annotate macros.xml @ 5:8fc50fe60127 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit d1f8cb0c56e082656c5d4a8729e612bdc5b6e3cc"
author iuc
date Sat, 27 Nov 2021 09:48:57 +0000
parents f50807720df1
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
92496521fd39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
1 <?xml version="1.0"?>
92496521fd39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
2 <macros>
92496521fd39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
3 <xml name="citations">
92496521fd39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
4 <citations>
92496521fd39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
5 <citation type="doi">10.1371/journal.pcbi.1004401</citation>
92496521fd39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
6 <yield />
92496521fd39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
7 </citations>
92496521fd39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
8 </xml>
5
8fc50fe60127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit d1f8cb0c56e082656c5d4a8729e612bdc5b6e3cc"
iuc
parents: 4
diff changeset
9 <xml name="bio_tools">
8fc50fe60127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit d1f8cb0c56e082656c5d4a8729e612bdc5b6e3cc"
iuc
parents: 4
diff changeset
10 <xrefs>
8fc50fe60127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit d1f8cb0c56e082656c5d4a8729e612bdc5b6e3cc"
iuc
parents: 4
diff changeset
11 <xref type="bio.tools">transit</xref>
8fc50fe60127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit d1f8cb0c56e082656c5d4a8729e612bdc5b6e3cc"
iuc
parents: 4
diff changeset
12 </xrefs>
8fc50fe60127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit d1f8cb0c56e082656c5d4a8729e612bdc5b6e3cc"
iuc
parents: 4
diff changeset
13 </xml>
0
92496521fd39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
14 <xml name="requirements">
92496521fd39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
15 <requirements>
5
8fc50fe60127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit d1f8cb0c56e082656c5d4a8729e612bdc5b6e3cc"
iuc
parents: 4
diff changeset
16 <requirement type="package" version="@TOOL_VERSION@">transit</requirement>
0
92496521fd39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
17 <yield />
92496521fd39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
18 </requirements>
92496521fd39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
19 </xml>
5
8fc50fe60127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit d1f8cb0c56e082656c5d4a8729e612bdc5b6e3cc"
iuc
parents: 4
diff changeset
20 <token name="@TOOL_VERSION@">3.0.2</token>
8fc50fe60127 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit d1f8cb0c56e082656c5d4a8729e612bdc5b6e3cc"
iuc
parents: 4
diff changeset
21 <token name="@VERSION_SUFFIX@">1</token>
0
92496521fd39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
22 <xml name="outputs">
92496521fd39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
23 <yield />
92496521fd39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
24 <data name="sites" from_work_dir="transit_out.txt" format="tabular" label="${tool.name} on ${on_string} Sites" />
92496521fd39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
25 </xml>
3
ecce0cbe659f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit bd061799ebd49ada1a666d0815720c18291728da"
iuc
parents: 2
diff changeset
26 <xml name="handle_replicates">
ecce0cbe659f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit bd061799ebd49ada1a666d0815720c18291728da"
iuc
parents: 2
diff changeset
27 <param name="handle_replicates" type="select" label="How to handle replicates" value="Mean">
ecce0cbe659f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit bd061799ebd49ada1a666d0815720c18291728da"
iuc
parents: 2
diff changeset
28 <option value="Sum">Sum</option>
0
92496521fd39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
29 <option value="Mean">Mean</option>
92496521fd39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
30 </param>
92496521fd39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
31 </xml>
92496521fd39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
32 <xml name="inputs">
92496521fd39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
33 <conditional name="mode">
92496521fd39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
34 <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.">
92496521fd39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
35 <option value="Batch">Batch</option>
92496521fd39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
36 <option value="Replicates">Replicates</option>
92496521fd39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
37 </param>
92496521fd39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
38 <when value="Batch">
92496521fd39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
39 <param name="inputs" type="data" format="wig,tabular" multiple="false" label="Input .wig files" />
92496521fd39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
40 </when>
92496521fd39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
41 <when value="Replicates">
92496521fd39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
42 <param name="inputs" type="data" format="wig,tabular" multiple="true" label="Input .wig files" />
92496521fd39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
43 </when>
92496521fd39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
44 </conditional>
92496521fd39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
45 <yield />
92496521fd39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
46 <param name="annotation" type="data" format="gff3,tabular" label="Input annotation" />
92496521fd39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
47 </xml>
92496521fd39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
48 <xml name="ignore_tas">
92496521fd39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
49 <param name="nterm" argument="-iN" type="float" value="0" min="0" max="1" label="Ignore TAs occuring at given fraction of the N terminus." />
92496521fd39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
50 <param name="cterm" argument="-iC" type="float" value="0" min="0" max="1" label="Ignore TAs occuring at given fraction of the C terminus." />
92496521fd39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
51 </xml>
2
c980be2c002c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents: 1
diff changeset
52 <xml name="normal">
c980be2c002c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents: 1
diff changeset
53 <param name="normalization" argument="-n" type="select" label="Normalization method" value="TTR">
c980be2c002c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents: 1
diff changeset
54 <option value="TTR">TTR</option>
c980be2c002c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents: 1
diff changeset
55 <option value="nonorm">No Normalization</option>
c980be2c002c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents: 1
diff changeset
56 <option value="nzmean">Non-Zero Mean</option>
c980be2c002c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents: 1
diff changeset
57 <option value="totreads">Total read counts</option>
c980be2c002c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents: 1
diff changeset
58 <option value="zinfnb">Zero inflated Negative Binomial model</option>
c980be2c002c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents: 1
diff changeset
59 <option value="quantile">Quantile Normalization</option>
c980be2c002c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents: 1
diff changeset
60 <option value="betageom">Beta-Geometric Correction</option>
c980be2c002c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents: 1
diff changeset
61 </param>
c980be2c002c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents: 1
diff changeset
62 </xml>
0
92496521fd39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
63 <xml name="standard_inputs">
92496521fd39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
64 <expand macro="inputs" />
92496521fd39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
65 <yield />
92496521fd39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
66 <expand macro="ignore_tas" />
2
c980be2c002c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents: 1
diff changeset
67 <expand macro="normal" />
0
92496521fd39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
68 </xml>
92496521fd39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
69 <token name="@LINK_INPUTS@">
92496521fd39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
70 <![CDATA[
92496521fd39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
71 #if str($mode.replicates) == 'Batch':
92496521fd39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
72 #set $input_files = $mode.inputs
92496521fd39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
73 #else:
92496521fd39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
74 #set $input_files = ','.join(['input_file_%d.wig' % idx for idx, _ in enumerate(str($mode.inputs).split(','))])
92496521fd39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
75 #for idx, filename in enumerate(str($mode.inputs).split(',')):
92496521fd39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
76 ln -s '$filename' input_file_${idx}.wig &&
92496521fd39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
77 #end for
92496521fd39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
78 #end if
92496521fd39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
79 ln -s '$annotation' annotation.dat &&
92496521fd39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
80 ]]>
92496521fd39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
81 </token>
92496521fd39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
82 <token name="@STANDARD_OPTIONS@">
92496521fd39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
83 -iN $nterm
92496521fd39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
84 -tC $cterm
2
c980be2c002c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
iuc
parents: 1
diff changeset
85 -n $normalization
3
ecce0cbe659f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit bd061799ebd49ada1a666d0815720c18291728da"
iuc
parents: 2
diff changeset
86 -r $handle_replicates
0
92496521fd39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
87 </token>
92496521fd39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
88 </macros>