Mercurial > repos > ppericard > viscorvar

annotate viscorvar_networkvar.xml @ 2:c8533e9298e5 draft

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"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
author ppericard
date Fri, 23 Oct 2020 10:15:56 +0000
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children df8428358b7f
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1 <tool id="viscorvar_networkvar" name="visCorVar networkVar" version="@TOOL_VERSION@+galaxy1" 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="Input computeMatSimilarity RData file"
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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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54
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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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74 Bla bla...
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76 -----------------
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77 Workflow position
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78 -----------------
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80 **Upstream tools**
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81
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82 ================================ ============================================= =========
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83 Name Output file Format
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84 ================================ ============================================= =========
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85 visCorVar.computeMatSimilarity viscorvar_computematsimilarity_output.RData rdata
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86 -------------------------------- --------------------------------------------- ---------
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87 visCorVar.circleCor viscorvar_circlecor_selected_var.tsv tabular
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88 -------------------------------- --------------------------------------------- ---------
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89 visCorVar.matCorAddVar viscorvar_matcoraddvar_response_var.tsv tabular
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90 ================================ ============================================= =========
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91
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92 ---------------------------------------------------
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94 -----------
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95 Input files
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96 -----------
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98 +-------------------------------------------------------+------------+
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99 | Parameter : num + label | Format |
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100 +=======================================================+============+
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101 | 1 : Rdata visCorVar.computeMatSimilarity output | rdata |
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102 +-------------------------------------------------------+------------+
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103 | 2 : *_selected_var.tsv visCorVar.circleCor output | tabular |
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104 +-------------------------------------------------------+------------+
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105 | 3 : *_response_var.tsv visCorVar.matCorAddVar output | tabular |
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106 +-------------------------------------------------------+------------+
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107
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108 ----------
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109 Parameters
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110 ----------
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111
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112 @HELP_MANUAL@
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113
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114 ------------
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115 Output files
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116 ------------
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117
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118 viscorvar_networkvar_graph.graphml
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119 GraphML file
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120
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121 ]]></help>
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122
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123 <expand macro="citations" />
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124
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125 </tool>