Mercurial > repos > iuc > transit_resampling

comparison macros.xml @ 0:043a6feaa8bc draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
author iuc
date Mon, 22 Apr 2019 14:42:47 -0400
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children 73a3ea18ec71
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-1:000000000000 0:043a6feaa8bc
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@">2.3.3</token>
16 <xml name="outputs">
17 <yield />
18 <data name="sites" from_work_dir="transit_out.txt" format="tabular" label="${tool.name} on ${on_string} Sites" />
19 </xml>
20 <xml name="replicates">
21 <param name="replicates" type="select" label="How to handle replicates">
22 <option value="Mean">Mean</option>
23 <option value="Sum">Sum</option>
24 </param>
25 </xml>
26 <xml name="inputs">
27 <conditional name="mode">
28 <param name="replicates" type="select" label="Operation mode" help="If set to 'Batch', transit will run and produce one output for each input file. If set to 'Replicates', transit will run once on all the input files.">
29 <option value="Batch">Batch</option>
30 <option value="Replicates">Replicates</option>
31 </param>
32 <when value="Batch">
33 <param name="inputs" type="data" format="wig,tabular" multiple="false" label="Input .wig files" />
34 </when>
35 <when value="Replicates">
36 <param name="inputs" type="data" format="wig,tabular" multiple="true" label="Input .wig files" />
37 </when>
38 </conditional>
39 <yield />
40 <param name="annotation" type="data" format="gff3,tabular" label="Input annotation" />
41 </xml>
42 <xml name="ignore_tas">
43 <param name="nterm" argument="-iN" type="float" value="0" min="0" max="1" label="Ignore TAs occuring at given fraction of the N terminus." />
44 <param name="cterm" argument="-iC" type="float" value="0" min="0" max="1" label="Ignore TAs occuring at given fraction of the C terminus." />
45 </xml>
46 <xml name="standard_inputs">
47 <expand macro="inputs" />
48 <yield />
49 <expand macro="ignore_tas" />
50 </xml>
51 <token name="@LINK_INPUTS@">
52 <![CDATA[
53 #if str($mode.replicates) == 'Batch':
54 #set $input_files = $mode.inputs
55 #else:
56 #set $input_files = ','.join(['input_file_%d.wig' % idx for idx, _ in enumerate(str($mode.inputs).split(','))])
57 #for idx, filename in enumerate(str($mode.inputs).split(',')):
58 ln -s '$filename' input_file_${idx}.wig &&
59 #end for
60 #end if
61 ln -s '$annotation' annotation.dat &&
62 ]]>
63 </token>
64 <token name="@STANDARD_OPTIONS@">
65 -iN $nterm
66 -tC $cterm
67 </token>
68 </macros>