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comparison cpm_tpm_rpk.xml @ 1:b74bab5157c4 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
author artbio
date Tue, 05 Feb 2019 19:51:38 -0500
parents 35d032c46a4e
children 563337e780ce
comparison
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0:35d032c46a4e 1:b74bab5157c4
1 <tool id="cpm_tpm_rpk" name="Generate CPM, TPM, RPK" version="0.1.0"> 1 <tool id="cpm_tpm_rpk" name="Generate CPM, TPM, RPK" version="0.2.0">
2 <description>from raw counts expression values</description> 2 <description>from raw counts expression values</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement> 4 <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement>
5 <requirement type="package" version="0.13=r3.3.2_0">r-rtsne</requirement>
6 <requirement type="package" version="2.2.1=r3.3.2_0">r-ggplot2</requirement>
5 </requirements> 7 </requirements>
6 <stdio> 8 <stdio>
7 <exit_code range="1:" level="fatal" description="Tool exception" /> 9 <exit_code range="1:" level="fatal" description="Tool exception" />
8 </stdio> 10 </stdio>
9 <command detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
10 Rscript $__tool_directory__/cpm_tpm_rpk.R 12 Rscript $__tool_directory__/cpm_tpm_rpk.R
11 -d $input 13 -d $input
12 -t $option.type_transfo 14 -t $option.type_transfo
13 -s $input_sep 15 -s $input_sep
14 -c $input_header 16 -c $input_header
15 #if $option.type_transfo == "tpm": 17 #if $option.type_transfo == "tpm":
16 -f $option.gene_file 18 -f $option.gene_file
17 --gene_sep $option.gene_sep 19 --gene_sep $option.gene_sep
18 --gene_header $option.gene_header 20 --gene_header $option.gene_header
19 #end if 21 #end if
20 #if $option.type_transfo == "rpk": 22 #if $option.type_transfo == "rpk":
21 -f $option.gene_file 23 -f $option.gene_file
22 --gene_sep $option.gene_sep 24 --gene_sep $option.gene_sep
23 --gene_header $option.gene_header 25 --gene_header $option.gene_header
24 #end if 26 #end if
25 -l $log 27 -l $log
26 #if $log == "FALSE": 28 #if $log == "FALSE":
27 -o ${output} 29 -o ${output}
28 #end if 30 #else if $log == "TRUE":
29 #if $log == "TRUE": 31 -o ${output_log}
30 -o ${output_log} 32 #end if
31 #end if 33 #if $visu_option.visualisation == "tsne":
34 --tsne 'TRUE'
35 --seed '$visu_option.seed'
36 --perp '$visu_option.perp'
37 --theta '$visu_option.theta'
38 --tsne_out '$tsne_out'
39 #end if
32 ]]></command> 40 ]]></command>
33 <inputs> 41 <inputs>
34 <param name="input" type="data" format="txt" label="Raw counts of expression data"/> 42 <param name="input" type="data" format="txt" label="Raw counts of expression data"/>
35 <param name="input_sep" type="select" label="Input column separator"> 43 <param name="input_sep" type="select" label="Input column separator">
36 <option value="tab" selected="true">Tabs</option> 44 <option value="tab" selected="true">Tabs</option>
42 </param> 50 </param>
43 <param name="input_header" type="select" label="Consider first line of input file as header?"> 51 <param name="input_header" type="select" label="Consider first line of input file as header?">
44 <option value="TRUE" selected="true">Yes</option> 52 <option value="TRUE" selected="true">Yes</option>
45 <option value="FALSE">No</option> 53 <option value="FALSE">No</option>
46 </param> 54 </param>
47 <conditional name="option"> 55 <conditional name="option">
48 <param name="type_transfo" type="select" label="Type of transformation"> 56 <param name="type_transfo" type="select" label="Type of transformation">
49 <option value="cpm" selected="true">CPM</option> 57 <option value="cpm" selected="true">CPM</option>
50 <option value="tpm">TPM</option> 58 <option value="tpm">TPM</option>
51 <option value="rpk">RPK</option> 59 <option value="rpk">RPK</option>
52 </param>
53 <when value="tpm">
54 <param name="gene_file" type="data" format="txt" label="Gene length file"/>
55 <param name="gene_sep" type="select" label="Gene length column separator">
56 <option value="tab" selected="true">Tabs</option>
57 <option value=",">Commas</option>
58 <option value="\ ">Whitespaces</option>
59 <option value=".">Dots</option>
60 <option value="_">Underscores</option>
61 <option value="-">Dashes</option>
62 </param> 60 </param>
63 <param name="gene_header" type="select" label="Consider first line of gene length file as header ?"> 61 <when value="tpm">
64 <option value="TRUE" selected="true">Yes</option> 62 <param name="gene_file" type="data" format="txt" label="Gene length file"/>
65 <option value="FALSE">No</option> 63 <param name="gene_sep" type="select" label="Gene length column separator">
66 </param> 64 <option value="tab" selected="true">Tabs</option>
67 </when> 65 <option value=",">Commas</option>
68 <when value="rpk"> 66 <option value="\ ">Whitespaces</option>
69 <param name="gene_file" type="data" format="txt" label="Gene length file"/> 67 <option value=".">Dots</option>
70 <param name="gene_sep" type="select" label="Gene length column separator"> 68 <option value="_">Underscores</option>
