Mercurial > repos > iuc > transit_tn5gaps

comparison transit_tn5gaps.xml @ 1:c68753eedf72 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit bd061799ebd49ada1a666d0815720c18291728da"
author iuc
date Wed, 16 Oct 2019 04:32:50 -0400
parents e4f44f327cf1
children 4aaabd55eab8
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0:e4f44f327cf1 1:c68753eedf72
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="transit_tn5gaps" name="Tn5Gaps" version="@VERSION@+galaxy1"> 2 <tool id="transit_tn5gaps" name="Tn5Gaps" version="@VERSION@+galaxy2">
3 <description>- determine essential genes</description> 3 <description>- determine essential genes</description>
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
12 -m $smallest 12 -m $smallest
13 ]]> 13 ]]>
14 </command> 14 </command>
15 <inputs> 15 <inputs>
16 <expand macro="standard_inputs"> 16 <expand macro="standard_inputs">
17 <expand macro="handle_replicates" />
17 <param name="smallest" argument="-m" type="integer" value="1" label="Smallest read-count to consider" /> 18 <param name="smallest" argument="-m" type="integer" value="1" label="Smallest read-count to consider" />
18 </expand> 19 </expand>
19 </inputs> 20 </inputs>
20 <outputs> 21 <outputs>
21 <expand macro="outputs" /> 22 <expand macro="outputs" />
57 58
58 ------------------- 59 -------------------
59 60
60 Optional Arguments: 61 Optional Arguments:
61 -m <integer> := Smallest read-count to consider. Default: -m 1 62 -m <integer> := Smallest read-count to consider. Default: -m 1
62 -r <string> := How to handle replicates. Sum or Mean. Default: -r Sum 63 -r <string> := How to handle replicates. Sum or Mean. Default: -r Mean
63 --iN <float> := Ignore TAs occuring at given fraction of the N terminus. Default: -iN 0.0 64 --iN <float> := Ignore TAs occuring at given fraction of the N terminus. Default: -iN 0.0
64 --iC <float> := Ignore TAs occuring at given fraction of the C terminus. Default: -iC 0.0 65 --iC <float> := Ignore TAs occuring at given fraction of the C terminus. Default: -iC 0.0
65 -n <string> := Determines which normalization method to use. Default -n TTR 66 -n <string> := Determines which normalization method to use. Default -n TTR
67
66 68
67 - Minimum Read: The minimum read count that is considered a true read. Because the Gumbel method depends on determining gaps of TA sites lacking insertions, it may be susceptible to spurious reads (e.g. errors). The default value of 1 will consider all reads as true reads. A value of 2, for example, will ignore read counts of 1. 69 - Minimum Read: The minimum read count that is considered a true read. Because the Gumbel method depends on determining gaps of TA sites lacking insertions, it may be susceptible to spurious reads (e.g. errors). The default value of 1 will consider all reads as true reads. A value of 2, for example, will ignore read counts of 1.
68 - Replicates: Determines how to deal with replicates by averaging the read-counts or summing read counts across datasets. This should not have an affect for the Gumbel method, aside from potentially affecting spurious reads. 70 - Replicates: Determines how to deal with replicates by averaging the read-counts or summing read counts across datasets. This should not have an affect for the Gumbel method, aside from potentially affecting spurious reads.
69 - Normalisation : 71 - Normalisation :
70 - TTR (Default) : Trimmed Total Reads (TTR), normalized by the total read-counts (like totreads), but trims top and bottom 5% of read-counts. This is the recommended normalization method for most cases as it has the beneffit of normalizing for difference in saturation in the context of resampling. 72 - TTR (Default) : Trimmed Total Reads (TTR), normalized by the total read-counts (like totreads), but trims top and bottom 5% of read-counts. This is the recommended normalization method for most cases as it has the beneffit of normalizing for difference in saturation in the context of resampling.