Mercurial > repos > artbio > cpm_tpm_rpk

comparison cpm_tpm_rpk.xml @ 3:8b1020c25f0f draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 9149001c65de633ddfd2f91cf208074e40482ce3
author artbio
date Fri, 12 Apr 2019 12:01:35 -0400
parents 563337e780ce
children be358a1ebf67
comparison
equal deleted inserted replaced
2:563337e780ce 3:8b1020c25f0f
1 <tool id="cpm_tpm_rpk" name="Generate CPM, TPM, RPK" version="0.3.0"> 1 <tool id="cpm_tpm_rpk" name="Generate CPM, TPM, RPK" version="0.4.0">
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>
62 <conditional name="option"> 62 <conditional name="option">
63 <param name="type_transfo" type="select" label="Type of transformation"> 63 <param name="type_transfo" type="select" label="Type of transformation">
64 <option value="cpm" selected="true">CPM</option> 64 <option value="cpm" selected="true">CPM</option>
65 <option value="tpm">TPM</option> 65 <option value="tpm">TPM</option>
66 <option value="rpk">RPK</option> 66 <option value="rpk">RPK</option>
67 <option value="none">NONE</option>
67 </param> 68 </param>
68 <when value="tpm"> 69 <when value="tpm">
69 <param name="gene_file" type="data" format="txt" label="Gene length file"/> 70 <param name="gene_file" type="data" format="txt" label="Gene length file"/>
70 <param name="gene_sep" type="select" label="Gene length column separator"> 71 <param name="gene_sep" type="select" label="Gene length column separator">
71 <option value="tab" selected="true">Tabs</option> 72 <option value="tab" selected="true">Tabs</option>
94 <option value="TRUE" selected="true">Yes</option> 95 <option value="TRUE" selected="true">Yes</option>
95 <option value="FALSE">No</option> 96 <option value="FALSE">No</option>
96 </param> 97 </param>
97 </when> 98 </when>
98 <when value="cpm"> 99 <when value="cpm">
100 </when>
101 <when value="none">
99 </when> 102 </when>
100 </conditional> 103 </conditional>
101 <param name="log" type="select" label="Data should be log transformed ?"> 104 <param name="log" type="select" label="Data should be log transformed ?">
102 <option value="FALSE" selected="true">No</option> 105 <option value="FALSE" selected="true">No</option>
103 <option value="TRUE">Yes</option> 106 <option value="TRUE">Yes</option>
106 <param name="visualisation" type="select" label="Visualisation of data with various dimensionality reduction methods" > 109 <param name="visualisation" type="select" label="Visualisation of data with various dimensionality reduction methods" >
107 <option value="no" selected="true">No visualisation</option> 110 <option value="no" selected="true">No visualisation</option>
108 <option value="yes" >t-SNE and PCA</option> 111 <option value="yes" >t-SNE and PCA</option>
109 </param> 112 </param>
110 <when value="yes"> 113 <when value="yes">
111 <param name="seed" value="49.0" type="float" label="Seed value for reproducibility" help="Set to 49 as default" /> 114 <param name="seed" value="49.0" type="float" label="Seed value for reproducibility of t-SNE" help="Set to 49 as default" />
112 <param name="perp" value="10.0" type="float" label="perplexity" help="should be less than ((nbre observations)-1)/3" /> 115 <param name="perp" value="10.0" type="float" label="perplexity (t-SNE)" help="should be less than ((nbre observations)-1)/3" />
113 <param name="theta" value="1.0" type="float" label="theta"/> 116 <param name="theta" value="1.0" type="float" label="theta (t-SNE)"/>
114 <param name="tsne_labels" type="select" label="Add labels to points in the t-SNE plot" > 117 <param name="tsne_labels" type="select" label="Add labels to points plots" >
115 <option value="no" selected="true">No Labels</option> 118 <option value="no" selected="true">No Labels</option>
116 <option value="yes" >Label points</option> 119 <option value="yes" >Label points</option>
117 </param> 120 </param>
118 </when> 121 </when>
119 <when value="no" /> 122 <when value="no" />
133 <filter>visu_option['visualisation'] == 'yes'</filter> 136 <filter>visu_option['visualisation'] == 'yes'</filter>
134 </data> 137 </data>
135 </outputs> 138 </outputs>
136 <tests> 139 <tests>
137 <!-- test t-SNE --> 140 <!-- test t-SNE -->
141 <test>
142 <param name="input" value="none.tab" ftype="tabular"/>
143 <param name="type_transfo" value="none"/>
144 <param name="log" value="FALSE"/>
145 <param name="visualisation" value="yes"/>
146 <param name="seed" value="49"/>
147 <param name="perp" value="10"/>
148 <param name="theta" value="1" />
149 <param name="tsne_labels" value="yes" />
150 <output name="output" file="none.tab" ftype="tabular"/>
151 <output name="tsne_out" file="none_tsne.pdf" ftype="pdf"/>
152 <output name="pca_out" file="none_pca.pdf" ftype="pdf"/>
153 </test>
138 <test> 154 <test>
139 <param name="input" value="counts.tab" ftype="tabular"/> 155 <param name="input" value="counts.tab" ftype="tabular"/>
140 <param name="type_transfo" value="cpm"/> 156 <param name="type_transfo" value="cpm"/>
141 <param name="log" value="TRUE"/> 157 <param name="log" value="TRUE"/>
142 <param name="visualisation" value="yes"/> 158 <param name="visualisation" value="yes"/>