Mercurial > repos > iuc > transit_tn5gaps
changeset 1:c68753eedf72 draft
"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 |
| files | macros.xml transit_tn5gaps.xml |
| diffstat | 2 files changed, 8 insertions(+), 5 deletions(-) [+] |
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--- a/macros.xml Tue Oct 08 08:24:46 2019 -0400 +++ b/macros.xml Wed Oct 16 04:32:50 2019 -0400 @@ -18,10 +18,10 @@ <yield /> <data name="sites" from_work_dir="transit_out.txt" format="tabular" label="${tool.name} on ${on_string} Sites" /> </xml> - <xml name="replicates"> - <param name="replicates" type="select" label="How to handle replicates"> + <xml name="handle_replicates"> + <param name="handle_replicates" type="select" label="How to handle replicates" value="Mean"> + <option value="Sum">Sum</option> <option value="Mean">Mean</option> - <option value="Sum">Sum</option> </param> </xml> <xml name="inputs"> @@ -78,5 +78,6 @@ -iN $nterm -tC $cterm -n $normalization + -r $handle_replicates </token> </macros>
--- a/transit_tn5gaps.xml Tue Oct 08 08:24:46 2019 -0400 +++ b/transit_tn5gaps.xml Wed Oct 16 04:32:50 2019 -0400 @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="transit_tn5gaps" name="Tn5Gaps" version="@VERSION@+galaxy1"> +<tool id="transit_tn5gaps" name="Tn5Gaps" version="@VERSION@+galaxy2"> <description>- determine essential genes</description> <macros> <import>macros.xml</import> @@ -14,6 +14,7 @@ </command> <inputs> <expand macro="standard_inputs"> + <expand macro="handle_replicates" /> <param name="smallest" argument="-m" type="integer" value="1" label="Smallest read-count to consider" /> </expand> </inputs> @@ -59,11 +60,12 @@ Optional Arguments: -m <integer> := Smallest read-count to consider. Default: -m 1 - -r <string> := How to handle replicates. Sum or Mean. Default: -r Sum + -r <string> := How to handle replicates. Sum or Mean. Default: -r Mean --iN <float> := Ignore TAs occuring at given fraction of the N terminus. Default: -iN 0.0 --iC <float> := Ignore TAs occuring at given fraction of the C terminus. Default: -iC 0.0 -n <string> := Determines which normalization method to use. Default -n TTR + - 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. - 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. - Normalisation :