Mercurial > repos > iuc > transit_hmm

diff transit_hmm.xml @ 11:7f82912d2d8e draft default tip

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/transit/ commit 0daaffac75df549583b6d834113608c2dbacb1d3
author iuc
date Tue, 27 May 2025 19:59:03 +0000
parents 0f499c16998a
children
line wrap: on
line diff
--- a/transit_hmm.xml	Sat Nov 27 09:47:33 2021 +0000
+++ b/transit_hmm.xml	Tue May 27 19:59:03 2025 +0000
@@ -10,7 +10,8 @@
     	@LINK_INPUTS@
         transit hmm $input_files annotation.dat transit_out.txt
         @STANDARD_OPTIONS@
-        $loess
+         -r $handle_replicates
+         $loess
         ]]>
     </command>
     <inputs>
@@ -120,6 +121,19 @@
 =============================================   ========================================================================================================================
 
 Note: Libraries that are too sparse (e.g. < 30%) or which contain very low read-counts may be problematic for the HMM method, causing it to label too many Growth-Defect genes
+
+
+-------------------
+
+**More Information**
+
+-------------------
+
+See  `TRANSIT documentation`
+
+- TRANSIT: https://transit.readthedocs.io/en/v@TOOL_VERSION@/index.html
+- `TRANSIT Gumbel`: https://transit.readthedocs.io/en/v@TOOL_VERSION@/transit_methods.html#hmm
+
 ]]></help>
 
     <expand macro="citations" />