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comparison transit_resampling.xml @ 11:daf2c40fc3f6 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 0daaffac75df549583b6d834113608c2dbacb1d3
author iuc
date Tue, 27 May 2025 19:58:37 +0000
parents 8863f1733e36
children
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10:8863f1733e36 11:daf2c40fc3f6
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="transit_resampling" name="TRANSIT Resampling" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 2 <tool id="transit_resampling" name="TRANSIT Resampling" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
3 <description>- determine per-gene p-values</description> 3 <description>- determine per-gene p-values</description>
4 <expand macro="bio_tools"/> 4 <expand macro="bio_tools"/>
5 <macros> 5 <macros>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
7 </macros> 7 </macros>
10 @LINK_INPUTS@ 10 @LINK_INPUTS@
11 #set $control_files = ','.join(['control_file_%d.wig' % idx for idx, _ in enumerate(str($controls).split(','))]) 11 #set $control_files = ','.join(['control_file_%d.wig' % idx for idx, _ in enumerate(str($controls).split(','))])
12 #for idx, filename in enumerate(str($controls).split(',')): 12 #for idx, filename in enumerate(str($controls).split(',')):
13 ln -s '$filename' control_file_${idx}.wig && 13 ln -s '$filename' control_file_${idx}.wig &&
14 #end for 14 #end for
15 transit resampling $input_files $control_files annotation.dat transit_out.txt 15 transit resampling $control_files $input_files annotation.dat transit_out.txt
16 @STANDARD_OPTIONS@ 16 @STANDARD_OPTIONS@
17 -s $samples $histogram $adaptive $exclude_zero $pseudo $loess 17 -s $samples $histogram $adaptive $exclude_zero $pseudo $loess
18 ]]> 18 ]]>
19 </command> 19 </command>
20 <inputs> 20 <inputs>
21 <expand macro="standard_inputs"> 21 <expand macro="standard_inputs">
22 <expand macro="handle_replicates" />
23 <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" />
24 <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" />
25 <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" />
26 <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" />
27 <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" />
33 <outputs> 32 <outputs>
34 <expand macro="outputs" /> 33 <expand macro="outputs" />
35 </outputs> 34 </outputs>
36 <tests> 35 <tests>
37 <test> 36 <test>
38 <param name="inputs" ftype="wig" value="transit-in1-rep1.wig,transit-in1-rep2.wig" /> 37 <conditional name="mode">
38 <param name="replicates" value="Replicates" />
39 <param name="inputs" ftype="wig" value="transit-in1-rep1.wig,transit-in1-rep2.wig" />
40 </conditional>
39 <param name="controls" ftype="wig" value="transit-co1-rep1.wig,transit-co1-rep2.wig,transit-co1-rep3.wig" /> 41 <param name="controls" ftype="wig" value="transit-co1-rep1.wig,transit-co1-rep2.wig,transit-co1-rep3.wig" />
40 <param name="annotation" ftype="tabular" value="transit-in1.prot" /> 42 <param name="annotation" ftype="tabular" value="transit-in1.prot" />
41 <param name="samples" value="1000" /> 43 <param name="samples" value="1000" />
42 <param name="replicates" value="Replicates" />
43 <output name="sites" file="resampling-sites1.txt" ftype="tabular" compare="sim_size" /> 44 <output name="sites" file="resampling-sites1.txt" ftype="tabular" compare="sim_size" />
44 </test> 45 </test>
45 </tests> 46 </tests>
46 47
47 <help> 48 <help>
85 -h := Output histogram of the permutations for each gene. Default: Off. 86 -h := Output histogram of the permutations for each gene. Default: Off.
86 -a := Perform adaptive resampling. Default: Off. 87 -a := Perform adaptive resampling. Default: Off.
87 -ez := Exclude rows with zero accross conditions. Default: Off 88 -ez := Exclude rows with zero accross conditions. Default: Off
88 --pc := Pseudocounts to be added at each site. Default: 0 89 --pc := Pseudocounts to be added at each site. Default: 0
89 -l := Perform LOESS Correction; Helps remove possible genomic position bias. Default: Off. 90 -l := Perform LOESS Correction; Helps remove possible genomic position bias. Default: Off.
90 -r <string> := How to handle replicates. Sum, Mean. Default: -r Mean
91 --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
92 --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
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. 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.
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. 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.
95 95
142 142
143 ------------------- 143 -------------------
144 144
145 See `TRANSIT documentation` 145 See `TRANSIT documentation`
146 146
147 - TRANSIT: https://transit.readthedocs.io/en/latest/index.html 147 - TRANSIT: https://transit.readthedocs.io/en/v@TOOL_VERSION@/index.html
148 - `TRANSIT Gumbel`: https://transit.readthedocs.io/en/latest/transit_methods.html#re-sampling 148 - `TRANSIT Gumbel`: https://transit.readthedocs.io/en/v@TOOL_VERSION@/transit_methods.html#re-sampling
149 ]]></help> 149 ]]></help>
150 150
151 <expand macro="citations" /> 151 <expand macro="citations" />
152 </tool> 152 </tool>