Mercurial > repos > ppericard > viscorvar

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"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 21d09ff286a496ff475f32626d88dd42423ae663"
author ppericard
date Tue, 07 Sep 2021 10:40:08 +0000
parents d4e9f7546dfa
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1 <tool id="viscorvar_matcoraddvar" name="visCorVar matCorAddVar" version="@TOOL_VERSION@+galaxy0" profile="16.04" workflow_compatible="true">
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3 <description>determine the correlation circles that can be overlaid and compute the correlations</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_matcoraddvar.R
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17 --input_rdata ${input_rdata}
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18 --block_Y_file ${block_Y}
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20 ##--cutoff_comp ${cutoff_comp}
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21 --cutoff_comp 0.75
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22 #if str($var_of_interest_file) !='':
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23 --interest_var_file ${var_of_interest_file}
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24 #end if
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26 --output_rdata ${output_rdata}
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27 --output_response_var ${output_response_var}
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28 --output_blocks_comb ${output_blocks_comb}
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30 ]]></command>
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32 <inputs>
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33 <param name="input_rdata" type="data" format="rdata"
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34 label="Input RData file from block.SPLSDA"
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35 help="this is the RData output file from the block.splsda function" />
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36 <param name="block_Y" type="data" format="tabular"
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37 label="Block Y"
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38 help="Block Y is a table. A column corresponds to a phenotype and determines which sample is associated with this phenotype or not (value equals to 1 or 0). For the file structure, see below in the section Input files" />
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39 <!-- Fichier avec noms de gènes/variables, donné par l'utilisateur -->
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40 <param name="var_of_interest_file" type="data" format="txt" optional="true"
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41 label="Variables of interest (Optional)"
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42 help="variables not belonging to any block will not be considered. For the file structure, see below in the section Input files"/>
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43 <!-- <param name="cutoff_comp" type="float" value="0.775" min="0" max="1"
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44 label="Cutoff comp"
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45 help="[cutoff_comp] Two correlation circles will be superimposed if the correlation of their first and second axis is greater than cutoff_comp in absolute value." /> -->
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46 </inputs>
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48 <outputs>
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49 <data name="output_rdata" format="rdata" label="${tool.name}_output.RData" />
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50 <data name="output_response_var" format="tabular" label="${tool.name}_response_var.tsv" />
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51 <data name="output_blocks_comb" format="tabular" label="${tool.name}_blocks_comb.tsv" />
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52 </outputs>
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54 <tests>
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55 </tests>
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57 <help><![CDATA[
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59 @HELP_AUTHORS@
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61 ======================
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62 visCorVar matCorAddVar
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63 ======================
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65 -----------
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66 Description
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67 -----------
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68
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69 This tool is a pre-processing step of the pipeline. It computes the correlations
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70 between omics datasets variables, variables of interest (optional), response variables and
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71 the components which are output of the data integration. The variables of interest are omics
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72 datasets variables that will be added to the network. It also determines the omics datasets
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73 for which the correlated variables of these omics datasets can be visualized with correlation
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74 circles and networks.
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75
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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 mixOmics.block.splsda mixomics_blocksplsda_output.RData rdata
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86 ======================= =================================== ========
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87
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88 **Downstream tools**
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89
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90 ================================ ========================================= ========
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91 Name Output file Format
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92 ================================ ========================================= ========
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93 visCorVar.circleCor viscorvar_matcoraddvar_output.RData rdata
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94 -------------------------------- ----------------------------------------- --------
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95 visCorVar.computeMatSimilarity viscorvar_matcoraddvar_output.RData rdata
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96 -------------------------------- ----------------------------------------- --------
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97 visCorVar.networkVar viscorvar_matcoraddvar_response_var.tsv tabular
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98 ================================ ========================================= ========
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99
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100 ---------------------------------------------------
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101
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102 -----------
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103 Input files
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104 -----------
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105
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106 +-----------------------------------------+-----------+
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107 | Parameter : num + label | Format |
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108 +=========================================+===========+
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109 | 1 : Rdata mixOmics.block.splsda output | Rdata |
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110 +-----------------------------------------+-----------+
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111 | 2 : Block Y | tabular |
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112 +-----------------------------------------+-----------+
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113 | 3 : [opt] Variables of interest | txt |
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114 +-----------------------------------------+-----------+
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115
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116 2. Block Y structure
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117 Block Y is in tabular format (.tsv).
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118 This table contains the name of the samples in the first column.
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119 The other columns correspond to phenotypes.
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120 For each of these other columns, a column corresponds to a phenotype and determines which sample is associated with this phenotype or not (value equals to 1 or 0). The names of the samples in Block Y (transposed), in the sample metadata (transposed) and for all datasets have to be in the same order.
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121
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122 3. Variables of interest structure
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123 All the variables of interest are in the same column.
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124
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125 ----------
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126 Parameters
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127 ----------
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128
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129 @HELP_MANUAL@
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130
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131 ------------
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132 Output files
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133 ------------
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134
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135 viscorvar_matcoraddvar_output.RData
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136 | RData output
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137 | Contains the `matCorAddVar_result` R object containing the result of the matCorAddVar function
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138
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139 viscorvar_matcoraddvar_blocks_comb.tsv
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140 | viscorvar_matcoraddvar_blocks_comb.tsv contains the block names whose correlation circles can be overlaid
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141
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142 ]]></help>
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143
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144 <expand macro="citations" />
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145
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146 </tool>