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comparison sleuth.xml @ 2:d6b5fc94062c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 10e44e324ee754d81a1b9d990ee0932b37e7a9bc
author iuc
date Thu, 08 Jun 2023 19:57:53 +0000
parents d3e447dd52c8
children 2c3d294dbe42
comparison
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1:d3e447dd52c8 2:d6b5fc94062c
65 ]]></command> 65 ]]></command>
66 <inputs> 66 <inputs>
67 <conditional name="experiment_design"> 67 <conditional name="experiment_design">
68 <param name="selector" type="select" label="Experiment design" help="If you have multiple experimental conditions, you should use propably the complex design mode. In the help section you can find more information."> 68 <param name="selector" type="select" label="Experiment design" help="If you have multiple experimental conditions, you should use propably the complex design mode. In the help section you can find more information.">
69 <option value="single">Simple design mode (one experimental factor)</option> 69 <option value="single">Simple design mode (one experimental factor)</option>
70 <option value="complex">Complex design mode (two experimental factors)</option> 70 <option value="complex">Complex design mode (two or more experimental factors)</option>
71 </param> 71 </param>
72 <when value="single"> 72 <when value="single">
73 <repeat name="rep_factorLevel" title="Factor level" min="2" default="2"> 73 <repeat name="rep_factorLevel" title="Factor level" min="2" default="2">
74 <param name="factorLevel" type="text" value="FactorLevel" label="Specify a factor level, typical values could be 'tumor', 'normal', 'treated' or 'control'" 74 <param name="factorLevel" type="text" value="FactorLevel" label="Specify a factor level, typical values could be 'tumor', 'normal', 'treated' or 'control'"
75 help="Only letters, numbers and underscores will be retained in this field"> 75 help="Only letters, numbers and underscores will be retained in this field">
80 <param name="countsFile" type="data" format="h5" multiple="true" label="Counts file(s)"/> 80 <param name="countsFile" type="data" format="h5" multiple="true" label="Counts file(s)"/>
81 </repeat> 81 </repeat>
82 </when> 82 </when>
83 <when value="complex"> 83 <when value="complex">
84 <param name="countsFile" type="data_collection" format="h5" multiple="true" label="Counts file(s)"/> 84 <param name="countsFile" type="data_collection" format="h5" multiple="true" label="Counts file(s)"/>
85 <param argument="--metadata_file" type="data" format="txt" label="Input metadata file" help="You can find more details about it in the help section" /> 85 <param argument="--metadata_file" type="data" format="txt" label="Input metadata file" help="You can find more details about the format of the design table in the help section." />
86 </when> 86 </when>
87 </conditional> 87 </conditional>
88 <section name="advanced_options" title="Advanced options" expanded="true"> 88 <section name="advanced_options" title="Advanced options" expanded="true">
89 <param argument="normalization" type="boolean" truevalue="--normalize" falsevalue="" checked="true" label="Normalize data" 89 <param argument="normalization" type="boolean" truevalue="--normalize" falsevalue="" checked="true" label="Normalize data"
90 help="If this is set to false, bootstraps will not be read and transformation of the data will not be done. This should 90 help="If this is set to false, bootstraps will not be read and transformation of the data will not be done. This should
131 </assert_contents> 131 </assert_contents>
132 </output> 132 </output>
133 <output name="pca_plot" file="test01_pca.pdf" ftype="pdf" compare="sim_size"/> 133 <output name="pca_plot" file="test01_pca.pdf" ftype="pdf" compare="sim_size"/>
134 <output name="density_plot" file="test01_density.pdf" ftype="pdf" compare="sim_size"/> 134 <output name="density_plot" file="test01_density.pdf" ftype="pdf" compare="sim_size"/>
135 </test> 135 </test>
136 <test expect_num_outputs="3"> 136 <test expect_num_outputs="3">
137 <conditional name="experiment_design"> 137 <conditional name="experiment_design">
138 <param name="selector" value="complex"/> 138 <param name="selector" value="complex"/>
139 <param name="countsFile"> 139 <param name="countsFile">
140 <collection type="list"> 140 <collection type="list">
141 <element name="kallisto_output_01.h5" ftype="h5" value="kallisto_output_01.h5"/> 141 <element name="kallisto_output_01.h5" ftype="h5" value="kallisto_output_01.h5"/>
