Mercurial > repos > artbio > cpm_tpm_rpk

comparison 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
comparison
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1:b74bab5157c4 2:563337e780ce
1 <tool id="cpm_tpm_rpk" name="Generate CPM, TPM, RPK" version="0.2.0"> 1 <tool id="cpm_tpm_rpk" name="Generate CPM, TPM, RPK" version="0.3.0">
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> 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> 6 <requirement type="package" version="2.2.1=r3.3.2_0">r-ggplot2</requirement>
7 <requirement type="package" version="0.4.1=r3.3.2_0">r-ggfortify</requirement>
7 </requirements> 8 </requirements>
8 <stdio> 9 <stdio>
9 <exit_code range="1:" level="fatal" description="Tool exception" /> 10 <exit_code range="1:" level="fatal" description="Tool exception" />
10 </stdio> 11 </stdio>
11 <command detect_errors="exit_code"><![CDATA[ 12 <command detect_errors="exit_code"><![CDATA[
28 #if $log == "FALSE": 29 #if $log == "FALSE":
29 -o ${output} 30 -o ${output}
30 #else if $log == "TRUE": 31 #else if $log == "TRUE":
31 -o ${output_log} 32 -o ${output_log}
32 #end if 33 #end if
33 #if $visu_option.visualisation == "tsne": 34 #if $visu_option.visualisation == "yes":
34 --tsne 'TRUE' 35 --visu 'TRUE'
36 #if $visu_option.tsne_labels == "yes":
37 --tsne_labels 'TRUE'
38 #else
39 --tsne_labels 'FALSE'
40 #end if
35 --seed '$visu_option.seed' 41 --seed '$visu_option.seed'
36 --perp '$visu_option.perp' 42 --perp '$visu_option.perp'
37 --theta '$visu_option.theta' 43 --theta '$visu_option.theta'
38 --tsne_out '$tsne_out' 44 --tsne_out '$tsne_out'
45 --pca_out '$pca_out'
39 #end if 46 #end if
40 ]]></command> 47 ]]></command>
41 <inputs> 48 <inputs>
42 <param name="input" type="data" format="txt" label="Raw counts of expression data"/> 49 <param name="input" type="data" format="txt" label="Raw counts of expression data"/>
43 <param name="input_sep" type="select" label="Input column separator"> 50 <param name="input_sep" type="select" label="Input column separator">
96 <option value="TRUE">Yes</option> 103 <option value="TRUE">Yes</option>
97 </param> 104 </param>
98 <conditional name="visu_option"> 105 <conditional name="visu_option">
99 <param name="visualisation" type="select" label="Visualisation of data with various dimensionality reduction methods" > 106 <param name="visualisation" type="select" label="Visualisation of data with various dimensionality reduction methods" >
100 <option value="no" selected="true">No visualisation</option> 107 <option value="no" selected="true">No visualisation</option>
101 <option value="tsne" >tsne</option> 108 <option value="yes" >t-SNE and PCA</option>
102 </param> 109 </param>
103 <when value="tsne"> 110 <when value="yes">
104 <param name="seed" value="42.0" type="float" label="Seed value for reproducibiity" help="Set to 42 as default" /> 111 <param name="seed" value="49.0" type="float" label="Seed value for reproducibility" help="Set to 49 as default" />
105 <param name="perp" value="10.0" type="float" label="perplexity"/> 112 <param name="perp" value="10.0" type="float" label="perplexity" help="should be less than ((nbre observations)-1)/3" />
106 <param name="theta" value="1.0" type="float" label="theta"/> 113 <param name="theta" value="1.0" type="float" label="theta"/>
114 <param name="tsne_labels" type="select" label="Add labels to points in the t-SNE plot" >
115 <option value="no" selected="true">No Labels</option>
116 <option value="yes" >Label points</option>
117 </param>
107 </when> 118 </when>
108 <when value="no" /> 119 <when value="no" />
109 </conditional> 120 </conditional>
110 </inputs> 121 </inputs>
111 <outputs> 122 <outputs>
114 </data> 125 </data>
115 <data name="output_log" format="tabular" label="log2(${option.type_transfo} +1) from ${on_string}"> 126 <data name="output_log" format="tabular" label="log2(${option.type_transfo} +1) from ${on_string}">
116 <filter>log == "TRUE"</filter> 127 <filter>log == "TRUE"</filter>
117 </data> 128 </data>
118 <data name="tsne_out" format="pdf" label="tsne from ${on_string}"> 129 <data name="tsne_out" format="pdf" label="tsne from ${on_string}">
119 <filter>visu_option['visualisation'] == 'tsne'</filter> 130 <filter>visu_option['visualisation'] == 'yes'</filter>
131 </data>
132 <data name="pca_out" format="pdf" label="PCA from ${on_string}">
133 <filter>visu_option['visualisation'] == 'yes'</filter>
120 </data> 134 </data>
121 </outputs> 135 </outputs>
122 <tests> 136 <tests>
123 <!-- test t-SNE --> 137 <!-- test t-SNE -->
124 <test> 138 <test>
125 <param name="input" value="counts.tab" ftype="tabular"/> 139 <param name="input" value="counts.tab" ftype="tabular"/>
126 <param name="type_transfo" value="cpm"/> 140 <param name="type_transfo" value="cpm"/>
127 <param name="visualisation" value="tsne"/> 141 <param name="log" value="TRUE"/>
142 <param name="visualisation" value="yes"/>
128 <param name="seed" value="49"/> 143 <param name="seed" value="49"/>
129 <param name="perp" value="2"/> 144 <param name="perp" value="2"/>
130 <param name="theta" value="1" /> 145 <param name="theta" value="1" />
131 <output name="output" file="cpm.tab" ftype="tabular"/> 146 <param name="tsne_labels" value="yes" />
147 <output name="output" file="logcpm.tab" ftype="tabular"/>
132 <output name="tsne_out" file="tsne.pdf" ftype="pdf"/> 148 <output name="tsne_out" file="tsne.pdf" ftype="pdf"/>
149 <output name="pca_out" file="pca.pdf" ftype="pdf"/>
150 </test>
151 <test>
152 <param name="input" value="counts.tab" ftype="tabular"/>
153 <param name="type_transfo" value="tpm"/>
154 <param name="gene_file" value="gene_length.tab" ftype="tabular"/>
155 <param name="log" value="TRUE"/>
156 <param name="visualisation" value="yes"/>
157 <param name="seed" value="49"/>
158 <param name="perp" value="2"/>
159 <param name="theta" value="1" />
160 <param name="tsne_labels" value="no" />
161 <output name="output" file="logtpm.tab" ftype="tabular"/>
162 <output name="tsne_out" file="tsne.nolab.pdf" ftype="pdf"/>
163 <output name="pca_out" file="pca.nolab.pdf" ftype="pdf"/>
133 </test> 164 </test>
134 <!-- test without t-SNE --> 165 <!-- test without t-SNE -->
135 <test> 166 <test>
136 <param name="input" value="counts.tab" ftype="tabular"/> 167 <param name="input" value="counts.tab" ftype="tabular"/>
137 <param name="type_transfo" value="cpm"/> 168 <param name="type_transfo" value="cpm"/>