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comparison deseq2.xml @ 42:6ef2cba4e35a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
author iuc
date Fri, 26 Aug 2022 11:15:32 +0000
parents 0a0a3388e3f2
children 621ddf5967d2
comparison
equal deleted inserted replaced
41:0a0a3388e3f2 42:6ef2cba4e35a
89 -e $advanced_options.esf 89 -e $advanced_options.esf
90 #end if 90 #end if
91 -t $advanced_options.fit_type 91 -t $advanced_options.fit_type
92 #if $batch_factors: 92 #if $batch_factors:
93 --batch_factors '$batch_factors' 93 --batch_factors '$batch_factors'
94 #end if
95 #if $advanced_options.prefilter_conditional.prefilter:
96 $advanced_options.prefilter_conditional.prefilter
97 -V $advanced_options.prefilter_conditional.prefilter_value
94 #end if 98 #end if
95 #if $advanced_options.outlier_replace_off: 99 #if $advanced_options.outlier_replace_off:
96 -a 100 -a
97 #end if 101 #end if
98 #if $advanced_options.outlier_filter_off: 102 #if $advanced_options.outlier_filter_off:
192 help="When there are more than 2 replicates for a given sample, the DESeq2 will automatically 196 help="When there are more than 2 replicates for a given sample, the DESeq2 will automatically
193 filter genes which contain a Cook’s distance above a cutoff" /> 197 filter genes which contain a Cook’s distance above a cutoff" />
194 <param name="auto_mean_filter_off" type="boolean" truevalue="1" falsevalue="0" checked="false" 198 <param name="auto_mean_filter_off" type="boolean" truevalue="1" falsevalue="0" checked="false"
195 label="Turn off independent filtering" 199 label="Turn off independent filtering"
196 help=" DESeq2 performs independent filtering by default using the mean of normalized counts as a filter statistic" /> 200 help=" DESeq2 performs independent filtering by default using the mean of normalized counts as a filter statistic" />
201 <conditional name="prefilter_conditional">
202 <param name="prefilter" type="select" label="Perform pre-filtering" help="While it is not necessary to pre-filter
203 low count genes before running the DESeq2 functions, there are two reasons which make pre-filtering useful:
204 by removing rows in which there are very few reads, we reduce the required memory, and we increase the speed.
205 It can also improve visualizations, as features with no information for differential expression are not plotted.">
206 <option value="-P">Enabled</option>
207 <option value="" selected="true">Disabled</option>
208 </param>
209 <when value="-P">
210 <param name="prefilter_value" type="integer" min="0" value="10" label="Pre-filter value" help="Keep only rows that have at least N reads total." />
211 </when>
212 <when value=""/>
213 </conditional>
197 </section> 214 </section>
198 <section name="output_options" title="Output options"> 215 <section name="output_options" title="Output options">
199 <param name="output_selector" type="select" multiple="True" optional="true" display="checkboxes" label="Output selector"> 216 <param name="output_selector" type="select" multiple="True" optional="true" display="checkboxes" label="Output selector">
200 <option value="pdf" selected="True">Generate plots for visualizing the analysis results</option> 217 <option value="pdf" selected="True">Generate plots for visualizing the analysis results</option>
201 <option value="sizefactors" >Output sample size factors</option> 218 <option value="sizefactors" >Output sample size factors</option>
270 </assert_contents> 287 </assert_contents>
271 </output> 288 </output>
272 <output name="deseq_out" > 289 <output name="deseq_out" >
273 <assert_contents> 290 <assert_contents>
274 <has_text_matching expression="FBgn0003360\t1933\.9504.*\t-2\.8399.*\t0\.1309.*\t-21\.68.*\t.*e-104\t.*e-101" /> 291 <has_text_matching expression="FBgn0003360\t1933\.9504.*\t-2\.8399.*\t0\.1309.*\t-21\.68.*\t.*e-104\t.*e-101" />
292 <has_n_lines n="3999"/>
275 </assert_contents> 293 </assert_contents>
276 </output> 294 </output>
277 </test> 295 </test>
278 <!--Ensure additional batch factor correction works --> 296 <!--Ensure additional batch factor correction works -->
279 <test expect_num_outputs="2"> 297 <test expect_num_outputs="2">
577 <has_text_matching expression="sailfish_quant\.sf4\.tab\t0\.8\d+" /> 595 <has_text_matching expression="sailfish_quant\.sf4\.tab\t0\.8\d+" />
578 <has_text_matching expression="sailfish_quant\.sf3\.tab\t1\.0\d+" /> 596 <has_text_matching expression="sailfish_quant\.sf3\.tab\t1\.0\d+" />
579 </assert_contents> 597 </assert_contents>
580 </output> 598 </output>
581 </test> 599 </test>
600 <!--Test prefilter parameter -->
601 <test expect_num_outputs="2">
602 <repeat name="rep_factorName">
603 <param name="factorName" value="Treatment"/>
604 <repeat name="rep_factorLevel">
605 <param name="factorLevel" value="Treated"/>
606 <param name="countsFile" value="GSM461179_treat_single.counts,GSM461180_treat_paired.counts,GSM461181_treat_paired.counts"/>
607 </repeat>
608 <repeat name="rep_factorLevel">
609 <param name="factorLevel" value="Untreated"/>
610 <param name="countsFile" value="GSM461176_untreat_single.counts,GSM461177_untreat_paired.counts,GSM461178_untreat_paired.counts,GSM461182_untreat_single.counts"/>
611 </repeat>
612 </repeat>
613 <section name="advanced_options">
614 <conditional name="prefilter_conditional">
615 <param name="prefilter" value="-P"/>
616 <param name="prefilter_value" value="10"/>
617 </conditional>
618 </section>
619 <section name="output_options">
620 <param name="output_selector" value="normCounts"/>
621 </section>
622 <output name="counts_out">
623 <assert_contents>
624 <has_n_lines n="2922"/>
625 </assert_contents>
626 </output>
627 <output name="deseq_out" >
628 <assert_contents>
629 <has_n_lines n="2921"/> <!-- Smallen value when compared with the first test-->
630 </assert_contents>
631 </output>
632 </test>
582 </tests> 633 </tests>
583 <help><![CDATA[ 634 <help><![CDATA[
584 .. class:: infomark 635 .. class:: infomark
585 636
586 **What it does** 637 **What it does**