Mercurial > repos > iuc > transit_tn5gaps

annotate macros.xml @ 1:c68753eedf72 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit bd061799ebd49ada1a666d0815720c18291728da"
author iuc
date Wed, 16 Oct 2019 04:32:50 -0400
parents e4f44f327cf1
children 4aaabd55eab8
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
1 <?xml version="1.0"?>
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
2 <macros>
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
3 <xml name="citations">
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
4 <citations>
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
5 <citation type="doi">10.1371/journal.pcbi.1004401</citation>
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
6 <yield />
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
7 </citations>
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
8 </xml>
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
9 <xml name="requirements">
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
10 <requirements>
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
11 <requirement type="package" version="@VERSION@">transit</requirement>
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
12 <requirement type="package" version="3.7">python</requirement>
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
13 <yield />
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
14 </requirements>
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
15 </xml>
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
16 <token name="@VERSION@">3.0.1</token>
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
17 <xml name="outputs">
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
18 <yield />
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
19 <data name="sites" from_work_dir="transit_out.txt" format="tabular" label="${tool.name} on ${on_string} Sites" />
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
20 </xml>
1
c68753eedf72 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit bd061799ebd49ada1a666d0815720c18291728da"
iuc
parents: 0
diff changeset
21 <xml name="handle_replicates">
c68753eedf72 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit bd061799ebd49ada1a666d0815720c18291728da"
iuc
parents: 0
diff changeset
22 <param name="handle_replicates" type="select" label="How to handle replicates" value="Mean">
c68753eedf72 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit bd061799ebd49ada1a666d0815720c18291728da"
iuc
parents: 0
diff changeset
23 <option value="Sum">Sum</option>
0
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
24 <option value="Mean">Mean</option>
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
25 </param>
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
26 </xml>
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
27 <xml name="inputs">
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
28 <conditional name="mode">
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
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.">
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
30 <option value="Batch">Batch</option>
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
31 <option value="Replicates">Replicates</option>
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
32 </param>
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
33 <when value="Batch">
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
34 <param name="inputs" type="data" format="wig,tabular" multiple="false" label="Input .wig files" />
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
35 </when>
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
36 <when value="Replicates">
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
37 <param name="inputs" type="data" format="wig,tabular" multiple="true" label="Input .wig files" />
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
38 </when>
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
39 </conditional>
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
40 <yield />
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
41 <param name="annotation" type="data" format="gff3,tabular" label="Input annotation" />
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
42 </xml>
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
43 <xml name="ignore_tas">
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
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." />
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
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." />
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
46 </xml>
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
47 <xml name="normal">
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
48 <param name="normalization" argument="-n" type="select" label="Normalization method" value="TTR">
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
49 <option value="TTR">TTR</option>
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
50 <option value="nonorm">No Normalization</option>
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
51 <option value="nzmean">Non-Zero Mean</option>
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
52 <option value="totreads">Total read counts</option>
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
53 <option value="zinfnb">Zero inflated Negative Binomial model</option>
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
54 <option value="quantile">Quantile Normalization</option>
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
55 <option value="betageom">Beta-Geometric Correction</option>
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
56 </param>
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
57 </xml>
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
58 <xml name="standard_inputs">
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
59 <expand macro="inputs" />
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
60 <yield />
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
61 <expand macro="ignore_tas" />
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
62 <expand macro="normal" />
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
63 </xml>
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
64 <token name="@LINK_INPUTS@">
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
65 <![CDATA[
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
66 #if str($mode.replicates) == 'Batch':
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
67 #set $input_files = $mode.inputs
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
68 #else:
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
69 #set $input_files = ','.join(['input_file_%d.wig' % idx for idx, _ in enumerate(str($mode.inputs).split(','))])
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
70 #for idx, filename in enumerate(str($mode.inputs).split(',')):
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
71 ln -s '$filename' input_file_${idx}.wig &&
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
72 #end for
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
73 #end if
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
74 ln -s '$annotation' annotation.dat &&
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
75 ]]>
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
76 </token>
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
77 <token name="@STANDARD_OPTIONS@">
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
78 -iN $nterm
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
79 -tC $cterm
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
80 -n $normalization
1
c68753eedf72 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit bd061799ebd49ada1a666d0815720c18291728da"
iuc
parents: 0
diff changeset
81 -r $handle_replicates
0
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
82 </token>
e4f44f327cf1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents:
diff changeset
83 </macros>