Mercurial > repos > artbio > cpm_tpm_rpk

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk commit 8cca5f05212cd25113955fb9c11801f4047c12b4
author artbio
date Wed, 03 Jul 2024 14:39:26 +0000
parents d2575928b824
children
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7
f00c1c34565e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk commit 8cca5f05212cd25113955fb9c11801f4047c12b4
artbio
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1 <tool id="cpm_tpm_rpk" name="Generate CPM, TPM, RPKM" version="0.6.0">
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="1.7.5">r-optparse</requirement>
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5 <requirement type="package" version="0.17">r-rtsne</requirement>
f00c1c34565e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk commit 8cca5f05212cd25113955fb9c11801f4047c12b4
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6 <requirement type="package" version="3.5.1">r-ggplot2</requirement>
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7 <requirement type="package" version="0.4.17">r-ggfortify</requirement>
4
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8 <requirement type="package" version="1.4.4">r-reshape2</requirement>
0
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9 </requirements>
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10 <stdio>
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11 <exit_code range="1:" level="fatal" description="Tool exception" />
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12 </stdio>
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13 <command detect_errors="exit_code"><![CDATA[
1
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14 Rscript $__tool_directory__/cpm_tpm_rpk.R
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15 -d $input
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16 -t $option.type_transfo
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17 -s $input_sep
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18 -c $input_header
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19 #if $option.type_transfo == "tpm":
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20 -f $option.gene_file
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21 --gene_sep $option.gene_sep
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22 --gene_header $option.gene_header
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23 #end if
7
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24 #if $option.type_transfo == "rpkm":
1
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25 -f $option.gene_file
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26 --gene_sep $option.gene_sep
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27 --gene_header $option.gene_header
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28 #end if
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29 -l $log
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30 #if $log == "FALSE":
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31 -o ${output}
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32 #else if $log == "TRUE":
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33 -o ${output_log}
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34 #end if
2
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35 #if $visu_option.visualisation == "yes":
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36 --visu 'TRUE'
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37 #if $visu_option.tsne_labels == "yes":
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38 --tsne_labels 'TRUE'
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39 #else
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40 --tsne_labels 'FALSE'
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41 #end if
1
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42 --seed '$visu_option.seed'
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43 --perp '$visu_option.perp'
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44 --theta '$visu_option.theta'
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45 --tsne_out '$tsne_out'
2
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46 --pca_out '$pca_out'
1
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47 #end if
0
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48 ]]></command>
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49 <inputs>
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50 <param name="input" type="data" format="txt" label="Raw counts of expression data"/>
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51 <param name="input_sep" type="select" label="Input column separator">
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52 <option value="tab" selected="true">Tabs</option>
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53 <option value=",">Comma</option>
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54 <option value="\ ">Whitespace</option>
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55 <option value=".">Dots</option>
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56 <option value="_">Underscores</option>
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57 <option value="-">Dashes</option>
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58 </param>
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59 <param name="input_header" type="select" label="Consider first line of input file as header?">
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60 <option value="TRUE" selected="true">Yes</option>
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61 <option value="FALSE">No</option>
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62 </param>
1
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63 <conditional name="option">
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64 <param name="type_transfo" type="select" label="Type of transformation">
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65 <option value="cpm" selected="true">CPM</option>
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66 <option value="tpm">TPM</option>
7
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67 <option value="rpkm">RPKM</option>
3
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68 <option value="none">NONE</option>
0
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69 </param>
1
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70 <when value="tpm">
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71 <param name="gene_file" type="data" format="txt" label="Gene length file"/>
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72 <param name="gene_sep" type="select" label="Gene length column separator">
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73 <option value="tab" selected="true">Tabs</option>
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74 <option value=",">Commas</option>
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75 <option value="\ ">Whitespaces</option>
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76 <option value=".">Dots</option>
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77 <option value="_">Underscores</option>
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78 <option value="-">Dashes</option>
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79 </param>
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80 <param name="gene_header" type="select" label="Consider first line of gene length file as header ?">
