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comparison deseq2.xml @ 24:71bacea10eee draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
author iuc
date Sat, 29 Feb 2020 17:08:08 -0500
parents e5c8afac22a7
children de44f8eff84a
comparison
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23:0696db066a5b 24:71bacea10eee
1 <tool id="deseq2" name="DESeq2" version="2.11.40.6"> 1 <tool id="deseq2" name="DESeq2" version="2.11.40.6+galaxy1">
2 <description>Determines differentially expressed features from count tables</description> 2 <description>Determines differentially expressed features from count tables</description>
3 <macros> 3 <macros>
4 <import>deseq2_macros.xml</import> 4 <import>deseq2_macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
215 <action name="column_names" type="metadata" default="GeneID,Base mean,log2(FC),StdErr,Wald-Stats,P-value,P-adj" /> 215 <action name="column_names" type="metadata" default="GeneID,Base mean,log2(FC),StdErr,Wald-Stats,P-value,P-adj" />
216 </actions> 216 </actions>
217 </data> 217 </data>
218 <collection name="split_output" type="list" label="DESeq2 result files on ${on_string}"> 218 <collection name="split_output" type="list" label="DESeq2 result files on ${on_string}">
219 <filter>many_contrasts is True</filter> 219 <filter>many_contrasts is True</filter>
220 <discover_datasets pattern="None.(?P&lt;designation&gt;.+_vs_.+)" format="tabular" directory="." visible="false"/> 220 <discover_datasets pattern="(?P&lt;designation&gt;.+_vs_.+)" format="tabular" directory="." visible="false"/>
221 </collection> 221 </collection>
222 <data name="plots" format="pdf" label="DESeq2 plots on ${on_string}"> 222 <data name="plots" format="pdf" label="DESeq2 plots on ${on_string}">
223 <filter>pdf == True</filter> 223 <filter>pdf == True</filter>
224 </data> 224 </data>
225 <data name="counts_out" format="tabular" label="Normalized counts file on ${on_string}"> 225 <data name="counts_out" format="tabular" label="Normalized counts file on ${on_string}">
443 <assert_contents> 443 <assert_contents>
444 <has_text_matching expression="HOXC11\t0.557.*\t0.324.*\t0.437.*\t0.741.*\t0.458.*\t0.999.*"/> 444 <has_text_matching expression="HOXC11\t0.557.*\t0.324.*\t0.437.*\t0.741.*\t0.458.*\t0.999.*"/>
445 </assert_contents> 445 </assert_contents>
446 </output> 446 </output>
447 </test> 447 </test>
448 <!--Ensure many_contrasts produces output collection -->
449 <test expect_num_outputs="1">
450 <param name="select_data|how" value="group_tags"/>
451 <param name="select_data|countsFile">
452 <collection type="list">
453 <element name="1" value="sailfish/sailfish_quant.sf1.tab" tags="group:primary:treated"/>
454 <element name="2" value="sailfish/sailfish_quant.sf2.tab" tags="group:primary:treated"/>
455 <element name="3" value="sailfish/sailfish_quant.sf3.tab" tags="group:primary:treated"/>
456 <element name="4" value="sailfish/sailfish_quant.sf4.tab" tags="group:primary:untreated"/>
457 <element name="5" value="sailfish/sailfish_quant.sf5.tab" tags="group:primary:untreated"/>
458 <element name="6" value="sailfish/sailfish_quant.sf6.tab" tags="group:primary:untreated"/>
459 </collection>
460 </param>
461 <repeat name="rep_factorName">
462 <param name="factorName" value="Treatment"/>
463 <repeat name="rep_factorLevel">
464 <param name="factorLevel" value="Treated"/>
465 <param name="groups" value="primary:treated"/>
466 </repeat>
467 <repeat name="rep_factorLevel">
468 <param name="factorLevel" value="Untreated"/>
469 <param name="groups" value="primary:untreated"/>
470 </repeat>
471 </repeat>
472 <param name="pdf" value="False"/>
473 <param name="tximport_selector" value="tximport"/>
474 <param name="txtype" value="sailfish"/>
475 <param name="mapping_format_selector" value="tabular"/>
476 <param name="tabular_file" value="tx2gene.tab"/>
477 <param name="many_contrasts" value="true"/>
478 <output_collection name="split_output" type="list" count="1">
479 <element name="Treatment_Treated_vs_Untreated">
480 <assert_contents>
481 <has_text_matching expression="HOXC11\t0.557.*\t0.324.*\t0.437.*\t0.741.*\t0.458.*\t0.999.*"/>
482 </assert_contents>
483 </element>
484 </output_collection>
485 </test>
448 </tests> 486 </tests>
449 <help><![CDATA[ 487 <help><![CDATA[
450 .. class:: infomark 488 .. class:: infomark
451 489
452 **What it does** 490 **What it does**