opts">
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118 <param name="advanced_opts_selector" type="select" label="Advanced Options">
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119 <option value="hide" selected="True">Hide</option>
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120 <option value="show">Show</option>
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121 </param>
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122 <when value="hide"></when>
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123 <when value="show">
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124
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125 <conditional name="param_type">
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126 <param name="param_type_selector" type="select" label="Choose the type of parameters">
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127 <option value="locarna">LocARNA defaults</option>
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128 <option value="gclust" selected="True">GrapClust defaults(changeable)</option>
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129 </param>
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130 <when value="gclust">
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131
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132 <param name="p" type="float" value="0.001" size="5" label="minimal probability" help="-p"/>
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133 <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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134 <param argument="tau" type="integer" value="50" min="0" max="200" label="Sequence contribution at structure match in percent"/>
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135 <param name="max_diff" type="integer" value="100" size="5" label="maximal difference for alignment traces" help="--max-diff"/>
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136
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137 <param name="struct_weight" argument="struct-weight"
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138 label="Structure weight" type="integer"
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139 value="180" min="0" max="800" />
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140 <param name="indel_opening" argument="indel-opening"
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141 label="Indel opening score" type="integer"
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142 value="-400" max="0" min="-1500" />
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143 <param argument="indel" label="Indel score" type="integer"
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144 value="-200" min="-1000" max="0" />
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145
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146 <param name="alifold_consensus_dp"
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147 type="boolean" checked="True"
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148 truevalue="--alifold-consensus-dp" falsevalue=" "
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149 label="Compute consensus dot plot by alifold" />
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150
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151 </when>
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152 <when value="locarna">
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153 </when>
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154 </conditional>
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155
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156 </when>
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157 </conditional>
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158
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159 </inputs>
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160 <outputs>
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161 <data name="final_stats" format="txt" from_work_dir="RESULTS/cluster.final.stats" label="cluster.final.stats" />
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162 <data name="tableForEval" format="tabular" from_work_dir="RESULTS/fullTab.tabular" label="tableForEval" />
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163 <data name="final_soft" format="txt" from_work_dir="RESULTS/partitions/final_partition.soft" label="soft_part" />
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164 <data name="final_used_cmsearch" format="txt" from_work_dir="RESULTS/partitions/final_partition.used_cmsearch" label="final_partition_used_cmsearch" />
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165 <data name="evaluation" format="txt" from_work_dir="RESULTS/evaluation.txt" label="evaluation_of_clusters" />
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166 <data name="combined_cm_out" format="txt" from_work_dir="combined_cm_out" label="combined_cmsearch_output" />
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167 <collection name="clusters" type="list" label="CLUSTERS">
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168 <discover_datasets pattern="(?P&lt;name&gt;^.*\.all$)" directory="RESULTS" />
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169 </collection>
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170 <collection name="partitions" type="list" label="Partitions">
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171 <discover_datasets pattern="(?P&lt;name&gt;^.*$)" directory="RESULTS/partitions" />
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172 </collection>
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173 <collection name="topSecondaryStruct" type="list" label="Top $results_top_num alirna.ps">
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174 <discover_datasets format="png" pattern="(?P&lt;name&gt;^.*\.alirna.png$)" />
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175 </collection>
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176 <collection name="topDot" type="list" label="Top $results_top_num aln.ps">
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177 <discover_datasets format="png" pattern="(?P&lt;name&gt;^.*\.aln.png$)" />
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178 </collection>
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179 <collection name="rscapePlot" type="list" label="R-scape Plot">
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180 <discover_datasets format="pdf" pattern="(?P&lt;name&gt;^.*\.pdf$)" />
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181 </collection>
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182 <data name="RESULTS_zip" format="zip" from_work_dir="RESULTS.zip" label="RESULTS.zip" />
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183 </outputs>
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184 <tests>
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185 <test>
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186 <param name="FASTA" value="FASTA.zip" ftype="searchgui_archive"/>
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187 <param name="cmsearch_results" value="1.1.tree,1.2.tree"/>
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188 <param name="model_tree_files" value="1.1.model.tree.fa,1.2.model.tree.fa"/>
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189 <param name="combined_cm_out" value="combined_cm_out"/>
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190 <param name="partition_type" value="0"/>
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191 <param name="cut_type" value="0"/>
