Mercurial > repos > iuc > cemitool

annotate cemitool.xml @ 0:3f9ff31c88bb draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
author iuc
date Mon, 10 Oct 2022 16:55:19 +0000
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3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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1 <tool id="cemitool" name="CEMiTool" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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2 <description>gene co-expression network analyses</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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6 <expand macro='xrefs'/>
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7 <expand macro="requirements" />
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8 <command detect_errors="exit_code"><![CDATA[
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9 Rscript '$__tool_directory__/CEMiTool.R'
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10 -M '$expression_matrix'
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11 #if $annotation
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12 -A '$annotation'
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13 #end if
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14 #if $pathways
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15 -P '$pathways'
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16 #end if
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17 #if $interactions
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18 -I '$interactions'
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19 #end if
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20 -f $advanced_parameters.filter
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21 -i $advanced_parameters.filter_pval
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22 -a $advanced_parameters.apply_vst
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23 -n $advanced_parameters.n_genes
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24 -e $advanced_parameters.eps
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25 -c $advanced_parameters.cor_method
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26 -y $advanced_parameters.cor_function
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27 -x $advanced_parameters.network_type
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28 -t $advanced_parameters.tom_type
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29 -m $advanced_parameters.merge_similar
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30 -r $advanced_parameters.rank_method
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31 -g $advanced_parameters.min_ngen
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32 -d $advanced_parameters.diss_thresh
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33 -h $advanced_parameters.center_func
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34 -o $advanced_parameters.ora_pval
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35 -l $advanced_parameters.gsea_scale
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36 -w $advanced_parameters.gsea_min_size
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37 -z $advanced_parameters.gsea_max_size
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38 -v $advanced_parameters.sample_column_name
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39 ]]></command>
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40 <inputs>
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41 <param name="expression_matrix" type="data" format="tabular" label="Expression matrix"/>
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42 <param name="annotation" type="data" format="tabular" optional="true" label="Sample annotation"
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43 help="It allows to build a more complete object and generate richer reports about the
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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44 expression data. Sample annotation can be supplied in a data.frame that specifies a
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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45 class for each sample. Classes can represent different conditions, phenotypes, cell lines,
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46 time points, etc. " />
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47 <param name="pathways" type="data" format="tabular,txt" label="Pathways list" optional="true" help="CEMiTool can
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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48 determine which biological functions are associated with the modules by performing an over
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49 representation analysis (ORA). To do this you must provide a pathway list in the form of GMT
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50 file. CEMiTool will then analyze how these pathways are represented in the modules." />
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51 <param name="interactions" type="data" format="tabular" optional="true" label="Interactions data" help="Interaction data,
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52 such as protein-protein interactions can be added in order to generate annotated module graphs.
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53 Interaction files contains two columns for interacting pairs of genes"/>
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54 <param name="outputs" type="select" multiple="true" display="checkboxes" label="Outputs selector">
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55 <option value="report" selected="true">Report</option>
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56 <option value="tables">Tables</option>
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57 <option value="plots">Plots</option>
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58 </param>
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59 <section name="advanced_parameters" title="Advanced parameters">
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60 <param argument="filter" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Filter" help="If enabled, it will filter expression data" />
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61 <param argument="filter_pval" type="float" min="0" max="1" value="0.1" label="Filter P-value" help="P-value threshold for filtering" />
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62 <param argument="apply_vst" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="VST" help="If enabled, it apply Variance Stabilizing Transform before filtering genes" />
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63 <param argument="n_genes" type="integer" min="0" value="1000" label="Number of genes" help="Number of genes left after filtering" />
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64 <param argument="eps" type="float" min="0" max="1" value="0.1" label="EPS" help="A value for accepted R-squared interval between subsequent beta values" />
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65 <param name="cor_method" type="select" label="Correlation method" help="Correlation coefficient to be computed">
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66 <option value="pearson">Pearson</option>
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67 <option value="spearman">Spearman</option>
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68 </param>
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69 <param name="cor_function" type="select" label="Correlation function" help="Correlation function to be used">
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70 <option value="cor">Correlation (cor)</option>
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71 <option value="bicor">Biweight Midcorrelation (bicor)</option>
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72 </param>
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73 <param name="network_type" type="select" label="Network type" help="Indicates if network type should be computed as 'signed' or 'unsigned'">
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74 <option value="signed">Signed</option>
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75 <option value="unsigned" selected="true">Unsigned</option>
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76 </param>
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77 <param name="tom_type" type="select" label="TOM type" help="Indicates if TOM type should be computed as 'signed' or 'unsigned'">
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78 <option value="signed">Signed</option>
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79 <option value="unsigned">Unsigned</option>
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80 </param>
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81 <param argument="merge_similar" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Merge similar" help="If enabled, merge similar modules" />
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82 <param argument="rank_method" type="select" label="Rank method" help="Indicate how to rank genes">
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83 <option value="mean">Mean</option>
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84 <option value="median">Median</option>
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85 </param>
