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comparison transit_resampling.xml @ 0:8ccb1b841efb draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
author iuc
date Mon, 17 Dec 2018 11:02:16 -0500
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-1:000000000000 0:8ccb1b841efb
1 <?xml version="1.0"?>
2 <tool id="transit_resampling" name="Resampling" version="@VERSION@+galaxy0">
3 <description>- determine per-gene p-values</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <command detect_errors="exit_code"><![CDATA[
9 @LINK_INPUTS@
10 #set $control_files = ','.join(['control_file_%d.wig' % idx for idx, _ in enumerate(str($controls).split(','))])
11 #for idx, filename in enumerate(str($controls).split(',')):
12 ln -s '$filename' control_file_${idx}.wig &&
13 #end for
14 transit resampling $input_files $control_files annotation.dat transit_out.txt
15 @STANDARD_OPTIONS@
16 -s $samples -n $normalization $histogram $adaptive $exclude_zero $pseudo $loess
17 ]]>
18 </command>
19 <inputs>
20 <expand macro="standard_inputs">
21 <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="normalization" argument="-n" type="select" label="Normalization method">
24 <option value="TTR">TTR</option>
25 </param>
26 <param name="histogram" argument="-h" type="boolean" truevalue="-h" falsevalue="" label="Output histogram of the permutations" />
27 <param name="adaptive" argument="-a" type="boolean" truevalue="-a" falsevalue="" label="Perform adaptive resampling" />
28 <param name="exclude_zero" argument="-ez" type="boolean" truevalue="-ez" falsevalue="" label="Exclude rows with zero accross conditions" />
29 <param name="pseudo" argument="-pc" type="boolean" truevalue="-pc" falsevalue="" label="Add pseudocounts at each site" />
30 <param name="loess" argument="-l" type="boolean" truevalue="-l" falsevalue="" label="Perform LOESS Correction" help="Helps remove possible genomic position bias." />
31
32 </expand>
33 </inputs>
34 <outputs>
35 <expand macro="outputs" />
36 </outputs>
37 <tests>
38 <test>
39 <param name="inputs" ftype="wig" value="transit-in1-rep1.wig,transit-in1-rep2.wig" />
40 <param name="controls" ftype="wig" value="transit-co1-rep1.wig,transit-co1-rep2.wig,transit-co1-rep3.wig" />
41 <param name="annotation" ftype="gff3" value="transit-in1.gff3" />
42 <param name="samples" value="1000" />
43 <param name="burnin" value="100" />
44 <output name="sites" file="resampling-sites1.txt" ftype="tabular" compare="sim_size" />
45 </test>
46 </tests>
47 <help>
48 <![CDATA[
49 The re-sampling method is a comparative analysis the allows that can be used to determine conditional essentiality of genes. It is based on a permutation test, and is capable of determining read-counts that are significantly different across conditions.
50 ]]></help>
51 <expand macro="citations" />
52 </tool>