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comparison ruvseq.xml @ 1:99e0c629d3a2 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 9ed3d83cc447ee897af867362bf1dd67af8a11c2
author iuc
date Tue, 26 Mar 2019 06:24:17 -0400
parents 5f56d460bce3
children a32619eef8b9
comparison
equal deleted inserted replaced
0:5f56d460bce3 1:99e0c629d3a2
1 <tool id="ruvseq" name="Remove Unwanted Variation" version="1.12.0"> 1 <tool id="ruvseq" name="Remove Unwanted Variation" version="1.16.0">
2 <description>from RNA-seq data</description> 2 <description>from RNA-seq data</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.12.0">bioconductor-ruvseq</requirement> 4 <requirement type="package" version="1.16.0">bioconductor-ruvseq</requirement>
5 <requirement type="package" version="1.18.1">bioconductor-deseq2</requirement> 5 <requirement type="package" version="1.22.1">bioconductor-deseq2</requirement>
6 <requirement type="package" version="1.6.0">bioconductor-tximport</requirement> 6 <requirement type="package" version="1.10.0">bioconductor-tximport</requirement>
7 <requirement type="package" version="1.30.0">bioconductor-genomicfeatures</requirement> 7 <requirement type="package" version="1.34.1">bioconductor-genomicfeatures</requirement>
8 <requirement type="package" version="0.6.5">r-ggrepel</requirement> 8 <requirement type="package" version="0.8.0">r-ggrepel</requirement>
9 <requirement type="package" version="1.20.2">r-getopt</requirement>
9 </requirements> 10 </requirements>
10 <stdio> 11 <stdio>
11 <regex match="Execution halted" 12 <regex match="Execution halted"
12 source="both" 13 source="both"
13 level="fatal" 14 level="fatal"
42 43
43 $header 44 $header
44 45
45 --min_k $min_k 46 --min_k $min_k
46 --max_k $max_k 47 --max_k $max_k
48 --min_mean_count $min_mean_count
47 49
48 #if $tximport.tximport_selector == 'tximport': 50 #if $tximport.tximport_selector == 'tximport':
49 --txtype $tximport.txtype 51 --txtype $tximport.txtype
50 #if $tximport.mapping_format.mapping_format_selector == 'gtf': 52 #if $tximport.mapping_format.mapping_format_selector == 'gtf':
51 --tx2gene mapping.gtf 53 --tx2gene mapping.gtf
134 <output name="plots" file="ruvseq_diag.pdf" ftype="pdf" compare="sim_size"/> 136 <output name="plots" file="ruvseq_diag.pdf" ftype="pdf" compare="sim_size"/>
135 <output_collection name="unwanted_variation" type="list"> 137 <output_collection name="unwanted_variation" type="list">
136 <element name="batch_effects_control_method_k1"> 138 <element name="batch_effects_control_method_k1">
137 <assert_contents> 139 <assert_contents>
138 <has_text_matching expression="identifier\tcondition\tW_1"/> 140 <has_text_matching expression="identifier\tcondition\tW_1"/>
139 <has_text_matching expression="GSM461179.*\tTreated\t-0.49.*"/> 141 <has_text_matching expression="GSM461179.*\tTreated\t\-.+"/>
140 </assert_contents> 142 </assert_contents>
141 </element> 143 </element>
142 <element name="batch_effects_replicate_method_k1"> 144 <element name="batch_effects_replicate_method_k1">
143 <assert_contents> 145 <assert_contents>
144 <has_text_matching expression="identifier\tcondition\tW_1"/> 146 <has_text_matching expression="identifier\tcondition\tW_1"/>
145 <has_text_matching expression="GSM461179.*\tTreated\t-0.25.*"/> 147 <has_text_matching expression="GSM461179.*\tTreated\t\-.+"/>
146 </assert_contents> 148 </assert_contents>
147 </element> 149 </element>
148 <element name="batch_effects_residual_method_k1"> 150 <element name="batch_effects_residual_method_k1">
149 <assert_contents> 151 <assert_contents>
150 <has_text_matching expression="identifier\tcondition\tW_1"/> 152 <has_text_matching expression="identifier\tcondition\tW_1"/>
151 <has_text_matching expression="GSM461179.*\tTreated\t-0.60.*"/> 153 <has_text_matching expression="GSM461179.*\tTreated\t\-.+"/>
152 </assert_contents> 154 </assert_contents>
153 </element> 155 </element>
154 </output_collection> 156 </output_collection>
155 </test> 157 </test>
156 <!--Ensure counts files without header works --> 158 <!--Ensure counts files without header works -->
168 <output name="plots" file="ruvseq_diag.pdf" ftype="pdf" compare="sim_size"/> 170 <output name="plots" file="ruvseq_diag.pdf" ftype="pdf" compare="sim_size"/>