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86 <param argument="min_ngen" type="integer" min="0" value="30" label="Minimal number of genes per module"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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87 <param argument="diss_thresh" type="float" min="0" max="1" value="0.8" label="Merging correlation threshold" help="Module merging correlation threshold for eigengene similarity" />
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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88 <param argument="center_func" type="select" label="Cetrality measure to show in the plot">
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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89 <option value="mean">Mean</option>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
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90 <option value="median">Median</option>
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91 </param>
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92 <param argument="ora_pval" type="float" min="0" max="1" value="0.05" label="P-value for overrepresentation analysis"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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93 <param argument="gsea_scale" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Z-score transformation for GSEA analysis" help="If enabled, it applies z-score transformation" />
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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94 <param argument="gsea_min_size" type="integer" min="0" value="15" label="Minimum size of gene sets for GSEA analysis"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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95 <param argument="gsea_max_size" type="integer" min="0" value="1000" label="Maximum size of gene sets for GSEA analysis"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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96 <param argument="sample_column_name" type="text" value="SampleName" label="Sample column name" help="This is only required if an annotation file is provided">
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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97 <sanitizer invalid_char="">
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98 <valid initial="string.letters,string.digits">
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99 <add value="_" />
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100 <add value="-" />
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101 <add value=":" />
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102 </valid>
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103 </sanitizer>
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104 <validator type="regex">[0-9a-zA-Z:-_]+</validator>
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105 </param>
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106 </section>
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107 </inputs>
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108 <outputs>
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109 <collection name="plots" type="list" label="${tool.name} on ${on_string}: Plots">
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110 <discover_datasets pattern="__designation_and_ext__" format="pdf" directory="Plots" />
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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111 <filter>"plots" in outputs</filter>
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112 </collection>
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113 <data name="module" format="tabular" from_work_dir="Tables/module.tsv" label="${tool.name} on ${on_string}: Module">
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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114 <filter>"tables" in outputs</filter>
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115 </data>
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116 <data name="modules_genes" format="tabular" from_work_dir="Tables/modules_genes.gmt" label="${tool.name} on ${on_string}: Module genes">
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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117 <filter>"tables" in outputs</filter>
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118 </data>
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119 <data name="parameters" format="tabular" from_work_dir="Tables/parameters.tsv" label="${tool.name} on ${on_string}: Parameters">
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120 <filter>"tables" in outputs</filter>
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121 </data>
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122 <data name="selected_genes" format="txt" from_work_dir="Tables/selected_genes.txt" label="${tool.name} on ${on_string}: Selected genes">
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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123 <filter>"tables" in outputs</filter>
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124 </data>
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125 <data name="summary_eigengene" format="tabular" from_work_dir="Tables/summary_eigengene.tsv" label="${tool.name} on ${on_string}: Summary eigengenes">
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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126 <filter>"tables" in outputs</filter>
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127 </data>
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128 <data name="summary_mean" format="tabular" from_work_dir="Tables/summary_mean.tsv" label="${tool.name} on ${on_string}: Summary mean">
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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129 <filter>"tables" in outputs</filter>
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130 </data>
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131 <data name="summary_median" format="tabular" from_work_dir="Tables/summary_median.tsv" label="${tool.name} on ${on_string}: Summary median">
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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132 <filter>"tables" in outputs</filter>
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133 </data>
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134 <data name="interactions_output" format="tabular" from_work_dir="Tables/interactions.tsv" label="${tool.name} on ${on_string}: Interactions">
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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135 <filter>"tables" in outputs</filter>
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136 <filter>interactions</filter>
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137 </data>
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138 <data name='output_html' format='html' from_work_dir="Reports/Report/report.html" label="${tool.name} on ${on_string}: HTML report">
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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139 <filter>"report" in outputs</filter>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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140 </data>
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141 </outputs>
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142 <tests>
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143 <test expect_num_outputs="1">
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144 <!--Test expression matrix input-->
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145 <param name="expression_matrix" value="expression_matrix.tab"/>
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146 <param name="outputs" value="report"/>
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147 <section name="advanced_parameters">
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148 <param name="filter" value="True"/>
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149 <param name="filter_pval" value="0.1"/>
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150 <param name="apply_vst" value="false"/>
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151 <param name="n_genes" value="1000"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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152 <param name="eps" value="0.1"/>
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153 <param name="cor_method" value="pearson"/>
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154 <param name="cor_function" value="cor"/>
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155 <param name="network_type" value="signed"/>
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156 <param name="tom_type" value="signed"/>
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157 <param name="merge_similar" value="false"/>
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158 <param name="rank_method" value="mean"/>
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159 <param name="min_ngen" value="30"/>
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160 <param name="diss_thresh" value="0.8"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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161 <param name="center_func" value="mean"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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162 <param name="ora_pval" value="0.05"/>
