Mercurial > repos > ppericard > viscorvar

annotate viscorvar_networkvar.xml @ 4:d4e9f7546dfa draft

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"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 579dc54316e8ede493f86f434a87d3d7b692b023"
author ppericard
date Tue, 17 Nov 2020 13:01:44 +0000
parents df8428358b7f
children 88c1fd2ac110
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1 <tool id="viscorvar_networkvar" name="visCorVar networkVar" version="@TOOL_VERSION@+galaxy0" profile="16.04" workflow_compatible="true">
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3 <description>creates a network between selected variables of datasets and the response variables. In the network, the similarity between two variables is associated with the link between these two variables.</description>
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5 <macros>
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6 <import>macros.xml</import>
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7 <import>macros_viscorvar.xml</import>
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8 </macros>
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10 <expand macro="requirements"/>
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11 <expand macro="stdio"/>
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13 <command detect_errors="aggressive"><![CDATA[
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15 @COMMAND_RSCRIPT@/viscorvar_networkvar.R
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17 --mat_similarity_rdata ${mat_similarity_rdata}
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18 --var_list_file ${var_list_file}
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19 --response_var ${select_response_var}
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21 --output_graph ${output_graph}
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23 @COMMAND_LOG_EXIT@
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25 ]]></command>
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27 <inputs>
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28 <param name="mat_similarity_rdata" type="data" format="rdata"
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29 label="this is the RData output file from the computeMatSimilarity function"
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30 help="output RData file from computeMatSimilarity"/>
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31 <param name="var_list_file" type="data" format="tabular"
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32 label="Variables list file"
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33 help="selected variables output tabular file from circleCor"/>
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35 <!-- Fichier avec noms de gènes/variables, donné par l'utilisateur -->
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36 <!-- <param name="var_of_interest_file" type="data" format="txt" optional="true"
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37 label="Variables of interest (Optional)"
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38 help="these variables have to belong to datasets that can be superimposed"/> -->
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40 <param name="response_var_list" type="data" format="tabular"
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41 label="List of response variables"
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42 help="output *_response_var.tsv file from matCorAddVar"/>
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43 <param name="select_response_var" type="select" display="checkboxes" multiple="true"
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44 label="Response variables"
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45 help="response variables that will be plotted in the network">
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46 <!-- <param name="select_responses_var" type="select" multiple="true" label="Response variables"> -->
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47 <options from_dataset="response_var_list">
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48 <column name="value" index="0"/>
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49 <filter type="unique_value" column="0"/>
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50 <filter type="sort_by" name="sorted_value" column="0"/>
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51 </options>
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52 </param>
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53 </inputs>
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55 <outputs>
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56 <data name="output_graph" format="xml" label="${tool.name}_graph.graphml" />
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57 </outputs>
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59 <tests>
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60 </tests>
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62 <help><![CDATA[
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64 @HELP_AUTHORS@
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66 ====================
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67 visCorVar networkVar
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68 ====================
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70 -----------
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71 Description
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72 -----------
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73
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74 This tool creates a network of correlated variables for omics datasets. The determination of
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75 the omics datasets which can be visualized is made by the tool matCorAddVar. This network can
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76 be exported to graphml format and visualized with Cytoscape. The link between two variables
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77 is associated with the correlation between two variables : a threshold can be used in
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78 Cytoscape to get a network of variables whose correlation is greater than this threshold
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79 in absolute value.
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81 -----------------
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82 Workflow position
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83 -----------------
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84
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85 **Upstream tools**
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86
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87 ================================ ============================================= =========
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88 Name Output file Format
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89 ================================ ============================================= =========
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90 visCorVar.computeMatSimilarity viscorvar_computematsimilarity_output.RData rdata
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91 -------------------------------- --------------------------------------------- ---------
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92 visCorVar.circleCor viscorvar_circlecor_selected_var.tsv tabular
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93 -------------------------------- --------------------------------------------- ---------
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94 visCorVar.matCorAddVar viscorvar_matcoraddvar_response_var.tsv tabular
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95 ================================ ============================================= =========
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96
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97 ---------------------------------------------------
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99 -----------
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100 Input files
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101 -----------
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102
3
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103 +-----------------------------------------------------------+-----------+
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104 | Parameter : num + label | Format |
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105 +===========================================================+===========+
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106 | 1 : Rdata visCorVar.computeMatSimilarity output | rdata |
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107 +-----------------------------------------------------------+-----------+
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108 | 2 : ``*``_selected_var.tsv visCorVar.circleCor output | tabular |
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109 +-----------------------------------------------------------+-----------+
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110 | 3 : ``*``_response_var.tsv visCorVar.matCorAddVar output | tabular |
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111 +-----------------------------------------------------------+-----------+
2
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113 ----------
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114 Parameters
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115 ----------
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116
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117 @HELP_MANUAL@
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118
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119 ------------
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120 Output files
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121 ------------
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122
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123 viscorvar_networkvar_graph.graphml
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124 GraphML file
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125
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126 ]]></help>
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127
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128 <expand macro="citations" />
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129
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130 </tool>