comparison transit_resampling.xml @ 3:0e0618c96ca4 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit bd061799ebd49ada1a666d0815720c18291728da"

2:335197e8f75e

<?xml version="1.0"?>
<tool id="transit_resampling" name="Resampling" version="@VERSION@+galaxy1">
    <description>- determine per-gene p-values</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />

        -s $samples $histogram $adaptive $exclude_zero $pseudo $loess
        ]]>
    </command>
    <inputs>
        <expand macro="standard_inputs">
            <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" />
            <param name="adaptive" argument="-a" type="boolean" truevalue="-a" falsevalue="" label="Perform adaptive resampling" />
            <param name="exclude_zero" argument="-ez" type="boolean" truevalue="-ez" falsevalue="" label="Exclude rows with zero accross conditions" />

-h              :=  Output histogram of the permutations for each gene. Default: Off.
-a              :=  Perform adaptive resampling. Default: Off.
-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.
--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.
--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.

3:0e0618c96ca4

<?xml version="1.0"?>
<tool id="transit_resampling" name="Resampling" version="@VERSION@+galaxy2">
    <description>- determine per-gene p-values</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />

        -s $samples $histogram $adaptive $exclude_zero $pseudo $loess
        ]]>
    </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" />
            <param name="adaptive" argument="-a" type="boolean" truevalue="-a" falsevalue="" label="Perform adaptive resampling" />
            <param name="exclude_zero" argument="-ez" type="boolean" truevalue="-ez" falsevalue="" label="Exclude rows with zero accross conditions" />

-h              :=  Output histogram of the permutations for each gene. Default: Off.
-a              :=  Perform adaptive resampling. Default: Off.
-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.
--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.