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81 <option value="TRUE" selected="true">Yes</option>
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82 <option value="FALSE">No</option>
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artbio
parents: 0
diff changeset
83 </param>
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
84 </when>
7
f00c1c34565e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk commit 8cca5f05212cd25113955fb9c11801f4047c12b4
artbio
parents: 6
diff changeset
85 <when value="rpkm">
1
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
86 <param name="gene_file" type="data" format="txt" label="Gene length file"/>
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
87 <param name="gene_sep" type="select" label="Gene length column separator">
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
88 <option value="tab" selected="true">Tabs</option>
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
89 <option value=",">Commas</option>
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
90 <option value="\ ">Whitespaces</option>
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
91 <option value=".">Dots</option>
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
92 <option value="_">Underscores</option>
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
93 <option value="-">Dashes</option>
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
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94 </param>
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
95 <param name="gene_header" type="select" label="Consider first line of gene length file as header ?">
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
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96 <option value="TRUE" selected="true">Yes</option>
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
97 <option value="FALSE">No</option>
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
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98 </param>
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
99 </when>
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
100 <when value="cpm">
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
101 </when>
3
8b1020c25f0f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 9149001c65de633ddfd2f91cf208074e40482ce3
artbio
parents: 2
diff changeset
102 <when value="none">
8b1020c25f0f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 9149001c65de633ddfd2f91cf208074e40482ce3
artbio
parents: 2
diff changeset
103 </when>
1
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
104 </conditional>
0
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
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105 <param name="log" type="select" label="Data should be log transformed ?">
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
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106 <option value="FALSE" selected="true">No</option>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
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107 <option value="TRUE">Yes</option>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
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108 </param>
1
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
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109 <conditional name="visu_option">
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
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110 <param name="visualisation" type="select" label="Visualisation of data with various dimensionality reduction methods" >
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
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111 <option value="no" selected="true">No visualisation</option>
2
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artbio
parents: 1
diff changeset
112 <option value="yes" >t-SNE and PCA</option>
1
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
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113 </param>
2
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
artbio
parents: 1
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114 <when value="yes">
3
8b1020c25f0f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 9149001c65de633ddfd2f91cf208074e40482ce3
artbio
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115 <param name="seed" value="49.0" type="float" label="Seed value for reproducibility of t-SNE" help="Set to 49 as default" />
8b1020c25f0f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 9149001c65de633ddfd2f91cf208074e40482ce3
artbio
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116 <param name="perp" value="10.0" type="float" label="perplexity (t-SNE)" help="should be less than ((nbre observations)-1)/3" />
8b1020c25f0f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 9149001c65de633ddfd2f91cf208074e40482ce3
artbio
parents: 2
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117 <param name="theta" value="1.0" type="float" label="theta (t-SNE)"/>
8b1020c25f0f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 9149001c65de633ddfd2f91cf208074e40482ce3
artbio
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118 <param name="tsne_labels" type="select" label="Add labels to points plots" >
2
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
artbio
parents: 1
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119 <option value="no" selected="true">No Labels</option>
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
artbio
parents: 1
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120 <option value="yes" >Label points</option>
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
artbio
parents: 1
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121 </param>
1
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
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122 </when>
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
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123 <when value="no" />
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
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124 </conditional>
0
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
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125 </inputs>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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126 <outputs>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
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127 <data name="output" format="tabular" label="${option.type_transfo} from ${on_string}">
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
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128 <filter>log == "FALSE"</filter>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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129 </data>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
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130 <data name="output_log" format="tabular" label="log2(${option.type_transfo} +1) from ${on_string}">
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
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131 <filter>log == "TRUE"</filter>
1
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
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132 </data>
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
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133 <data name="tsne_out" format="pdf" label="tsne from ${on_string}">
2
