Mercurial > repos > ppericard > viscorvar

annotate viscorvar_circlecor.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
parents
children df8428358b7f
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1 <tool id="viscorvar_circlecor" name="visCorVar circleCor" version="@TOOL_VERSION@+galaxy1" 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
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33 <inputs>
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34 <param name="input_rdata" type="data" format="rdata"
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35 label="Input RData file"
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36 help="output RData from matCorAddVar"/>
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37 <param name="blocks_vec_list" type="data" format="tabular"
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38 label="List of blocks vector."
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39 help="output *_blocks_comb.tsv file from matCorAddVar"/>
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40 <param name="select_blocks" type="select"
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41 label="Blocks"
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42 help="list of the blocks that are to be superimposed">
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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="select 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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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 Bla bla...
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93
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94 -----------------
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95 Workflow position
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96 -----------------
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97
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98 **Upstream tools**
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99
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100 ======================== ===================================== ========
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101 Name Output file Format
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102 ======================== ===================================== ========
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103 visCorVar.matCorAddVar viscorvar_matcoraddvar_output.RData rdata
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104 ======================== ===================================== ========
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105
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106 **Downstream tools**
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107
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108 ====================== ====================================== =========
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109 Name Output file Format
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110 ====================== ====================================== =========
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111 visCorVar.networkVar viscorvar_circlecor_selected_var.tsv tabular
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112 ====================== ====================================== =========
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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 Input files
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118 -----------
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119
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120 +-------------------------------------------------------+-----------+
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121 | Parameter : num + label | Format |
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122 +=======================================================+===========+
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123 | 1 : Rdata visCorVar.matCorAddVar output | rdata |
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124 +-------------------------------------------------------+-----------+
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125 | 2 : \*_blocks_comb.tsv visCorVar.matCorAddVar output | tabular |
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126 +-------------------------------------------------------+-----------+
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127 | 3 : \*_response_var.tsv visCorVar.matCorAddVar output | tabular |
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128 +-------------------------------------------------------+-----------+
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129
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130 ----------
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131 Parameters
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132 ----------
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133
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134 @HELP_MANUAL@
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135
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136 ------------
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137 Output files
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138 ------------
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139
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140 viscorvar_circlecor.pdf
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141 Correlation circle pdf file
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142
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143 viscorvar_circlecor_selected_var.tsv
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144 List of variables selected in the correlation circle
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145
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146 ]]></help>
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147
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148 <expand macro="citations" />
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149
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150 </tool>