Mercurial > repos > iuc > mageck_test

comparison mageck_test.xml @ 4:38073c236d71 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 4478aabdcb10e4787450b1b23944defa7dc38ffe
author iuc
date Mon, 04 Jun 2018 10:58:16 -0400
parents 81bbbddcf285
children 9b4f4533c9ee
comparison
equal deleted inserted replaced
3:afa81ef5f1c3 4:38073c236d71
158 <!-- Ensure MAGeCK's default output works --> 158 <!-- Ensure MAGeCK's default output works -->
159 <test expect_num_outputs="2"> 159 <test expect_num_outputs="2">
160 <param name="count_table" value="in.test.sample.txt" ftype="tabular" /> 160 <param name="count_table" value="in.test.sample.txt" ftype="tabular" />
161 <param name="treatment_id" value="HL60_final,KBM7_final" /> 161 <param name="treatment_id" value="HL60_final,KBM7_final" />
162 <param name="control_id" value="HL60_initial,KBM7_initial" /> 162 <param name="control_id" value="HL60_initial,KBM7_initial" />
163 <output name="gene_summary" file="out.test.gene_summary.txt"/> 163 <output name="gene_summary">
164 <output name="sgrna_summary" file="out.test.sgrna_summary.txt"/> 164 <assert_contents>
165 <has_text_matching expression="id\tnum\tneg|score\tneg|p-value\tneg|fdr\tneg|rank\tneg|goodsgrna\tneg|lfc\tpos|score\tpos|p-value\tpos|fdr\tpos|rank\tpos|goodsgrna\tpos|lfc" />
166 <has_text_matching expression="ACD.*10.*0.9996.*-0.0296" />
167 </assert_contents>
168 </output>
169 <output name="sgrna_summary">
170 <assert_contents>
171 <has_text_matching expression="sgrna\tGene\tcontrol_count\ttreatment_count\tcontrol_mean\ttreat_mean\tLFC\tcontrol_var\tadj_var\tscore\tp.low\tp.high\tp.twosided\tFDR\thigh_in_treatment" />
172 <has_text_matching expression="ADCK3_m227149144.*ADCK3.*263.11.*189.27.*False" />
173 </assert_contents>
174 </output>
165 </test> 175 </test>
166 <!-- Ensure MAGeCK's additional outputs works --> 176 <!-- Ensure MAGeCK's additional outputs works -->
167 <test expect_num_outputs="7"> 177 <test expect_num_outputs="7">
168 <param name="count_table" value="in.test.sample.txt" ftype="tabular" /> 178 <param name="count_table" value="in.test.sample.txt" ftype="tabular" />
169 <param name="treatment_id" value="HL60_final,KBM7_final" /> 179 <param name="treatment_id" value="HL60_final,KBM7_final" />
170 <param name="control_id" value="HL60_initial,KBM7_initial" /> 180 <param name="control_id" value="HL60_initial,KBM7_initial" />
171 <param name="out_log" value="True" /> 181 <param name="out_log" value="True" />
172 <param name="normcounts" value="True" /> 182 <param name="normcounts" value="True" />
173 <param name="pdfreport" value="True" /> 183 <param name="pdfreport" value="True" />
174 <param name="rfilesOpt" value="True" /> 184 <param name="rfilesOpt" value="True" />
175 <output name="gene_summary" file="out.test.gene_summary.txt"/> 185 <output name="gene_summary">
176 <output name="sgrna_summary" file="out.test.sgrna_summary.txt"/> 186 <assert_contents>
187 <has_text_matching expression="id\tnum\tneg|score\tneg|p-value\tneg|fdr\tneg|rank\tneg|goodsgrna\tneg|lfc\tpos|score\tpos|p-value\tpos|fdr\tpos|rank\tpos|goodsgrna\tpos|lfc" />
188 <has_text_matching expression="ACD.*10.*0.9996.*-0.0296" />
189 </assert_contents>
190 </output>
191 <output name="sgrna_summary">
192 <assert_contents>
193 <has_text_matching expression="sgrna\tGene\tcontrol_count\ttreatment_count\tcontrol_mean\ttreat_mean\tLFC\tcontrol_var\tadj_var\tscore\tp.low\tp.high\tp.twosided\tFDR\thigh_in_treatment" />
194 <has_text_matching expression="ADCK3_m227149144.*ADCK3.*263.11.*189.27.*False" />
195 </assert_contents>
196 </output>
197 <output name="log">
198 <assert_contents>
199 <has_text_matching expression="Welcome to MAGeCK" />
200 </assert_contents>
201 </output>
202 <output name="rscript">
203 <assert_contents>
204 <has_text_matching expression="output_summary.tex" />
205 </assert_contents>
206 </output>
207 <output name="rnwfile">
208 <assert_contents>
209 <has_text_matching expression="This is a template file for Sweave used in MAGeCK" />
210 </assert_contents>
211 </output>
212 <output name="plots" file="out.test.plots.pdf" compare="sim_size"/>
177 <output name="normcounts" file="out.test.normalized.txt"/> 213 <output name="normcounts" file="out.test.normalized.txt"/>
178 <output name="log" file="out.test.log.txt" compare="sim_size"/>
179 <output name="plots" file="out.test.plots.pdf" compare="sim_size"/>
180 <output name="rscript" file="out.test.R" />
181 <output name="rnwfile" file="output_summary.Rnw" />
182 </test> 214 </test>
183 </tests> 215 </tests>
184 216
185 <help><![CDATA[ 217 <help><![CDATA[
186 .. class:: infomark 218 .. class:: infomark