Mercurial > repos > iuc > transit_gumbel
changeset 3:ecce0cbe659f draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit bd061799ebd49ada1a666d0815720c18291728da"
| author | iuc |
|---|---|
| date | Wed, 16 Oct 2019 04:32:08 -0400 |
| parents | c980be2c002c |
| children | f50807720df1 |
| files | macros.xml transit_gumbel.xml |
| diffstat | 2 files changed, 7 insertions(+), 5 deletions(-) [+] |
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--- a/macros.xml Tue Oct 08 08:24:12 2019 -0400 +++ b/macros.xml Wed Oct 16 04:32:08 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_gumbel.xml Tue Oct 08 08:24:12 2019 -0400 +++ b/transit_gumbel.xml Wed Oct 16 04:32:08 2019 -0400 @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="transit_gumbel" name="Gumbel" version="@VERSION@+galaxy1"> +<tool id="transit_gumbel" name="Gumbel" 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="samples" argument="-s" type="integer" value="10000" label="Number of samples" /> <param name="burnin" argument="-b" type="integer" value="500" label="Number of Burn-in samples" /> <param name="smallest" argument="-m" type="integer" value="1" label="Smallest read-count to consider" /> @@ -68,7 +69,7 @@ -b <integer> := Number of Burn-in samples. Default -b 500 -m <integer> := Smallest read-count to consider. Default: -m 1 -t <integer> := Trims all but every t-th value. Default: -t 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