Mercurial > repos > nml > csvtk_correlation

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"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
author nml
date Tue, 19 May 2020 17:25:59 -0400
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0
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1 <tool id="csvtk_correlation" name="csvtk-correlation" version="@VERSION@+@GALAXY_VERSION@">
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2 <description> calculate pearson correlation</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="version_cmd" />
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8 <command detect_errors="exit_code"><![CDATA[
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9
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10 ###################
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11 ## Start Command ##
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12 ###################
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13
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14 csvtk corr --num-cpus "\${GALAXY_SLOTS:-1}"
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15
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16 ## Add additional flags as specified ##
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17 #######################################
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18 $global_param.illegal_rows
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19 $global_param.empty_rows
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20 $global_param.header
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21 $global_param.lazy_quotes
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22
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23 ## Set Tabular input/output flag if input is tabular ##
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24 #######################################################
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25 #if $in_1.is_of_type("tabular"):
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26 -t -T
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27 #end if
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28
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29 ## Specify fields ##
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30 ####################
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31 -f '$in_text'
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32
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33 ## Set Input ##
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34 ###############
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35 '$in_1'
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36
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37 ## other ##
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38 ###########
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39 $ignore_nan
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40 $log_values
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41 $passthrough
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42
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43 ## To output ##
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44 ###############
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45 &> corr
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46
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47 ]]></command>
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48 <inputs>
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49 <expand macro="singular_input" />
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50 <param name="in_text" type="text" argument="-f"
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51 label="Specify *two* column names"
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52 help="Input the exact spelling of the two input column names wanted with a comma (,) separating them. Ex. 'Length,GC Content'">
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53 <expand macro="text_sanitizer" />
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54 </param>
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55 <param name="ignore_nan" type="boolean" checked="false" argument="-i"
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56 truevalue="-i"
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57 falsevalue=""
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58 label="Ignore non-numeric values in columns"
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59 help="Needed to be set to yes to avoid returning NaN if there is a non-numeric value"
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60 />
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61 <param name="log_values" type="boolean" checked="false" argument="-L"
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62 truevalue="-L"
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63 falsevalue=""
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64 label="Log10 transformed Data"
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65 help="Calcute correlations on Log10 transformed data"
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66 />
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67 <param name="passthrough" type="boolean" checked="false" argument="-x"
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68 truevalue="-x"
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69 falsevalue=""
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70 label="passthrough mode (forward input to output)"
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71 />
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72 <expand macro="global_parameters" />
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73 </inputs>
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74 <outputs>
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75 <data format_source="in_1" name="corr" from_work_dir="corr" label="${in_1.name} correlation of ${in_text}" />
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76 </outputs>
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77 <tests>
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78 <test>
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79 <param name="in_1" value="XY_converted.csv" />
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80 <param name="in_text" value="X,Y" />
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81 <output name="corr" value="corr_1.csv" />
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82 </test>
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83 <test>
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84 <param name="in_1" value="XY_converted.tsv" />
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85 <param name="in_text" value="X,Y" />
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86 <param name="ignore_nan" value="true" />
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87 <param name="log_values" value="true" />
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88 <param name="passthrough" value="true" />
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89 <output name="corr" value="corr_2.tsv" />
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90 </test>
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91 </tests>
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92 <help><![CDATA[
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93
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94 Csvtk - Correlation Help
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95 ------------------------
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96
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97 Info
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98 ####
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99
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100 Csvtk Correlation calculates the pearson correlation between two columns specified by the column header
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101
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102 .. class:: warningmark
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103
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104 Single quotes are not allowed in text inputs!
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105
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106 @HELP_INPUT_DATA@
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107
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108
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109 Usage
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110 #####
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111
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112 To run csvtk-correlation, all you need is a valid (as defined above) CSV or TSV file with two numeric columns that you want to
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113 find the pearson correlation between. If the input data is Log10 transformed, remember to set the "Log10 transformed Data"
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114 slider to "Yes"
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115
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116 Output will be a singular line with the input column names, and the pearson correlation (integer between -1 to 1).
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117
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118
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119 **Example Correlation Input**
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120
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121 Input table:
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122
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123 +-------+--------+
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124 | Group | Length |
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125 +=======+========+
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126 | 1 | 1500 |
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127 +-------+--------+
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128 | 2 | 1000 |
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129 +-------+--------+
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130 | 1 | 1500 |
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131 +-------+--------+
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132 | 3 | 2000 |
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133 +-------+--------+
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134
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135 Our input for this would require us to specify our column input (-f) as "Group,Length" to allow the program to run
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136
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137 Our output would then look as such:
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138
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139 +-------+--------+--------+
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140 | Group | Length | 0.9999 |
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141 +-------+--------+--------+
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142
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143 --------
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144
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145
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146 @HELP_COLUMNS@
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147
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148
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149 @HELP_END_STATEMENT@
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150
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151
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152 ]]></help>
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153 <expand macro="citations" />
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154 </tool>