142 <element name="kallisto_output_02.h5" ftype="h5" value="kallisto_output_02.h5"/> 142 <element name="kallisto_output_02.h5" ftype="h5" value="kallisto_output_02.h5"/>
143 <element name="kallisto_output_03.h5" ftype="h5" value="kallisto_output_03.h5"/> 143 <element name="kallisto_output_03.h5" ftype="h5" value="kallisto_output_03.h5"/>
144 <element name="kallisto_output_04.h5" ftype="h5" value="kallisto_output_04.h5"/> 144 <element name="kallisto_output_04.h5" ftype="h5" value="kallisto_output_04.h5"/>
145 </collection> 145 </collection>
146 </param> 146 </param>
147 <param name="metadata_file" value="design.tab"/> 147 <param name="metadata_file" value="design_two_factors.tab"/>
148 </conditional> 148 </conditional>
149 <section name="advanced_options"> 149 <section name="advanced_options">
150 <param name="normalization" value="true"/> 150 <param name="normalization" value="true"/>
151 <param name="nbins" value="100"/> 151 <param name="nbins" value="100"/>
152 <param name="lwr" value="0.25"/> 152 <param name="lwr" value="0.25"/>
153 <param name="upr" value="0.75"/> 153 <param name="upr" value="0.75"/>
154 </section> 154 </section>
155 <output name="sleuth_table" ftype="tabular"> 155 <output name="sleuth_table" ftype="tabular">
156 <assert_contents> 156 <assert_contents>
157 <has_size value="756310" delta="100"/> 157 <has_size value="756310" delta="100"/>
158 <has_text text="ENST00000394894.8"/> 158 <has_text text="ENST00000394894.8"/>
159 <has_text text="ENST00000524187.1"/> 159 <has_text text="ENST00000524187.1"/>
160 </assert_contents> 160 </assert_contents>
161 </output> 161 </output>
162 <output name="pca_plot" file="test02_pca.pdf" ftype="pdf" compare="sim_size"/> 162 <output name="pca_plot" file="test02_pca.pdf" ftype="pdf" compare="sim_size"/>
163 <output name="density_plot" file="test02_density.pdf" ftype="pdf" compare="sim_size"/> 163 <output name="density_plot" file="test02_density.pdf" ftype="pdf" compare="sim_size"/>
164 </test> 164 </test>
165 <test expect_num_outputs="3">
166 <conditional name="experiment_design">
167 <param name="selector" value="complex"/>
168 <param name="countsFile">
169 <collection type="list">
170 <element name="kallisto_output_01.h5" ftype="h5" value="kallisto_output_01.h5"/>
171 <element name="kallisto_output_02.h5" ftype="h5" value="kallisto_output_02.h5"/>
172 <element name="kallisto_output_03.h5" ftype="h5" value="kallisto_output_03.h5"/>
173 <element name="kallisto_output_04.h5" ftype="h5" value="kallisto_output_04.h5"/>
174 </collection>
175 </param>
176 <param name="metadata_file" value="design_three_factors.tab"/>
177 </conditional>
178 <section name="advanced_options">
179 <param name="normalization" value="true"/>
180 <param name="nbins" value="100"/>
181 <param name="lwr" value="0.25"/>
182 <param name="upr" value="0.75"/>
183 </section>
184 <output name="sleuth_table" ftype="tabular">
185 <assert_contents>
186 <has_size value="756310" delta="100"/>
187 <has_text text="ENST00000394894.8"/>
188 <has_text text="ENST00000524187.1"/>
189 </assert_contents>
190 </output>
191 <output name="pca_plot" file="test03_pca.pdf" ftype="pdf" compare="sim_size"/>
192 <output name="density_plot" file="test03_density.pdf" ftype="pdf" compare="sim_size"/>
193 </test>
165 </tests> 194 </tests>
166 <help><![CDATA[ 195 <help><![CDATA[
167 196
168 .. class:: infomark 197 .. class:: infomark
169 198
194 filename_02.fastq.gz condition1 replicate2 223 filename_02.fastq.gz condition1 replicate2
195 filename_03.fastq.gz condition2 replicate1 224 filename_03.fastq.gz condition2 replicate1
196 filename_04.fastq.gz condition2 replicate2 225 filename_04.fastq.gz condition2 replicate2
197 226
198 227
199 The tabular file **requires to have the same column names** as the example (data_file, condition, sample). The data file column correspond to original FASTQ filenames uploaded to Galaxy. 228 The tabular file **requires to have at least three columns with the same names as the previous example** (path, condition, sample). The path column correspond to original FASTQ filenames uploaded to Galaxy.
200 Condition includes the information about the first factor, and sample includes information about the second factor. **Only alphanumeric characters, undescores and dots are allowed**. 229 Condition includes the information about the first factor, and sample includes information about the second factor. **Only alphanumeric characters, undescores and dots are allowed**.
230 Additional factors can be included in the design table.
201 231
202 ]]></help> 232 ]]></help>
203 <expand macro="citations" /> 233 <expand macro="citations" />
204 </tool> 234 </tool>