Mercurial > repos > rnateam > graphclust_postprocessing_no_align

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
author rnateam
date Sat, 27 Oct 2018 13:49:00 -0400
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0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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1 <tool id="graphclust_glob_report_no_align" name="Graphclust glob_report collect clusters" version="0.5" >
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2 <requirements>
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3 <requirement type="package" version="0.6.0">graphclust-wrappers</requirement>
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4 <requirement type="package" version='0.5'>perl-array-utils</requirement>
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5 <requirement type="package" version='0.18.1'>scikit-learn</requirement>
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6 <requirement type="package" version='1.8.10'>locarna</requirement>
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7 <requirement type="package" version='2.1'>rnaz</requirement>
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8 <requirement type="package" version="1.1.2">infernal</requirement>
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9 <requirement type="package" version='2.2.10'>viennarna</requirement>
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10 <requirement type="package" version='1.3.30'>graphicsmagick</requirement>
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11 <requirement type="package" version='0.6.1'>rscape</requirement>
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12 <requirement type="package" version='6.0'>unzip</requirement>
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13 </requirements>
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14 <command detect_errors="exit_code">
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15 <![CDATA[
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16 unzip $FASTA &> /dev/null &&
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17 mkdir ./CMSEARCH &&
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18 mkdir ./MODEL &&
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19 #import re
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20 #for $cms_res in $cmsearch_results:
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21 #set $safename_cm = re.sub('[^\w\-_\.]', '_', $cms_res.element_identifier)
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22 ln -f -s '$cms_res' ./CMSEARCH/$safename_cm &&
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23 #end for
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24 #for $mods in $model_tree_files:
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25 #set $safename_tr = re.sub('[^\w\-_\.]', '_', $mods.element_identifier)
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26 ln -f -s '$mods' ./MODEL/$safename_tr &&
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27 #end for
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28
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29 'glob_res.pl'
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30 $merge_cluster_ol
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31 $merge_overlap
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32 $min_cluster_size
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33 $cm_min_bitscore
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34 $cm_max_eval
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35 1 ## cm_bitscore_sig
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36 $partition_type ''
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37 $cut_type
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38 0 ## zero means do not align
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39 #if $iteration_num.iteration_num_selector:
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40 $iteration_num.CI
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41 $final_partition_soft
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42 $final_partition_used_cmsearch
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43 '$combined_cm'
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44
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45 #end if
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46
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47 &&
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48 python '$__tool_directory__/evaluation.py' FASTA/ RESULTS/
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49
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50 #if $cdhit:
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51 &&
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52 python '$__tool_directory__/addCdhitseqs.py' '$cdhit'
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53 #end if
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54 ]]>
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55 </command>
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56 <inputs>
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57 <param type="data" name="FASTA" format="zip" help="FASTA.zip from pre-processing step"/>
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58 <param type="data" name="cmsearch_results" format="tabular" multiple="True"
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59 help="Tabular cmsearch results of the candidate clusters from the cmsearch step"/>
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60 <param type="data" name="model_tree_files" format="txt" multiple="True" label="model-tree-stk"
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61 help="model.tree.stk files from pgma_graphclust candidate clustering step"/>
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62 <param name="partition_type" type="boolean" checked="True" truevalue="0" falsevalue="1" label="Hard partition"
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63 help="Whether to do hard partitioning (no overlap) or soft mode(cluster elements may overlap) "/>
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64 <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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65 <param name="cm_min_bitscore" type="integer" value="20" size="5" label="cm_min_bitscore" help=""/>
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66 <param name="cm_max_eval" type="float" value="0.001" size="5" label="cm_max_E-val" help=""/>
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67 <param type="data" name="cdhit" format="txt" optional="true" label="CD-HIT output"
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68 help="Optional CD-HIT pre-clustering output to be combined into the final clustering output"/>
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69 <param name="merge_cluster_ol" type="float" value="0.66" size="5" label="merge_cluster_ovelap"
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70 help="Overlapping ratio criteria to merge overlapping clusters or keep separate clusters (soft partitioning)"/>
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71 <param name="merge_overlap" type="float" value="0.51" size="5" label="merge_fraction_overlap"
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72 help="Overlapping ratio criteria to merge overlapping sequence fractions from same input sequence"/>
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73 <param name="min_cluster_size" type="integer" value="3" size="5" label="minimum cluster size"
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74 help="Minimum number of elements that can form a cluster. Higher values discard small clusters and may produce larger merged clusters"/>
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75 <!-- <param name="cm_bitscore_sig" type="integer" value="1" size="5" label="cm_bitscore_sig" help=""/> -->
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76
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77 <conditional name="iteration_num">
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78 <param name="iteration_num_selector" type="boolean" checked="no" label="Multiple iterations" help="for single iteration- NO, for multiple-YES"/>
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79 <when value="true">
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80 <param name="CI" type="integer" value="2" size="5" label="Number of current iteration "/>
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81 <param type="data" name="final_partition_soft" format="txt" />
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82 <param type="data" name="final_partition_used_cmsearch" format="txt" />
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83 <param type="data" name="combined_cm" format="txt" />
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84 </when>