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163 <param name="gsea_scale" value="true"/>
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164 <param name="gsea_min_size" value="15"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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165 <param name="gsea_max_size" value="1000"/>
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166 </section>
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167 <output name="output_html">
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168 <assert_contents>
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169 <has_text text="EPSTI1"/>
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170 <has_text text="RSAD2"/>
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171 <has_text text="XAF1"/>
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172 <has_text text="OAS2"/>
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173 <has_text text="Gene Set Enrichment Analysis"/>
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174 <has_text text="SPARC"/>
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175 </assert_contents>
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176 </output>
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177 </test>
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178
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179 <test expect_num_outputs="8">
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180 <!--Test all inputs and output tables-->
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181 <param name="expression_matrix" value="expression_matrix.tab"/>
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182 <param name="annotation" value="sample_annotation.tab"/>
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183 <param name="pathways" value="pathways.gmt"/>
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184 <param name="interactions" value="interactions.tab"/>
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185 <param name="outputs" value="tables"/>
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186 <section name="advanced_parameters">
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187 <param name="filter" value="True"/>
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188 <param name="filter_pval" value="0.1"/>
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189 <param name="apply_vst" value="false"/>
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190 <param name="n_genes" value="1000"/>
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191 <param name="eps" value="0.1"/>
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192 <param name="cor_method" value="pearson"/>
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193 <param name="cor_function" value="cor"/>
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194 <param name="network_type" value="signed"/>
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195 <param name="tom_type" value="signed"/>
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196 <param name="merge_similar" value="false"/>
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197 <param name="rank_method" value="mean"/>
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198 <param name="min_ngen" value="30"/>
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199 <param name="diss_thresh" value="0.8"/>
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200 <param name="center_func" value="mean"/>
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201 <param name="ora_pval" value="0.05"/>
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202 <param name="gsea_scale" value="true"/>
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203 <param name="gsea_min_size" value="15"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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204 <param name="gsea_max_size" value="1000"/>
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205 </section>
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206 <output name="module">
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207 <assert_contents>
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208 <has_n_lines n="110"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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209 <has_size value="2250" delta="200"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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210 </assert_contents>
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211 </output>
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212 <output name="modules_genes">
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213 <assert_contents>
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iuc
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diff changeset
214 <has_n_lines n="1"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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215 <has_size value="216" delta="10"/>
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216 </assert_contents>
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217 </output>
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218 <output name="parameters">
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219 <assert_contents>
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iuc
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220 <has_n_lines n="12"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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221 <has_size value="234" delta="10"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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222 </assert_contents>
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223 </output>
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224 <output name="selected_genes">
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225 <assert_contents>
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iuc
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diff changeset
226 <has_n_lines n="1000"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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227 <has_size value="6496" delta="10"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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228 </assert_contents>
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229 </output>
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230 <output name="summary_eigengene">
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231 <assert_contents>
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iuc
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diff changeset
232 <has_n_lines n="3"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
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233 <has_size value="2241" delta="10"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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234 </assert_contents>
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235 </output>
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236 <output name="summary_mean">
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237 <assert_contents>
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iuc
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diff changeset
238 <has_n_lines n="3"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
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239 <has_size value="2044" delta="50"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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240 </assert_contents>
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241 </output>
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242 <output name="summary_median">
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243 <assert_contents>
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iuc
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diff changeset
244 <has_n_lines n="3"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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diff changeset
245 <has_size value="1621" delta="10"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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246 </assert_contents>
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247 </output>
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diff changeset
248 <output name="interactions_output">
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249 <assert_contents>
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iuc
parents:
diff changeset
250 <has_n_lines n="277"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
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diff changeset
251 <has_size value="7736" delta="200"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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252 </assert_contents>
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253 </output>
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254 </test>
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iuc
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255
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
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diff changeset
256 <test expect_num_outputs="10">
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diff changeset
257 <!--Test custom inputs and plots-->