71 <option value="tab" selected="true">Tabs</option> 69 <option value="-">Dashes</option>
72 <option value=",">Commas</option> 70 </param>
73 <option value="\ ">Whitespaces</option> 71 <param name="gene_header" type="select" label="Consider first line of gene length file as header ?">
74 <option value=".">Dots</option> 72 <option value="TRUE" selected="true">Yes</option>
75 <option value="_">Underscores</option> 73 <option value="FALSE">No</option>
76 <option value="-">Dashes</option> 74 </param>
77 </param> 75 </when>
78 <param name="gene_header" type="select" label="Consider first line of gene length file as header ?"> 76 <when value="rpk">
79 <option value="TRUE" selected="true">Yes</option> 77 <param name="gene_file" type="data" format="txt" label="Gene length file"/>
80 <option value="FALSE">No</option> 78 <param name="gene_sep" type="select" label="Gene length column separator">
81 </param> 79 <option value="tab" selected="true">Tabs</option>
82 </when> 80 <option value=",">Commas</option>
83 <when value="cpm"> 81 <option value="\ ">Whitespaces</option>
84 </when> 82 <option value=".">Dots</option>
85 </conditional> 83 <option value="_">Underscores</option>
84 <option value="-">Dashes</option>
85 </param>
86 <param name="gene_header" type="select" label="Consider first line of gene length file as header ?">
87 <option value="TRUE" selected="true">Yes</option>
88 <option value="FALSE">No</option>
89 </param>
90 </when>
91 <when value="cpm">
92 </when>
93 </conditional>
86 <param name="log" type="select" label="Data should be log transformed ?"> 94 <param name="log" type="select" label="Data should be log transformed ?">
87 <option value="FALSE" selected="true">No</option> 95 <option value="FALSE" selected="true">No</option>
88 <option value="TRUE">Yes</option> 96 <option value="TRUE">Yes</option>
89 </param> 97 </param>
98 <conditional name="visu_option">
99 <param name="visualisation" type="select" label="Visualisation of data with various dimensionality reduction methods" >
100 <option value="no" selected="true">No visualisation</option>
101 <option value="tsne" >tsne</option>
102 </param>
103 <when value="tsne">
104 <param name="seed" value="42.0" type="float" label="Seed value for reproducibiity" help="Set to 42 as default" />
105 <param name="perp" value="10.0" type="float" label="perplexity"/>
106 <param name="theta" value="1.0" type="float" label="theta"/>
107 </when>
108 <when value="no" />
109 </conditional>
90 </inputs> 110 </inputs>
91 <outputs> 111 <outputs>
92 <data name="output" format="tabular" label="${option.type_transfo} from ${on_string}"> 112 <data name="output" format="tabular" label="${option.type_transfo} from ${on_string}">
93 <filter>log == "FALSE"</filter> 113 <filter>log == "FALSE"</filter>
94 </data> 114 </data>
95 <data name="output_log" format="tabular" label="log2(${option.type_transfo} +1) from ${on_string}"> 115 <data name="output_log" format="tabular" label="log2(${option.type_transfo} +1) from ${on_string}">
96 <filter>log == "TRUE"</filter> 116 <filter>log == "TRUE"</filter>
97 </data> 117 </data>
118 <data name="tsne_out" format="pdf" label="tsne from ${on_string}">
119 <filter>visu_option['visualisation'] == 'tsne'</filter>
120 </data>
98 </outputs> 121 </outputs>
99 <tests> 122 <tests>
123 <!-- test t-SNE -->
124 <test>
125 <param name="input" value="counts.tab" ftype="tabular"/>
126 <param name="type_transfo" value="cpm"/>
127 <param name="visualisation" value="tsne"/>
128 <param name="seed" value="49"/>
129 <param name="perp" value="2"/>
130 <param name="theta" value="1" />
131 <output name="output" file="cpm.tab" ftype="tabular"/>
132 <output name="tsne_out" file="tsne.pdf" ftype="pdf"/>
133 </test>
134 <!-- test without t-SNE -->
100 <test> 135 <test>
101 <param name="input" value="counts.tab" ftype="tabular"/> 136 <param name="input" value="counts.tab" ftype="tabular"/>
102 <param name="type_transfo" value="cpm"/> 137 <param name="type_transfo" value="cpm"/>
103 <output name="output" file="cpm.tab" ftype="tabular"/> 138 <output name="output" file="cpm.tab" ftype="tabular"/>
104 </test> 139 </test>
141 </tests> 176 </tests>
142 <help> 177 <help>
143 178
144 **What it does** 179 **What it does**
145 180
146 And returns a table of normalized expression values. 181 Takes a raw count expression matrix and returns a table of normalized expression values.
147 182
148 Normalization can be: 183 Normalization can be:
149 184
150 - CPM (Counts Per Million) are obtained by dividing counts by the library counts sum and multiplying the results by a million. 185 - CPM (Counts Per Million) are obtained by dividing counts by the library counts sum and multiplying the results by a million.
151 - RPK (Reads Per Kilobases) are obtained by dividing read counts by gene lengths (expressed in kilo-nucleotides). 186 - RPK (Reads Per Kilobases) are obtained by dividing read counts by gene lengths (expressed in kilo-nucleotides).