Mercurial > repos > iuc > transit_hmm

comparison 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
comparison
equal deleted inserted replaced
10:0f499c16998a 11:7f82912d2d8e
8 <expand macro="requirements" /> 8 <expand macro="requirements" />
9 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
10 @LINK_INPUTS@ 10 @LINK_INPUTS@
11 transit hmm $input_files annotation.dat transit_out.txt 11 transit hmm $input_files annotation.dat transit_out.txt
12 @STANDARD_OPTIONS@ 12 @STANDARD_OPTIONS@
13 $loess 13 -r $handle_replicates
14 $loess
14 ]]> 15 ]]>
15 </command> 16 </command>
16 <inputs> 17 <inputs>
17 <expand macro="standard_inputs"> 18 <expand macro="standard_inputs">
18 <expand macro="handle_replicates" /> 19 <expand macro="handle_replicates" />
118 Avg. Reads Mean read count within the gene 119 Avg. Reads Mean read count within the gene
119 State Call State Classification (ES = Essential, GD = Growth Defect, NE = Non-Essential, GA = Growth-Defect) 120 State Call State Classification (ES = Essential, GD = Growth Defect, NE = Non-Essential, GA = Growth-Defect)
120 ============================================= ======================================================================================================================== 121 ============================================= ========================================================================================================================
121 122
122 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 123 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
124
125
126 -------------------
127
128 **More Information**
129
130 -------------------
131
132 See `TRANSIT documentation`
133
134 - TRANSIT: https://transit.readthedocs.io/en/v@TOOL_VERSION@/index.html
135 - `TRANSIT Gumbel`: https://transit.readthedocs.io/en/v@TOOL_VERSION@/transit_methods.html#hmm
136
123 ]]></help> 137 ]]></help>
124 138
125 <expand macro="citations" /> 139 <expand macro="citations" />
126 </tool> 140 </tool>