Mercurial > repos > nml > csvtk_correlation
annotate corr.xml @ 0:62448f26c3fa draft default tip
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
author | nml |
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date | Tue, 19 May 2020 17:25:59 -0400 |
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0
62448f26c3fa
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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1 <tool id="csvtk_correlation" name="csvtk-correlation" version="@VERSION@+@GALAXY_VERSION@"> |
62448f26c3fa
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2 <description> calculate pearson correlation</description> |
62448f26c3fa
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3 <macros> |
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4 <import>macros.xml</import> |
62448f26c3fa
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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}" |
62448f26c3fa
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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 |
62448f26c3fa
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19 $global_param.empty_rows |
62448f26c3fa
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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20 $global_param.header |
62448f26c3fa
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21 $global_param.lazy_quotes |
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22 |
62448f26c3fa
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23 ## Set Tabular input/output flag if input is tabular ## |
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"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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24 ####################################################### |
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25 #if $in_1.is_of_type("tabular"): |
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26 -t -T |
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27 #end if |
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28 |
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29 ## Specify fields ## |
62448f26c3fa
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30 #################### |
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31 -f '$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 |
62448f26c3fa
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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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> |