Mercurial > repos > ppericard > viscorvar

annotate viscorvar_circlecor.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_circlecor" name="visCorVar circleCor" version="@TOOL_VERSION@+galaxy0" profile="16.04" workflow_compatible="true">
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3 <description>plots a correlation circle for the datasets whose correlation circles can be superimposed. This correlation circle contains the selected variables of these datasets which are included in a rectangle and the response 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_circlecor.R
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17 --input_rdata ${input_rdata}
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19 --blocks_vec ${select_blocks.value}
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20 --responses_var ${select_responses_var}
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21 --x_min ${x_min}
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22 --x_max ${x_max}
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23 --y_min ${y_min}
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24 --y_max ${y_max}
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26 --output_var ${output_var}
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27 --output_pdf ${output_pdf}
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29 @COMMAND_LOG_EXIT@
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31 ]]></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"
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35 help="this is the RData output file from the matCorAddVar function"/>
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36 <param name="blocks_vec_list" type="data" format="tabular"
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37 label="List of blocks vector."
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38 help="output *_blocks_comb.tsv file from matCorAddVar."/>
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39 <param name="select_blocks" type="select"
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40 label="Blocks"
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41 help="each element of List of blocks vector contain blocks for which selected variables can
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42 be visualized in the correlation circle">
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43 <options from_dataset="blocks_vec_list">
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44 <column name="value" index="0"/>
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45 <filter type="unique_value" column="0"/>
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46 <filter type="sort_by" name="sorted_value" column="0"/>
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47 </options>
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48 </param>
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49 <param name="responses_var_list" type="data" format="tabular"
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50 label="List of response variables."
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51 help="output *_response_var.tsv file from matCorAddVar"/>
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52 <param name="select_responses_var" type="select" display="checkboxes"
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53 multiple="true" label="Response variables"
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54 help="choose the response variables which will be plotted in the correlation circle">
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55 <!-- <param name="select_responses_var" type="select" multiple="true" label="Response variables"> -->
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56 <options from_dataset="responses_var_list">
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57 <column name="value" index="0"/>
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58 <filter type="unique_value" column="0"/>
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59 <filter type="sort_by" name="sorted_value" column="0"/>
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60 </options>
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61 </param>
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62 <param name="x_min" type="float" value="-1" min="-1" max="1"
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63 label="X min" help="" />
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64 <param name="x_max" type="float" value="1" min="-1" max="1"
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65 label="X max" help="" />
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66 <param name="y_min" type="float" value="-1" min="-1" max="1"
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67 label="Y min" help="" />
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68 <param name="y_max" type="float" value="1" min="-1" max="1"
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69 label="Y max" help="" />
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70 </inputs>
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71
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72 <outputs>
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73 <data name="output_var" format="tabular" label="${tool.name}_selected_var.tsv" />
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74 <data name="output_pdf" format="pdf" label="${tool.name}.pdf" />
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75 </outputs>
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76
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77 <tests>
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78 </tests>
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79
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80 <help><![CDATA[
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81
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82 @HELP_AUTHORS@
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83
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84 ===================
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85 visCorVar circleCor
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86 ===================
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87
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88 -----------
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89 Description
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90 -----------
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91
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92 This tool allows visualizing variables of omics datasets which are correlated with
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93 the response variables thanks to correlation circles. The determination of the omics
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94 datasets which can be visualized is made by the tool matCorAddVar. This tool performs
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95 a zoom in a rectangle to retrieve omics datasets variables which are correlated with a
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96 response variable.
2
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97
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98 -----------------
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99 Workflow position
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100 -----------------
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101
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102 **Upstream tools**
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103
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104 ======================== ===================================== ========
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105 Name Output file Format
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106 ======================== ===================================== ========
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107 visCorVar.matCorAddVar viscorvar_matcoraddvar_output.RData rdata
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108 ======================== ===================================== ========
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109
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110 **Downstream tools**
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111
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112 ====================== ====================================== =========
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113 Name Output file Format
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114 ====================== ====================================== =========
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115 visCorVar.networkVar viscorvar_circlecor_selected_var.tsv tabular
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116 ====================== ====================================== =========
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117
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118 ---------------------------------------------------
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119
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120 -----------
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121 Input files
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122 -----------
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123
3
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124 +-----------------------------------------------------------+-----------+
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125 | Parameter : num + label | Format |
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126 +===========================================================+===========+
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127 | 1 : Rdata visCorVar.matCorAddVar output | rdata |
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128 +-----------------------------------------------------------+-----------+
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129 | 2 : ``*``_blocks_comb.tsv visCorVar.matCorAddVar output | tabular |
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130 +-----------------------------------------------------------+-----------+
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131 | 3 : ``*``_response_var.tsv visCorVar.matCorAddVar output | tabular |
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132 +-----------------------------------------------------------+-----------+
2
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133
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134 ----------
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135 Parameters
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136 ----------
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137
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138 @HELP_MANUAL@
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139
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140 ------------
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141 Output files
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142 ------------
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143
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144 viscorvar_circlecor.pdf
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145 Correlation circle pdf file
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146
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147 viscorvar_circlecor_selected_var.tsv
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148 List of variables selected in the correlation circle
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149
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150 ]]></help>
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151
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152 <expand macro="citations" />
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153
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154 </tool>