169 <output_collection name="unwanted_variation" type="list"> 171 <output_collection name="unwanted_variation" type="list">
170 <element name="batch_effects_control_method_k1"> 172 <element name="batch_effects_control_method_k1">
171 <assert_contents> 173 <assert_contents>
172 <has_text_matching expression="identifier\tcondition\tW_1"/> 174 <has_text_matching expression="identifier\tcondition\tW_1"/>
173 <has_text_matching expression="GSM461179.*\tTreated\t-0.49.*"/> 175 <has_text_matching expression="GSM461179.*\tTreated\t\-.+"/>
174 </assert_contents> 176 </assert_contents>
175 </element> 177 </element>
176 <element name="batch_effects_replicate_method_k1"> 178 <element name="batch_effects_replicate_method_k1">
177 <assert_contents> 179 <assert_contents>
178 <has_text_matching expression="identifier\tcondition\tW_1"/> 180 <has_text_matching expression="identifier\tcondition\tW_1"/>
179 <has_text_matching expression="GSM461179.*\tTreated\t-0.25.*"/> 181 <has_text_matching expression="GSM461179.*\tTreated\t\-.+"/>
180 </assert_contents> 182 </assert_contents>
181 </element> 183 </element>
182 <element name="batch_effects_residual_method_k1"> 184 <element name="batch_effects_residual_method_k1">
183 <assert_contents> 185 <assert_contents>
184 <has_text_matching expression="identifier\tcondition\tW_1"/> 186 <has_text_matching expression="identifier\tcondition\tW_1"/>
185 <has_text_matching expression="GSM461179.*\tTreated\t-0.60.*"/> 187 <has_text_matching expression="GSM461179.*\tTreated\t\-.+"/>
186 </assert_contents> 188 </assert_contents>
187 </element> 189 </element>
188 </output_collection> 190 </output_collection>
189 </test> 191 </test>
190 <!--Ensure sailfish files work --> 192 <!--Ensure sailfish files work -->
200 <param name="pdf" value="true"/> 202 <param name="pdf" value="true"/>
201 <param name="tximport_selector" value="tximport"/> 203 <param name="tximport_selector" value="tximport"/>
202 <param name="txtype" value="sailfish"/> 204 <param name="txtype" value="sailfish"/>
203 <param name="mapping_format_selector" value="tabular"/> 205 <param name="mapping_format_selector" value="tabular"/>
204 <param name="tabular_file" value="tx2gene.tab"/> 206 <param name="tabular_file" value="tx2gene.tab"/>
207 <param name="min_mean_count" value="0"/>
205 <output name="plots" file="ruvseq_diag_sailfish.pdf" ftype="pdf" compare="sim_size"/> 208 <output name="plots" file="ruvseq_diag_sailfish.pdf" ftype="pdf" compare="sim_size"/>
206 <output_collection name="unwanted_variation" type="list"> 209 <output_collection name="unwanted_variation" type="list">
207 <element name="batch_effects_control_method_k1"> 210 <element name="batch_effects_control_method_k1">
208 <assert_contents> 211 <assert_contents>
209 <has_text_matching expression="identifier\tcondition\tW_1"/> 212 <has_text_matching expression="identifier\tcondition\tW_1"/>
210 <has_text_matching expression="sailfish_quant.sf1.tab\tTreated\t-0.28.*"/> 213 <has_text_matching expression=".*sailfish_quant.sf1.tab\tTreated\t.+"/>
211 </assert_contents> 214 </assert_contents>
212 </element> 215 </element>
213 <element name="batch_effects_replicate_method_k1"> 216 <element name="batch_effects_replicate_method_k1">
214 <assert_contents> 217 <assert_contents>
215 <has_text_matching expression="identifier\tcondition\tW_1"/> 218 <has_text_matching expression="identifier\tcondition\tW_1"/>
216 <has_text_matching expression="sailfish_quant.sf1.tab\tTreated\t-0.44.*"/> 219 <has_text_matching expression=".*sailfish_quant.sf1.tab\tTreated\t.+"/>
217 </assert_contents> 220 </assert_contents>
218 </element> 221 </element>
219 <element name="batch_effects_residual_method_k1"> 222 <element name="batch_effects_residual_method_k1">
220 <assert_contents> 223 <assert_contents>
221 <has_text_matching expression="identifier\tcondition\tW_1"/> 224 <has_text_matching expression="identifier\tcondition\tW_1"/>
222 <has_text_matching expression="sailfish_quant.sf1.tab\tTreated\t-0.22.*"/> 225 <has_text_matching expression=".*sailfish_quant.sf1.tab\tTreated\t.+"/>
223 </assert_contents> 226 </assert_contents>
224 </element> 227 </element>
225 </output_collection> 228 </output_collection>
226 </test> 229 </test>
227 </tests> 230 </tests>