Mercurial > repos > artbio > cpm_tpm_rpk

annotate cpm_tpm_rpk.xml @ 2:563337e780ce draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
author artbio
date Wed, 06 Feb 2019 19:31:57 -0500
parents b74bab5157c4
children 8b1020c25f0f
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2
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
artbio
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1 <tool id="cpm_tpm_rpk" name="Generate CPM, TPM, RPK" version="0.3.0">
0
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2 <description>from raw counts expression values</description>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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3 <requirements>
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4 <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement>
1
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5 <requirement type="package" version="0.13=r3.3.2_0">r-rtsne</requirement>
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6 <requirement type="package" version="2.2.1=r3.3.2_0">r-ggplot2</requirement>
2
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7 <requirement type="package" version="0.4.1=r3.3.2_0">r-ggfortify</requirement>
0
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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8 </requirements>
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9 <stdio>
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10 <exit_code range="1:" level="fatal" description="Tool exception" />
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11 </stdio>
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12 <command detect_errors="exit_code"><![CDATA[
1
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13 Rscript $__tool_directory__/cpm_tpm_rpk.R
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14 -d $input
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15 -t $option.type_transfo
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16 -s $input_sep
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17 -c $input_header
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18 #if $option.type_transfo == "tpm":
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19 -f $option.gene_file
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20 --gene_sep $option.gene_sep
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21 --gene_header $option.gene_header
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22 #end if
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23 #if $option.type_transfo == "rpk":
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24 -f $option.gene_file
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25 --gene_sep $option.gene_sep
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26 --gene_header $option.gene_header
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27 #end if
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28 -l $log
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29 #if $log == "FALSE":
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30 -o ${output}
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31 #else if $log == "TRUE":
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32 -o ${output_log}
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33 #end if
2
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34 #if $visu_option.visualisation == "yes":
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35 --visu 'TRUE'
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36 #if $visu_option.tsne_labels == "yes":
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37 --tsne_labels 'TRUE'
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38 #else
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39 --tsne_labels 'FALSE'
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40 #end if
1
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41 --seed '$visu_option.seed'
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42 --perp '$visu_option.perp'
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43 --theta '$visu_option.theta'
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44 --tsne_out '$tsne_out'
2
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45 --pca_out '$pca_out'
1
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46 #end if
0
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47 ]]></command>
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48 <inputs>
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49 <param name="input" type="data" format="txt" label="Raw counts of expression data"/>
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50 <param name="input_sep" type="select" label="Input column separator">
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51 <option value="tab" selected="true">Tabs</option>
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52 <option value=",">Comma</option>
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53 <option value="\ ">Whitespace</option>
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54 <option value=".">Dots</option>
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55 <option value="_">Underscores</option>
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56 <option value="-">Dashes</option>
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57 </param>
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58 <param name="input_header" type="select" label="Consider first line of input file as header?">
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59 <option value="TRUE" selected="true">Yes</option>
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60 <option value="FALSE">No</option>
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61 </param>
1
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62 <conditional name="option">
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63 <param name="type_transfo" type="select" label="Type of transformation">
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64 <option value="cpm" selected="true">CPM</option>
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65 <option value="tpm">TPM</option>
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66 <option value="rpk">RPK</option>
0
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67 </param>
1
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68 <when value="tpm">
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69 <param name="gene_file" type="data" format="txt" label="Gene length file"/>
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70 <param name="gene_sep" type="select" label="Gene length column separator">
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71 <option value="tab" selected="true">Tabs</option>
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72 <option value=",">Commas</option>
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73 <option value="\ ">Whitespaces</option>
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74 <option value=".">Dots</option>
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75 <option value="_">Underscores</option>
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76 <option value="-">Dashes</option>
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77 </param>
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78 <param name="gene_header" type="select" label="Consider first line of gene length file as header ?">
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79 <option value="TRUE" selected="true">Yes</option>
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80 <option value="FALSE">No</option>
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81 </param>
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artbio
parents: 0
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82 </when>
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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83 <when value="rpk">
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
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84 <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
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85 <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
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86 <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
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87 <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
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88 <option value="\ ">Whitespaces</option>
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
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89 <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
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90 <option value="_">Underscores</option>
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
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91 <option value="-">Dashes</option>
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
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92 </param>
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
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93 <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
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94 <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
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95 <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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96 </param>
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
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97 </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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98 <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
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99 </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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100 </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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101 <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
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102 <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
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103 <option value="TRUE">Yes</option>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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104 </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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105 <conditional name="visu_option">
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
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106 <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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107 <option value="no" selected="true">No visualisation</option>
2
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artbio
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108 <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
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109 </param>
2
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
artbio
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110 <when value="yes">
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
artbio
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111 <param name="seed" value="49.0" type="float" label="Seed value for reproducibility" help="Set to 49 as default" />
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
artbio
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112 <param name="perp" value="10.0" type="float" label="perplexity" help="should be less than ((nbre observations)-1)/3" />
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
artbio
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113 <param name="theta" value="1.0" type="float" label="theta"/>
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
artbio
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114 <param name="tsne_labels" type="select" label="Add labels to points in the t-SNE plot" >