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85 <when value="false" ></when>
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86 </conditional>
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87
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88 </inputs>
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89 <outputs>
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90 <data name="final_stats" format="txt" from_work_dir="RESULTS/cluster.final.stats" label="cluster.final.stats" />
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91 <data name="tableForEval" format="tabular" from_work_dir="RESULTS/fullTab.tabular" label="tableForEval" />
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92 <data name="final_soft" format="txt" from_work_dir="RESULTS/partitions/final_partition.soft" label="soft_part" />
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93 <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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94 <data name="evaluation" format="txt" from_work_dir="RESULTS/evaluation.txt" label="evaluation_of_clusters" />
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95 <data name="combined_cm_out" format="txt" from_work_dir="combined_cm_out" label="combined_cmsearch_output" />
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96 <collection name="clusters" type="list" label="CLUSTERS-cmsearch">
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97 <discover_datasets format="txt" pattern="(?P&lt;name&gt;^.*\.all$)" directory="RESULTS" />
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98 </collection>
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99 <collection name="allFastaSorted" type="list" label="cluster-sequences-sorted">
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100 <discover_datasets format="fasta" pattern="(?P&lt;name&gt;^.*\.sorted.fa$)" directory="RESULTS" />
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101 </collection>
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102
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103 <collection name="partitions" type="list" label="Partitions">
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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104 <discover_datasets pattern="(?P&lt;name&gt;^.*$)" directory="RESULTS/partitions" />
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105 </collection>
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106 <data name="RESULTS_zip" format="zip" from_work_dir="RESULTS.zip" label="RESULTS.zip" />
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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107 </outputs>
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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108 <tests>
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109 <test>
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110 <param name="FASTA" value="FASTA.zip" ftype="searchgui_archive"/>
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111 <param name="cmsearch_results" value="1.1.tree,1.2.tree"/>
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112 <param name="model_tree_files" value="1.1.model.tree.fa,1.2.model.tree.fa"/>
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113 <param name="partition_type" value="0"/>
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114 <param name="cut_type" value="0"/>
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115 <conditional name="iteration_num">
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116 <param name="iteration_num_selector" value="false"/>
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117 </conditional>
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118 <param name="merge_cluster_ol" value="0.66"/>
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119 <param name="merge_overlap" value="0.51"/>
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120 <param name="min_cluster_size" value="3"/>
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121 <param name="cm_min_bitscore" value="20"/>
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122 <param name="cm_max_eval" value="0.001"/>
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123 <!-- <param name="cm_bitscore_sig" value="0"/> -->
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124 <output name="final_stats" file="RESULTS/cluster.final.stats" />
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125 <output name="combined_cm_out" file="combined_cm_out"/>
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126 <output name="evaluation" file="evaluation1.txt"/>
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127 <output_collection name="clusters" type="list">
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128 <element name="1.cluster.all" file="RESULTS/1.cluster.all" compare="contains"/>
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129 <element name="2.cluster.all" file="RESULTS/2.cluster.all" compare="contains"/>
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130
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131 </output_collection>
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132 <output_collection name="partitions">
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133 <element name="final_overlap.map" file="RESULTS/partitions/final_overlap.map" compare="contains">
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134 <assert_contents>
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135 <has_text text="1.1 1.1 " />
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136 <has_text text="1.2 1.2" />
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137 </assert_contents>
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138 </element>
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139 <element name="final_overlap.matrix" file="RESULTS/partitions/final_overlap.matrix" compare="contains">
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140 <assert_contents>
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141 <has_text text="MODEL CLASS 0 0" />
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142 <!--has_text text="1.2" />
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143 <has_text text="1.1" /-->
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144 </assert_contents>
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145 </element>
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146 <element name="final_partition.hard.best" file="RESULTS/partitions/final_partition.hard.best" />
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147 <element name="final_partition.hard.merged" file="RESULTS/partitions/final_partition.hard.merged" />
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148 <element name="final_partition.soft" file="RESULTS/partitions/final_partition.soft" />
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149 <element name="final_partition.used_cmsearch" file="RESULTS/partitions/final_partition.used_cmsearch" compare="contains"/>
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150 </output_collection>
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151
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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152 <output name="RESULTS_zip" file="RESULTS.zip" ftype="zip" compare="sim_size" delta="20000"/>
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153
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154 </test>
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155 </tests>
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156 <help>
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157 <![CDATA[
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158
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159 **What it does**
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160
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161 Post-processing. Redundant clusters are merged and instances that belong to multiple clusters
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162 are assigned unambiguously. For every pair of clusters, the relative overlap (i.e. the fraction of
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163 instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%.
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164 Cluster members are finally ranked by their CM bitscore.
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165
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166 ]]>
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167 </help>
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168 <citations>
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169 <citation type="doi">10.5281/zenodo.597695</citation>
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170 </citations>
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171 </tool>