Mercurial > repos > iuc > deseq2

diff deseq2.xml @ 20:89d26b11d452 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
author iuc
date Thu, 06 Dec 2018 15:49:22 -0500
parents c56e0689e46e
children a6fc9228e1a0
line wrap: on
line diff
--- a/deseq2.xml	Tue Dec 04 08:19:06 2018 -0500
+++ b/deseq2.xml	Thu Dec 06 15:49:22 2018 -0500
@@ -348,7 +348,7 @@
                 </assert_contents>
             </output>
         </test>
-        <!--Ensure Sailfish/Salmon input with GFF3 annotation works-->
+        <!--Ensure Sailfish/Salmon input with GFF3 annotation from NCBI works-->
         <test expect_num_outputs="1">
             <repeat name="rep_factorName">
                 <param name="factorName" value="Treatment"/>
@@ -372,6 +372,30 @@
                 </assert_contents>
             </output>
         </test>
+        <!--Ensure Sailfish/Salmon input with GTF annotation from Ensembl works-->
+        <test expect_num_outputs="1">
+            <repeat name="rep_factorName">
+                <param name="factorName" value="Treatment"/>
+                <repeat name="rep_factorLevel">
+                    <param name="factorLevel" value="Treated"/>
+                    <param name="countsFile" value="sailfish_ensembl/sailfish_quant.sf1.tab,sailfish_ensembl/sailfish_quant.sf2.tab,sailfish_ensembl/sailfish_quant.sf3.tab"/>
+                </repeat>
+                <repeat name="rep_factorLevel">
+                    <param name="factorLevel" value="Untreated"/>
+                    <param name="countsFile" value="sailfish_ensembl/sailfish_quant.sf4.tab,sailfish_ensembl/sailfish_quant.sf5.tab,sailfish_ensembl/sailfish_quant.sf6.tab"/>
+                </repeat>
+            </repeat>
+            <param name="pdf" value="False"/>
+            <param name="tximport_selector" value="tximport"/>
+            <param name="txtype" value="sailfish"/>
+            <param name="mapping_format_selector" value="gtf"/>
+            <param name="gtf_file" value="Homo_sapiens.GRCh38.94.gtf" ftype="gtf"/>
+            <output name="deseq_out" >
+                <assert_contents>
+                    <has_text_matching expression="ENSG00000168671\t1.8841.*\t-0.1180.*\t0.7429.*\t-0.1589.*\t0.8737.*\t0.9999.*" />
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help><![CDATA[
 .. class:: infomark