Mercurial > repos > iuc > transit_tn5gaps

comparison macros.xml @ 0:1d91e33bb73b draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
author iuc
date Tue, 08 Oct 2019 08:22:57 -0400
parents
children 14173ac32110
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-1:000000000000 0:1d91e33bb73b
1 <?xml version="1.0"?>
2 <macros>
3 <xml name="citations">
4 <citations>
5 <citation type="doi">10.1371/journal.pcbi.1004401</citation>
6 <yield />
7 </citations>
8 </xml>
9 <xml name="requirements">
10 <requirements>
11 <requirement type="package" version="@VERSION@">transit</requirement>
12 <requirement type="package" version="3.7">python</requirement>
13 <yield />
14 </requirements>
15 </xml>
16 <token name="@VERSION@">3.0.1</token>
17 <xml name="outputs">
18 <yield />
19 <data name="sites" from_work_dir="transit_out.txt" format="tabular" label="${tool.name} on ${on_string} Sites" />
20 </xml>
21 <xml name="replicates">
22 <param name="replicates" type="select" label="How to handle replicates">
23 <option value="Mean">Mean</option>
24 <option value="Sum">Sum</option>
25 </param>
26 </xml>
27 <xml name="inputs">
28 <conditional name="mode">
29 <param name="replicates" type="select" label="Operation mode" help="If set to 'Batch', transit will run and produce one output for each input file. If set to 'Replicates', transit will run once on all the input files.">
30 <option value="Batch">Batch</option>
31 <option value="Replicates">Replicates</option>
32 </param>
33 <when value="Batch">
34 <param name="inputs" type="data" format="wig,tabular" multiple="false" label="Input .wig files" />
35 </when>
36 <when value="Replicates">
37 <param name="inputs" type="data" format="wig,tabular" multiple="true" label="Input .wig files" />
38 </when>
39 </conditional>
40 <yield />
41 <param name="annotation" type="data" format="gff3,tabular" label="Input annotation" />
42 </xml>
43 <xml name="ignore_tas">
44 <param name="nterm" argument="-iN" type="float" value="0" min="0" max="1" label="Ignore TAs occuring at given fraction of the N terminus." />
45 <param name="cterm" argument="-iC" type="float" value="0" min="0" max="1" label="Ignore TAs occuring at given fraction of the C terminus." />
46 </xml>
47 <xml name="normal">
48 <param name="normalization" argument="-n" type="select" label="Normalization method" value="TTR">
49 <option value="TTR">TTR</option>
50 <option value="nonorm">No Normalization</option>
51 <option value="nzmean">Non-Zero Mean</option>
52 <option value="totreads">Total read counts</option>
53 <option value="zinfnb">Zero inflated Negative Binomial model</option>
54 <option value="quantile">Quantile Normalization</option>
55 <option value="betageom">Beta-Geometric Correction</option>
56 </param>
57 </xml>
58 <xml name="standard_inputs">
59 <expand macro="inputs" />
60 <yield />
61 <expand macro="ignore_tas" />
62 <expand macro="normal" />
63 </xml>
64 <token name="@LINK_INPUTS@">
65 <![CDATA[
66 #if str($mode.replicates) == 'Batch':
67 #set $input_files = $mode.inputs
68 #else:
69 #set $input_files = ','.join(['input_file_%d.wig' % idx for idx, _ in enumerate(str($mode.inputs).split(','))])
70 #for idx, filename in enumerate(str($mode.inputs).split(',')):
71 ln -s '$filename' input_file_${idx}.wig &&
72 #end for
73 #end if
74 ln -s '$annotation' annotation.dat &&
75 ]]>
76 </token>
77 <token name="@STANDARD_OPTIONS@">
78 -iN $nterm
79 -tC $cterm
80 -n $normalization
81 </token>
82 </macros>