Mercurial > repos > artbio > cpm_tpm_rpk
comparison cpm_tpm_rpk.xml @ 3:8b1020c25f0f draft
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"/> |