Mercurial > repos > ppericard > viscorvar

annotate viscorvar_circlecor.xml @ 5:88c1fd2ac110 draft default tip

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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_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>
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30 <inputs>
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31 <param name="input_rdata" type="data" format="rdata"
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32 label="Input RData file"
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33 help="this is the RData output file from the matCorAddVar function"/>
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34 <param name="blocks_vec_list" type="data" format="tabular"
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35 label="List of blocks vector."
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36 help="output *_blocks_comb.tsv file from the matCorAddVar function."/>
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37 <param name="select_blocks" type="select"
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38 label="Blocks"
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39 help="each element of List of blocks vector contain blocks for which selected variables can
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40 be visualized in the correlation circle">
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41 <options from_dataset="blocks_vec_list">
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42 <column name="value" index="0"/>
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43 <filter type="unique_value" column="0"/>
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44 <filter type="sort_by" name="sorted_value" column="0"/>
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45 </options>
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46 </param>
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47 <param name="responses_var_list" type="data" format="tabular"
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48 label="List of response variables."
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49 help="output *_response_var.tsv file from the matCorAddVar function"/>
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50 <param name="select_responses_var" type="select" display="checkboxes"
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51 multiple="true" label="Response variables"
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52 help="choose the response variables which will be plotted in the correlation circle">
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53 <!-- <param name="select_responses_var" type="select" multiple="true" label="Response variables"> -->
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54 <options from_dataset="responses_var_list">
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55 <column name="value" index="0"/>
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56 <filter type="unique_value" column="0"/>
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57 <filter type="sort_by" name="sorted_value" column="0"/>
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58 </options>
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59 </param>
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60 <param name="x_min" type="float" value="-1" min="-1" max="1"
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61 label="X min" help="" />
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62 <param name="x_max" type="float" value="1" min="-1" max="1"
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63 label="X max" help="" />
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64 <param name="y_min" type="float" value="-1" min="-1" max="1"
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65 label="Y min" help="" />
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66 <param name="y_max" type="float" value="1" min="-1" max="1"
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67 label="Y max" help="" />
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68 </inputs>
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69
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70 <outputs>
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71 <data name="output_var" format="tabular" label="${tool.name}_selected_var.tsv" />
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72 <data name="output_pdf" format="pdf" label="${tool.name}.pdf" />
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73 </outputs>
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74
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75 <tests>
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76 </tests>
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78 <help><![CDATA[
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80 @HELP_AUTHORS@
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81
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82 ===================
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83 visCorVar circleCor
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84 ===================
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85
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86 -----------
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87 Description
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88 -----------
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89
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90 This tool allows visualizing variables of omics datasets which are correlated with response variables thanks to correlation circles. The determination of the omics
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91 datasets which can be visualized is made by the matCorAddVar tool. This tool performs
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92 a zoom in a rectangle to retrieve omics datasets variables which are correlated with a
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93 response variable.
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94
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95 -----------------
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96 Workflow position
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97 -----------------
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98
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99 **Upstream tools**
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100
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101 ======================== ===================================== ========
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102 Name Output file Format
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103 ======================== ===================================== ========
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104 visCorVar.matCorAddVar viscorvar_matcoraddvar_output.RData rdata
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105 ======================== ===================================== ========
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106
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107 **Downstream tools**
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108
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109 ====================== ====================================== =========
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110 Name Output file Format
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111 ====================== ====================================== =========
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112 visCorVar.networkVar viscorvar_circlecor_selected_var.tsv tabular
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113 ====================== ====================================== =========
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114
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115 ---------------------------------------------------
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116
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117 -----------
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118 Input files
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119 -----------
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120
3
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121 +-----------------------------------------------------------+-----------+
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122 | Parameter : num + label | Format |
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123 +===========================================================+===========+
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124 | 1 : Rdata visCorVar.matCorAddVar output | rdata |
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125 +-----------------------------------------------------------+-----------+
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126 | 2 : \*_blocks_comb.tsv visCorVar.matCorAddVar output | tabular |
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127 +-----------------------------------------------------------+-----------+
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128 | 3 : \*_response_var.tsv visCorVar.matCorAddVar output | tabular |
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129 +-----------------------------------------------------------+-----------+
2
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130
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131 ----------
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132 Parameters
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133 ----------
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134
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135 @HELP_MANUAL@
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136
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137 ------------
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138 Output files
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139 ------------
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140
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141 viscorvar_circlecor.pdf
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142 Correlation circle pdf file
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143
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144 viscorvar_circlecor_selected_var.tsv
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145 List of selected variables which are contained in a rectangle of the correlation circle
2
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146
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147 ]]></help>
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148
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149 <expand macro="citations" />
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150
5
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151 </tool>