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
artbio
parents: 1
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134 <filter>visu_option['visualisation'] == 'yes'</filter>
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135 </data>
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
artbio
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136 <data name="pca_out" format="pdf" label="PCA from ${on_string}">
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
artbio
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137 <filter>visu_option['visualisation'] == 'yes'</filter>
1
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
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138 </data>
0
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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139 </outputs>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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140 <tests>
1
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
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141 <!-- test t-SNE -->
4
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artbio
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142 <test expect_num_outputs="3">
3
8b1020c25f0f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 9149001c65de633ddfd2f91cf208074e40482ce3
artbio
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143 <param name="input" value="none.tab" ftype="tabular"/>
8b1020c25f0f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 9149001c65de633ddfd2f91cf208074e40482ce3
artbio
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144 <param name="type_transfo" value="none"/>
8b1020c25f0f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 9149001c65de633ddfd2f91cf208074e40482ce3
artbio
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145 <param name="log" value="FALSE"/>
8b1020c25f0f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 9149001c65de633ddfd2f91cf208074e40482ce3
artbio
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146 <param name="visualisation" value="yes"/>
8b1020c25f0f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 9149001c65de633ddfd2f91cf208074e40482ce3
artbio
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147 <param name="seed" value="49"/>
8b1020c25f0f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 9149001c65de633ddfd2f91cf208074e40482ce3
artbio
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148 <param name="perp" value="10"/>
8b1020c25f0f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 9149001c65de633ddfd2f91cf208074e40482ce3
artbio
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diff changeset
149 <param name="theta" value="1" />
8b1020c25f0f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 9149001c65de633ddfd2f91cf208074e40482ce3
artbio
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150 <param name="tsne_labels" value="yes" />
4
be358a1ebf67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit a8486c89b7ddabfb1e814c2c42f6c04d3896904c
artbio
parents: 3
diff changeset
151 <output name="output" file="none.tab" ftype="tabular" />
be358a1ebf67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit a8486c89b7ddabfb1e814c2c42f6c04d3896904c
artbio
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152 <output name="tsne_out" file="none_tsne.pdf" ftype="pdf" compare="sim_size" delta="1000" />
be358a1ebf67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit a8486c89b7ddabfb1e814c2c42f6c04d3896904c
artbio
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153 <output name="pca_out" file="none_pca.pdf" ftype="pdf" />
3
8b1020c25f0f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 9149001c65de633ddfd2f91cf208074e40482ce3
artbio
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154 </test>
4
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artbio
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155 <test expect_num_outputs="3">
1
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artbio
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156 <param name="input" value="counts.tab" ftype="tabular"/>
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
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157 <param name="type_transfo" value="cpm"/>
2
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
artbio
parents: 1
diff changeset
158 <param name="log" value="TRUE"/>
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
artbio
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159 <param name="visualisation" value="yes"/>
1
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
160 <param name="seed" value="49"/>
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
161 <param name="perp" value="2"/>
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
162 <param name="theta" value="1" />
2
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
artbio
parents: 1
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163 <param name="tsne_labels" value="yes" />
4
be358a1ebf67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit a8486c89b7ddabfb1e814c2c42f6c04d3896904c
artbio
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diff changeset
164 <output name="output" file="logcpm.tab" ftype="tabular" />
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artbio
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165 <output name="tsne_out" file="tsne.pdf" ftype="pdf" compare="sim_size" delta="1000" />
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166 <output name="pca_out" file="pca.pdf" ftype="pdf" />
2
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167 </test>
4
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168 <test expect_num_outputs="3">
2
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169 <param name="input" value="counts.tab" ftype="tabular"/>
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170 <param name="type_transfo" value="tpm"/>
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171 <param name="gene_file" value="gene_length.tab" ftype="tabular"/>
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172 <param name="log" value="TRUE"/>
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173 <param name="visualisation" value="yes"/>
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174 <param name="seed" value="49"/>
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175 <param name="perp" value="2"/>
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176 <param name="theta" value="1" />
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177 <param name="tsne_labels" value="no" />
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178 <output name="output" file="logtpm.tab" ftype="tabular" />
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179 <output name="tsne_out" file="tsne.nolab.pdf" ftype="pdf" compare="sim_size" delta="1000" />
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180 <output name="pca_out" file="pca.nolab.pdf" ftype="pdf" />
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181 </test>
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182 <!-- test without t-SNE -->
4
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183 <test expect_num_outputs="1">
0
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184 <param name="input" value="counts.tab" ftype="tabular"/>
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185 <param name="type_transfo" value="cpm"/>
