Mercurial > repos > artbio > gsc_cpm_tpm_rpk

annotate cpm_tpm_rpk.xml @ 0:ce3d027ec26b draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_cpm_tpm_rpk commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
author artbio
date Mon, 24 Jun 2019 13:37:16 -0400
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children 46507a10106c
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ce3d027ec26b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_cpm_tpm_rpk commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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1 <tool id="cpm_tpm_rpk" name="Generate CPM, TPM, RPK" version="0.9.0">
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2 <description>from raw counts expression values</description>
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3 <requirements>
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4 <requirement type="package" version="1.6.0">r-optparse</requirement>
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5 </requirements>
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6 <stdio>
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7 <exit_code range="1:" level="fatal" description="Tool exception" />
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8 </stdio>
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9 <command detect_errors="exit_code"><![CDATA[
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10 Rscript $__tool_directory__/cpm_tpm_rpk.R
ce3d027ec26b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_cpm_tpm_rpk commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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11 --data '$input'
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12 --type '$option.type_transfo'
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13 --sep '$input_sep'
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14 --colnames '$input_header'
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15 #if $option.type_transfo == "tpm":
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16 -f '$option.gene_file'
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17 --gene_sep $option.gene_sep
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18 --gene_header $option.gene_header
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19 #end if
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20 #if $option.type_transfo == "rpk":
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21 -f '$option.gene_file'
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22 --gene_sep '$option.gene_sep'
ce3d027ec26b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_cpm_tpm_rpk commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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23 --gene_header '$option.gene_header'
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24 #end if
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25 --log '$log'
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26 #if $log == "FALSE":
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27 -o ${output}
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28 #else if $log == "TRUE":
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29 -o ${output_log}
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30 #end if
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31 ]]></command>
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32 <inputs>
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33 <param name="input" type="data" format="txt,tabular" label="Raw counts of expression data"/>
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34 <param name="input_sep" type="select" label="Input column separator">
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35 <option value="tab" selected="true">Tabulation</option>
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36 <option value=",">Comma</option>
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37 </param>
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38 <param name="input_header" type="select" label="Consider first line of input file as header?">
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39 <option value="TRUE" selected="true">Yes</option>
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40 <option value="FALSE">No</option>
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41 </param>
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42 <conditional name="option">
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43 <param name="type_transfo" type="select" label="Type of transformation">
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44 <option value="cpm" selected="true">CPM</option>
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45 <option value="tpm">TPM</option>
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46 <option value="rpk">RPK</option>
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47 </param>
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48 <when value="tpm">
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49 <param name="gene_file" type="data" format="txt,tabular" label="Gene length file"/>
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50 <param name="gene_sep" type="select" label="Gene length column separator">
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51 <option value="tab" selected="true">Tabulation</option>
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52 <option value=",">Commas</option>
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53 </param>
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54 <param name="gene_header" type="select" label="Consider first line of gene length file as header ?">
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55 <option value="TRUE" selected="true">Yes</option>
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56 <option value="FALSE">No</option>
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57 </param>
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58 </when>
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59 <when value="rpk">
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60 <param name="gene_file" type="data" format="txt,tabular" label="Gene length file"/>
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61 <param name="gene_sep" type="select" label="Gene length column separator">
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62 <option value="tab" selected="true">Tabs</option>
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63 <option value=",">Commas</option>
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64 </param>
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65 <param name="gene_header" type="select" label="Consider first line of gene length file as header ?">
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66 <option value="TRUE" selected="true">Yes</option>
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67 <option value="FALSE">No</option>
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68 </param>
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69 </when>
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70 <when value="cpm">
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71 </when>
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72 </conditional>
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73 <param name="log" type="select" label="Data should be log transformed ?">
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74 <option value="FALSE" selected="true">No</option>
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75 <option value="TRUE">Yes</option>
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76 </param>
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77 </inputs>
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78 <outputs>
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79 <data name="output" format="tabular" label="${option.type_transfo} from ${on_string}">
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80 <filter>log == "FALSE"</filter>
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81 </data>
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82 <data name="output_log" format="tabular" label="log2(${option.type_transfo} +1) from ${on_string}">
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83 <filter>log == "TRUE"</filter>
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84 </data>
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85 </outputs>
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86 <tests>
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87 <test>
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88 <param name="input" value="counts.tab" ftype="tabular"/>
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89 <param name="type_transfo" value="cpm"/>
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90 <param name="log" value="TRUE"/>
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91 <output name="output" file="logcpm.tab" ftype="tabular"/>
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92 </test>
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93 <test>
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94 <param name="input" value="counts.tab" ftype="tabular"/>
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95 <param name="type_transfo" value="tpm"/>
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96 <param name="gene_file" value="gene_length.tab" ftype="tabular"/>
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97 <param name="log" value="TRUE"/>
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98 <output name="output" file="logtpm.tab" ftype="tabular"/>
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99 </test>
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100 <!-- test without t-SNE -->
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101 <test>
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102 <param name="input" value="counts.tab" ftype="tabular"/>
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103 <param name="type_transfo" value="cpm"/>
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104 <output name="output" file="cpm.tab" ftype="tabular"/>
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105 </test>
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106 <test>
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107 <param name="input" value="counts.tab" ftype="tabular"/>
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108 <param name="type_transfo" value="tpm"/>
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109 <param name="gene_file" value="gene_length.tab" ftype="tabular"/>
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110 <param name="gene_header" value="TRUE"/>
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111 <output name="output" file="tpm.tab" ftype="tabular"/>
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112 </test>
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113 <test>
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114 <param name="input" value="counts.tab" ftype="tabular"/>
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115 <param name="type_transfo" value="rpk"/>
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116 <param name="gene_file" value="gene_length.tab" ftype="tabular"/>
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117 <param name="gene_header" value="TRUE"/>
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118 <output name="output" file="rpk.tab" ftype="tabular"/>
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119 </test>
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120 <test>
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121 <param name="input" value="counts.tab" ftype="tabular"/>
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122 <param name="type_transfo" value="rpk"/>
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123 <param name="gene_file" value="gene_length.tab" ftype="tabular"/>
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124 <param name="gene_header" value="TRUE"/>
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125 <param name="log" value="TRUE"/>
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126 <output name="output" file="logrpk.tab" ftype="tabular"/>
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127 </test>
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128 </tests>
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129 <help>
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130
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131 **What it does**
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132
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133 Takes a raw count expression matrix and returns a table of normalized expression values.
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134
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135 Normalization can be:
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136
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137 - CPM (Counts Per Million) are obtained by dividing counts by the library counts sum and multiplying the results by a million.
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138 - RPK (Reads Per Kilobases) are obtained by dividing read counts by gene lengths (expressed in kilo-nucleotides).
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139 - TPM (Transcripts Per Million) are obtained by dividing RPK values by the sum of all RPK values in a sample and multiplying the results by 1 million.
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140
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141 RPK and TPM require a two-column correspondance table gene_name - gene length where the length is specified in nucleotide. Both these metrics are relevant only for sequencing of full length RNAs.
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142
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143 Note: First header row must NOT start with a '#' comment character
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144
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145 Computed values may be base-2 log-transformed (log2([CPM or RPK or TPM]+1))
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146
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147 </help>
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148 <citations>
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149 <citation type="bibtex">
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150 @Manual{,
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151 title = {R: A Language and Environment for Statistical Computing},
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152 author = {{R Core Team}},
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153 organization = {R Foundation for Statistical Computing},
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154 address = {Vienna, Austria},
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155 year = {2014},
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156 url = {http://www.R-project.org/},
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157 }
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158 </citation>
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159 </citations>
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160 </tool>