Mercurial > repos > iuc > funannotate_annotate

diff funannotate_annotate.xml @ 11:9c15ca7e764e draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate commit 9e3708d04faea0f1be4ea8918e859d6f2c7eb31d
author iuc
date Wed, 26 Jun 2024 09:41:52 +0000
parents d0336d67702b
children
line wrap: on
line diff
--- a/funannotate_annotate.xml	Sun Feb 11 00:08:00 2024 +0000
+++ b/funannotate_annotate.xml	Wed Jun 26 09:41:52 2024 +0000
@@ -26,6 +26,7 @@
 #end if
 
 --out output
+--tmpdir "\${_GALAXY_JOB_TMP_DIR:-/tmp}"
 
 --database '$database.fields.path'
 
@@ -76,7 +77,7 @@
 ## https://github.com/nextgenusfs/funannotate/issues/777
 ## The partial tbl files are combined by funannotate and are deleted below.
 ## The sqn files are discrete and are collected with discover_datasets.
-find output/annotate_results 
+find output/annotate_results
 -regex ".*part_[0-9]+\.\(tbl\)$"
 -delete
 
@@ -241,7 +242,7 @@
                     <assert_contents>
                         <has_text text="Seq-submit" />
                     </assert_contents>
-                </element>   
+                </element>
             </output_collection>
             <output name="fa_scaffolds">
                 <assert_contents>
@@ -335,7 +336,7 @@
                     <assert_contents>
                         <has_text text="Seq-submit" />
                     </assert_contents>
-                </element>   
+                </element>
             </output_collection>
             <output name="fa_scaffolds">
                 <assert_contents>