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186 <output name="output" file="cpm.tab" ftype="tabular"/>
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187 </test>
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188 <test expect_num_outputs="1">
0
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189 <param name="input" value="counts.tab" ftype="tabular"/>
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190 <param name="type_transfo" value="cpm"/>
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191 <param name="log" value="TRUE"/>
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192 <output name="output" file="logcpm.tab" ftype="tabular" />
0
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193 </test>
4
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194 <test expect_num_outputs="1">
0
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195 <param name="input" value="counts.tab" ftype="tabular"/>
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196 <param name="type_transfo" value="tpm"/>
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197 <param name="gene_file" value="gene_length.tab" ftype="tabular"/>
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198 <param name="gene_header" value="TRUE"/>
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199 <output name="output" file="tpm.tab" ftype="tabular"/>
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200 </test>
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201 <test expect_num_outputs="1">
0
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202 <param name="input" value="counts.tab" ftype="tabular"/>
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203 <param name="type_transfo" value="tpm"/>
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204 <param name="gene_file" value="gene_length.tab" ftype="tabular"/>
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205 <param name="gene_header" value="TRUE"/>
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206 <param name="log" value="TRUE"/>
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207 <output name="output" file="logtpm.tab" ftype="tabular" />
0
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208 </test>
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209 <test expect_num_outputs="1">
0
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210 <param name="input" value="counts.tab" ftype="tabular"/>
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211 <param name="type_transfo" value="rpkm"/>
0
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212 <param name="gene_file" value="gene_length.tab" ftype="tabular"/>
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213 <param name="gene_header" value="TRUE"/>
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214 <output name="output" file="rpkm.tab" ftype="tabular" />
0
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215 </test>
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216 <test expect_num_outputs="1">
0
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217 <param name="input" value="counts.tab" ftype="tabular"/>
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218 <param name="type_transfo" value="rpkm"/>
0
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219 <param name="gene_file" value="gene_length.tab" ftype="tabular"/>
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220 <param name="gene_header" value="TRUE"/>
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221 <param name="log" value="TRUE"/>
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222 <output name="output" file="logrpkm.tab" ftype="tabular" />
0
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223 </test>
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224 </tests>
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225 <help>
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226
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227 **What it does**
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228
1
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229 Takes a raw count expression matrix and returns a table of normalized expression values.
0
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230
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231 Normalization can be:
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232
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233 - 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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234 - RPK (Reads Per Kilobase) are obtained by dividing read counts by gene lengths (expressed as kilo-nucleotides).
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235 - RPKM (Reads Per Kilobase per Million of Counts) are obtained by dividing read counts by gene lengths (expressed in kilo-nucleotides) then by the sum of library counts (expressed as millions of reads)
0
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236 - 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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237
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238 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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239
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240 Note: do not comment you header line if you have header line in you tabular input (ie do not start the header line with a '#' character)
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241
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242 Computed values may be log-transformed (log2([CPM or RPK or TPM]+1))
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243
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244 </help>
4
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245 <citations>
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246 <citation type="bibtex">@Article{,
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247 title = {Visualizing High-Dimensional Data Using t-SNE},
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248 volume = {9},
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249 pages = {2579-2605},
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250 year = {2008},
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251 author = {L.J.P. {van der Maaten} and G.E. Hinton},
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252 journal = {Journal of Machine Learning Research},
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253 }
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254 </citation>
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255 <citation type="bibtex">@Manual{,
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256 title = {{ClusterR}: Gaussian Mixture Models, K-Means, Mini-Batch-Kmeans,
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257 K-Medoids and Affinity Propagation Clustering},
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258 author = {Lampros Mouselimis},
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259 year = {2019},
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260 note = {R package version 1.1.9},
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261 url = {https://github.com/mlampros/ClusterR},
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262 }
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263 </citation>
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264 </citations>
0
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265 </tool>