Mercurial > repos > iuc > transit_resampling

comparison transit_resampling.xml @ 8:32a5211380bc 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 04:29:26 -0400
parents 8ab1c8c909a7
children 9c8cae95df54
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7:8ab1c8c909a7 8:32a5211380bc
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="transit_resampling" name="Resampling" version="@VERSION@+galaxy1"> 2 <tool id="transit_resampling" name="Resampling" version="@VERSION@+galaxy2">
3 <description>- determine per-gene p-values</description> 3 <description>- determine per-gene p-values</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" />
16 -s $samples $histogram $adaptive $exclude_zero $pseudo $loess 16 -s $samples $histogram $adaptive $exclude_zero $pseudo $loess
17 ]]> 17 ]]>
18 </command> 18 </command>
19 <inputs> 19 <inputs>
20 <expand macro="standard_inputs"> 20 <expand macro="standard_inputs">
21 <expand macro="handle_replicates" />
21 <param name="controls" type="data" format="wig" multiple="true" label="Control .wig files" /> 22 <param name="controls" type="data" format="wig" multiple="true" label="Control .wig files" />
22 <param name="samples" argument="-s" type="integer" value="10000" label="Number of samples" /> 23 <param name="samples" argument="-s" type="integer" value="10000" label="Number of samples" />
23 <param name="histogram" argument="-h" type="boolean" truevalue="-h" falsevalue="" label="Output histogram of the permutations" /> 24 <param name="histogram" argument="-h" type="boolean" truevalue="-h" falsevalue="" label="Output histogram of the permutations" />
24 <param name="adaptive" argument="-a" type="boolean" truevalue="-a" falsevalue="" label="Perform adaptive resampling" /> 25 <param name="adaptive" argument="-a" type="boolean" truevalue="-a" falsevalue="" label="Perform adaptive resampling" />
25 <param name="exclude_zero" argument="-ez" type="boolean" truevalue="-ez" falsevalue="" label="Exclude rows with zero accross conditions" /> 26 <param name="exclude_zero" argument="-ez" type="boolean" truevalue="-ez" falsevalue="" label="Exclude rows with zero accross conditions" />
84 -h := Output histogram of the permutations for each gene. Default: Off. 85 -h := Output histogram of the permutations for each gene. Default: Off.
85 -a := Perform adaptive resampling. Default: Off. 86 -a := Perform adaptive resampling. Default: Off.
86 -ez := Exclude rows with zero accross conditions. Default: Off 87 -ez := Exclude rows with zero accross conditions. Default: Off
87 --pc := Pseudocounts to be added at each site. Default: 0 88 --pc := Pseudocounts to be added at each site. Default: 0
88 -l := Perform LOESS Correction; Helps remove possible genomic position bias. Default: Off. 89 -l := Perform LOESS Correction; Helps remove possible genomic position bias. Default: Off.
90 -r <string> := How to handle replicates. Sum, Mean. Default: -r Mean
89 --iN <float> := Ignore TAs occuring at given fraction of the N terminus. Default: 0.0 91 --iN <float> := Ignore TAs occuring at given fraction of the N terminus. Default: 0.0
90 --iC <float> := Ignore TAs occuring at given fraction of the C terminus. Default: 0.0 92 --iC <float> := Ignore TAs occuring at given fraction of the C terminus. Default: 0.0
91 --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. 93 --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.
92 --exp_lib := String of letters representing library of experimental files in order e.g. 'ABAB' Default: empty. Letters used must also be used in --ctrl_lib. If non-empty, resampling will limit permutations to within-libraries. 94 --exp_lib := String of letters representing library of experimental files in order e.g. 'ABAB' Default: empty. Letters used must also be used in --ctrl_lib. If non-empty, resampling will limit permutations to within-libraries.
93 95