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192 <conditional name="iteration_num">
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193 <param name="iteration_num_selector" value="false"/>
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194 </conditional>
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195 <param name="merge_cluster_ol" value="0.66"/>
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196 <param name="merge_overlap" value="0.51"/>
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197 <param name="min_cluster_size" value="3"/>
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198 <param name="cm_min_bitscore" value="20"/>
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199 <param name="cm_max_eval" value="0.001"/>
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200 <param name="cm_bitscore_sig" value="0"/>
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201 <output name="final_stats" file="RESULTS/cluster.final.stats" />
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202 <output_collection name="clusters" type="list">
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203 <element name="1.cluster.all" file="RESULTS/1.cluster.all" compare="contains"/>
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204 <element name="2.cluster.all" file="RESULTS/2.cluster.all" compare="contains"/>
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205
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206 </output_collection>
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207 <output_collection name="partitions">
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208 <element name="final_overlap.map" file="RESULTS/partitions/final_overlap.map" compare="contains">
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209 <assert_contents>
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210 <has_text text="1.1 1.1 " />
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211 <has_text text="1.2 1.2" />
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212 </assert_contents>
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213 </element>
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214 <element name="final_overlap.matrix" file="RESULTS/partitions/final_overlap.matrix" compare="contains">
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215 <assert_contents>
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216 <has_text text="MODEL CLASS 0 0" />
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217 <!--has_text text="1.2" />
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218 <has_text text="1.1" /-->
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219 </assert_contents>
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220 </element>
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221 <element name="final_partition.hard.best" file="RESULTS/partitions/final_partition.hard.best" />
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222 <element name="final_partition.hard.merged" file="RESULTS/partitions/final_partition.hard.merged" />
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223 <element name="final_partition.soft" file="RESULTS/partitions/final_partition.soft" />
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224 <element name="final_partition.used_cmsearch" file="RESULTS/partitions/final_partition.used_cmsearch" compare="contains"/>
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225 </output_collection>
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226 <param name="results_top_num" value="5"/>
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227 <output_collection name="topSecondaryStruct" type="list">
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228 <element name="1.cluster.top5.alirna.png" file="1.cluster.top5.alirna.png" ftype="png" compare="sim_size" />
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229 <element name="2.cluster.top5.alirna.png" file="2.cluster.top5.alirna.png" ftype="png" compare="sim_size" />
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230 </output_collection>
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231 <output_collection name="topDot" type="list">
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232 <element name="1.cluster.top5.aln.png" file="1.cluster.top5.aln.png" ftype="png" compare="sim_size" />
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233 <element name="2.cluster.top5.aln.png" file="2.cluster.top5.aln.png" ftype="png" compare="sim_size" />
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234 </output_collection>
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235
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236 <output_collection name="rscapePlot" type="list">
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237 <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" />
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238 <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" />
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239 </output_collection>
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240
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241 <output name="RESULTS_zip" file="RESULTS.zip" ftype="zip" compare="sim_size" delta="20000"/>
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242
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243 </test>
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244 </tests>
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245 <help>
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246 <![CDATA[
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247
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248 **What it does**
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249
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250 Post-processing. Redundant clusters are merged and instances that belong to multiple clusters
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251 are assigned unambiguously. For every pair of clusters, the relative overlap (i.e. the fraction of
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252 instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%.
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253 Cluster members are finally ranked by their CM bitscore.
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254
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255 ]]>
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256 </help>
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257 <citations>
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258 <citation type="bibtex">@inproceedings{costa2010fast,
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259 title={Fast neighborhood subgraph pairwise distance kernel},
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260 author={Costa, Fabrizio and De Grave, Kurt},
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261 booktitle={Proceedings of the 26th International Conference on Machine Learning},
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262 pages={255--262},
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263 year={2010},
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264 organization={Omnipress}
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265 }
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266 </citation>
f93c868203cc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults commit 4406735e44aba20859c252be39f4e99df28c7a92
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267 </citations>
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268 </tool>