Mercurial > repos > ppericard > viscorvar

annotate viscorvar_matcoraddvar.xml @ 3:df8428358b7f draft

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"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit d930da2982ffb689ba4fdf7599c8971f8c52339d"
author ppericard
date Fri, 23 Oct 2020 11:26:18 +0000
parents c8533e9298e5
children d4e9f7546dfa
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1 <tool id="viscorvar_matcoraddvar" name="visCorVar matCorAddVar" version="@TOOL_VERSION@+galaxy1" 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_LOG_EXIT@
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32 ]]></command>
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34 <inputs>
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35 <param name="input_rdata" type="data" format="rdata"
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36 label="Input RData file from block.SPLSDA"
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37 help="This is the RData output file from the block.splsda function." />
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38 <param name="block_Y" type="data" format="tabular"
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39 label="Block Y"
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40 help="[block_Y] (tabular format) This table contains the name of the samples in the first column. The other columns correspond to phenotypes. For each of these other columns, a column determines which sample is associated with this phenotype (value equals to 1) or not (value equals to 0). The name 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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41 <!-- Fichier avec noms de gènes/variables, donné par l'utilisateur -->
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42 <param name="var_of_interest_file" type="data" format="txt" optional="true"
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43 label="Variables of interest (Optional)"
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44 help="variables not belonging to any block will not be considered"/>
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45 <!-- <param name="cutoff_comp" type="float" value="0.775" min="0" max="1"
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46 label="Cutoff comp"
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47 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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48 </inputs>
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49
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50 <outputs>
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51 <data name="output_rdata" format="rdata" label="${tool.name}_output.RData" />
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52 <data name="output_response_var" format="tabular" label="${tool.name}_response_var.tsv" />
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53 <data name="output_blocks_comb" format="tabular" label="${tool.name}_blocks_comb.tsv" />
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54 </outputs>
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56 <tests>
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57 </tests>
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59 <help><![CDATA[
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61 @HELP_AUTHORS@
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63 ======================
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64 visCorVar matCorAddVar
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65 ======================
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67 -----------
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68 Description
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69 -----------
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71 Bla bla...
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73 -----------------
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74 Workflow position
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75 -----------------
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77 **Upstream tools**
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79 ======================= =================================== ========
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80 Name Output file Format
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81 ======================= =================================== ========
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82 mixOmics.block.splsda mixomics_blocksplsda_output.RData rdata
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83 ======================= =================================== ========
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85 **Downstream tools**
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87 ================================ ========================================= ========
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88 Name Output file Format
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89 ================================ ========================================= ========
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90 visCorVar.circleCor viscorvar_matcoraddvar_output.RData rdata
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91 -------------------------------- ----------------------------------------- --------
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92 visCorVar.computeMatSimilarity viscorvar_matcoraddvar_output.RData rdata
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93 -------------------------------- ----------------------------------------- --------
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94 visCorVar.networkVar viscorvar_matcoraddvar_response_var.tsv tabular
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95 ================================ ========================================= ========
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96
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97 ---------------------------------------------------
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99 -----------
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100 Input files
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101 -----------
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102
3
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103 +-----------------------------------------+-----------+
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104 | Parameter : num + label | Format |
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105 +=========================================+===========+
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106 | 1 : Rdata mixOmics.block.splsda output | Rdata |
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107 +-----------------------------------------+-----------+
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108 | 2 : Block Y | tabular |
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109 +-----------------------------------------+-----------+
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110 | 3 : [opt] Variables of interest | txt |
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111 +-----------------------------------------+-----------+
2
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113 ----------
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114 Parameters
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115 ----------
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116
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117 @HELP_MANUAL@
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118
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119 ------------
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120 Output files
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121 ------------
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123 viscorvar_matcoraddvar_output.RData
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124 RData output
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125
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126 viscorvar_matcoraddvar_response_var.tsv
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129 viscorvar_matcoraddvar_blocks_comb.tsv
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132 ]]></help>
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134 <expand macro="citations" />
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136 </tool>