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
artbio
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115 <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
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116 <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
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117 </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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118 </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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119 <when value="no" />
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artbio
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120 </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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121 </inputs>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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122 <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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123 <data name="output" format="tabular" label="${option.type_transfo} from ${on_string}">
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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124 <filter>log == "FALSE"</filter>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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125 </data>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
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126 <data name="output_log" format="tabular" label="log2(${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
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127 <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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128 </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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129 <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
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130 <filter>visu_option['visualisation'] == 'yes'</filter>
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131 </data>
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
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132 <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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133 <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
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134 </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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135 </outputs>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
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136 <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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137 <!-- test t-SNE -->
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138 <test>
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
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139 <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
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140 <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
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141 <param name="log" value="TRUE"/>
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
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142 <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
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143 <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
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144 <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
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145 <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
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146 <param name="tsne_labels" value="yes" />
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147 <output name="output" file="logcpm.tab" ftype="tabular"/>
1
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
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148 <output name="tsne_out" file="tsne.pdf" ftype="pdf"/>
2
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
artbio
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149 <output name="pca_out" file="pca.pdf" ftype="pdf"/>
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150 </test>
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151 <test>
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artbio
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152 <param name="input" value="counts.tab" ftype="tabular"/>
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
artbio
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153 <param name="type_transfo" value="tpm"/>
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artbio
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154 <param name="gene_file" value="gene_length.tab" ftype="tabular"/>
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
artbio
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155 <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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156 <param name="visualisation" value="yes"/>
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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157 <param name="seed" value="49"/>
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
artbio
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158 <param name="perp" value="2"/>
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="theta" value="1" />
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
artbio
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160 <param name="tsne_labels" value="no" />
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
artbio
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161 <output name="output" file="logtpm.tab" ftype="tabular"/>
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
artbio
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162 <output name="tsne_out" file="tsne.nolab.pdf" ftype="pdf"/>
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
artbio
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163 <output name="pca_out" file="pca.nolab.pdf" ftype="pdf"/>
1
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
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164 </test>
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165 <!-- test without t-SNE -->
0
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166 <test>
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167 <param name="input" value="counts.tab" ftype="tabular"/>
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168 <param name="type_transfo" value="cpm"/>
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169 <output name="output" file="cpm.tab" ftype="tabular"/>
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170 </test>
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171 <test>
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172 <param name="input" value="counts.tab" ftype="tabular"/>
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173 <param name="type_transfo" value="cpm"/>
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174 <param name="log" value="TRUE"/>
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175 <output name="output" file="logcpm.tab" ftype="tabular"/>
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176 </test>
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177 <test>
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178 <param name="input" value="counts.tab" ftype="tabular"/>
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179 <param name="type_transfo" value="tpm"/>
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180 <param name="gene_file" value="gene_length.tab" ftype="tabular"/>
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181 <param name="gene_header" value="TRUE"/>
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182 <output name="output" file="tpm.tab" ftype="tabular"/>
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183 </test>
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184 <test>
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185 <param name="input" value="counts.tab" ftype="tabular"/>
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186 <param name="type_transfo" value="tpm"/>
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187 <param name="gene_file" value="gene_length.tab" ftype="tabular"/>
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188 <param name="gene_header" value="TRUE"/>
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189 <param name="log" value="TRUE"/>
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190 <output name="output" file="logtpm.tab" ftype="tabular"/>
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191 </test>
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192 <test>
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193 <param name="input" value="counts.tab" ftype="tabular"/>
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194 <param name="type_transfo" value="rpk"/>
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195 <param name="gene_file" value="gene_length.tab" ftype="tabular"/>
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196 <param name="gene_header" value="TRUE"/>
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197 <output name="output" file="rpk.tab" ftype="tabular"/>
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198 </test>
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199 <test>
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200 <param name="input" value="counts.tab" ftype="tabular"/>
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201 <param name="type_transfo" value="rpk"/>
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202 <param name="gene_file" value="gene_length.tab" ftype="tabular"/>
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203 <param name="gene_header" value="TRUE"/>
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204 <param name="log" value="TRUE"/>
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205 <output name="output" file="logrpk.tab" ftype="tabular"/>
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206 </test>
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207 </tests>
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208 <help>
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209
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210 **What it does**
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211
1
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212 Takes a raw count expression matrix and returns a table of normalized expression values.
0
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213
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214 Normalization can be:
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215
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216 - 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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217 - RPK (Reads Per Kilobases) are obtained by dividing read counts by gene lengths (expressed in kilo-nucleotides).
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218 - 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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219
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220 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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221
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222 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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223
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224 Computed values may be log-transformed (log2([CPM or RPK or TPM]+1))
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225
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226 </help>
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227 </tool>