Mercurial > repos > iuc > transit_resampling
comparison transit_resampling.xml @ 3:0e0618c96ca4 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit bd061799ebd49ada1a666d0815720c18291728da"
author | iuc |
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date | Wed, 16 Oct 2019 04:31:43 -0400 |
parents | 335197e8f75e |
children | ad4d42fabf32 |
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2:335197e8f75e | 3:0e0618c96ca4 |
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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 |