Mercurial > repos > iuc > transit_resampling

comparison macros.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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children 1d1ca6b30fbb
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-1:000000000000 0:8ccb1b841efb
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 <yield />
13 </requirements>
14 </xml>
15 <token name="@VERSION@">2.3.1</token>
16 <xml name="outputs">
17 <yield />
18 <data name="sites" from_work_dir="transit_out.txt" format="tabular" label="${tool.name} on ${on_string} Sites" />
19 </xml>
20 <xml name="replicates">
21 <param name="replicates" type="select" label="How to handle replicates">
22 <option value="Mean">Mean</option>
23 <option value="Sum">Sum</option>
24 </param>
25 </xml>
26 <xml name="inputs">
27 <param name="inputs" type="data" format="wig" multiple="true" label="Input .wig files" />
28 <yield />
29 <param name="annotation" type="data" format="gff3" label="Input annotation" />
30 </xml>
31 <xml name="ignore_tas">
32 <param name="nterm" argument="-iN" type="float" value="0" min="0" max="1" label="Ignore TAs occuring at given fraction of the N terminus." />
33 <param name="cterm" argument="-iC" type="float" value="0" min="0" max="1" label="Ignore TAs occuring at given fraction of the C terminus." />
34 </xml>
35 <xml name="standard_inputs">
36 <expand macro="inputs" />
37 <yield />
38 <expand macro="ignore_tas" />
39 </xml>
40 <token name="@LINK_INPUTS@">
41 <![CDATA[
42 #set $input_files = ','.join(['input_file_%d.wig' % idx for idx, _ in enumerate(str($inputs).split(','))])
43 #for idx, filename in enumerate(str($inputs).split(',')):
44 ln -s '$filename' input_file_${idx}.wig &&
45 #end for
46 ln -s '$annotation' annotation.dat &&
47 ]]>
48 </token>
49 <token name="@STANDARD_OPTIONS@">
50 -iN $nterm
51 -tC $cterm
52 </token>
53 </macros>