| Previous changeset 2:335197e8f75e (2019-10-08) Next changeset 4:ad4d42fabf32 (2020-01-31) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit bd061799ebd49ada1a666d0815720c18291728da" |
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modified:
macros.xml transit_resampling.xml |
| b |
| diff -r 335197e8f75e -r 0e0618c96ca4 macros.xml --- a/macros.xml Tue Oct 08 08:23:54 2019 -0400 +++ b/macros.xml Wed Oct 16 04:31:43 2019 -0400 |
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| @@ -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> |
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| diff -r 335197e8f75e -r 0e0618c96ca4 transit_resampling.xml --- a/transit_resampling.xml Tue Oct 08 08:23:54 2019 -0400 +++ b/transit_resampling.xml Wed Oct 16 04:31:43 2019 -0400 |
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| @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="transit_resampling" name="Resampling" version="@VERSION@+galaxy1"> +<tool id="transit_resampling" name="Resampling" version="@VERSION@+galaxy2"> <description>- determine per-gene p-values</description> <macros> <import>macros.xml</import> @@ -18,6 +18,7 @@ </command> <inputs> <expand macro="standard_inputs"> + <expand macro="handle_replicates" /> <param name="controls" type="data" format="wig" multiple="true" label="Control .wig files" /> <param name="samples" argument="-s" type="integer" value="10000" label="Number of samples" /> <param name="histogram" argument="-h" type="boolean" truevalue="-h" falsevalue="" label="Output histogram of the permutations" /> @@ -86,6 +87,7 @@ -ez := Exclude rows with zero accross conditions. Default: Off --pc := Pseudocounts to be added at each site. Default: 0 -l := Perform LOESS Correction; Helps remove possible genomic position bias. Default: Off. +-r <string> := How to handle replicates. Sum, Mean. Default: -r Mean --iN <float> := Ignore TAs occuring at given fraction of the N terminus. Default: 0.0 --iC <float> := Ignore TAs occuring at given fraction of the C terminus. Default: 0.0 --ctrl_lib := String of letters representing library of control files in order e.g. 'AABB' Default: empty. Letters used must also be used in --exp_lib. If non-empty, resampling will limit permutations to within-libraries. |