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258 <param name="expression_matrix" value="expression_matrix.tab"/>
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iuc
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259 <param name="annotation" value="sample_annotation.tab"/>
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260 <param name="pathways" value="pathways.gmt"/>
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261 <param name="interactions" value="interactions.tab"/>
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262 <param name="outputs" value="report,tables,plots"/>
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263 <section name="advanced_parameters">
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264 <param name="filter" value="false"/>
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265 <param name="filter_pval" value="0.2"/>
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266 <param name="apply_vst" value="true"/>
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267 <param name="n_genes" value="2000"/>
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268 <param name="eps" value="0.1"/>
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269 <param name="cor_method" value="spearman"/>
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270 <param name="cor_function" value="bicor"/>
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271 <param name="network_type" value="unsigned"/>
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272 <param name="tom_type" value="unsigned"/>
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273 <param name="merge_similar" value="true"/>
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274 <param name="rank_method" value="median"/>
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275 <param name="min_ngen" value="35"/>
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276 <param name="diss_thresh" value="0.7"/>
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277 <param name="center_func" value="median"/>
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278 <param name="ora_pval" value="0.07"/>
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279 <param name="gsea_scale" value="false"/>
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280 <param name="gsea_min_size" value="10"/>
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281 <param name="gsea_max_size" value="1100"/>
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282 </section>
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283 <output name="module">
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284 <assert_contents>
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285 <has_n_lines n="1929"/>
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286 <has_size value="26528" delta="200"/>
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287 </assert_contents>
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288 </output>
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289 <output name="modules_genes">
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290 <assert_contents>
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291 <has_n_lines n="10"/>
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292 <has_size value="15814" delta="200"/>
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293 </assert_contents>
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294 </output>
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295 <output name="parameters">
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296 <assert_contents>
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iuc
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297 <has_n_lines n="12"/>
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298 <has_size value="234" delta="10"/>
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299 </assert_contents>
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300 </output>
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301 <output name="selected_genes">
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302 <assert_contents>
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iuc
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303 <has_n_lines n="1928"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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304 <has_size value="12570" delta="200"/>
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305 </assert_contents>
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306 </output>
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307 <output name="summary_eigengene">
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308 <assert_contents>
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iuc
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309 <has_n_lines n="12"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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310 <has_size value="9963" delta="200"/>
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311 </assert_contents>
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312 </output>
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313 <output name="summary_mean">
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314 <assert_contents>
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iuc
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315 <has_n_lines n="12"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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316 <has_size value="8898" delta="200"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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317 </assert_contents>
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318 </output>
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319 <output name="summary_median">
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320 <assert_contents>
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iuc
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321 <has_n_lines n="12"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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322 <has_size value="6574" delta="200"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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323 </assert_contents>
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324 </output>
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325 <output name="interactions_output">
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326 <assert_contents>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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327 <has_n_lines n="2579"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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328 <has_size value="55341" delta="200"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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329 </assert_contents>
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330 </output>
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331 <output_collection name="plots" type="list" count="10">
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332 <element name="profile" file="profiles.pdf" compare="sim_size" delta="100"/>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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333 </output_collection>
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334 </test>
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335
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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336 </tests>
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337 <help><![CDATA[
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338
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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339 .. class:: infomark
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340
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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341 **Purpose**
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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342
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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343 The CEMiTool R package provides users with an easy-to-use method to automatically implement gene co-expression network analyses, obtain key information about the
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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344 discovered gene modules using additional downstream analyses and retrieve publication-ready results via a high-quality interactive report.
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345
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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346 .. class:: infomark
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347
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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348 **Purpose**
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
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349
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350 ]]></help>
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
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351 <expand macro="citations" />
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
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352 </tool>