Mercurial > repos > iuc > trinity_stats

comparison macros.xml @ 0:ce94ad22e8c1 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c6eab3b60743dfa415dc135d657267cc8a0a31ce
author iuc
date Tue, 08 Aug 2023 09:00:45 +0000
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-1:000000000000 0:ce94ad22e8c1
1 <macros>
2 <xml name="requirements">
3 <requirements>
4 <requirement type="package" version="@TOOL_VERSION@">trinity</requirement>
5 <yield/>
6 </requirements>
7 </xml>
8 <xml name="bio_tools">
9 <xrefs>
10 <xref type="bio.tools">trinity</xref>
11 </xrefs>
12 </xml>
13 <token name="@TOOL_VERSION@">2.15.1</token>
14 <token name="@VERSION_SUFFIX@">0</token>
15
16 <token name="@COMMAND_PAIRED_STRAND_JACCARD@">
17 #if $pool.inputs.strand.is_strand_specific == 'true':
18 --SS_lib_type $pool.inputs.strand.library_type
19 #end if
20
21 $pool.inputs.jaccard_clip
22 </token>
23
24 <xml name="input_paired_strand_jaccard">
25 <conditional name="strand">
26 <param name="is_strand_specific" type="select" label="Strand specific data">
27 <option value="false">No</option>
28 <option value="true">Yes</option>
29 </param>
30 <when value="false" />
31 <when value="true">
32 <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific library type">
33 <option value="FR">Forward-Reverse</option>
34 <option value="RF">Reverse-Forward</option>
35 </param>
36 </when>
37 </conditional>
38 <param argument="--jaccard_clip" type="boolean" truevalue="--jaccard_clip" falsevalue="" checked="false" label="Jaccard Clip options" help="Set if you expect high gene density with UTR overlap"/>
39 </xml>
40
41 <xml name="is_strand_specific_f_r">
42 <conditional name="strand">
43 <param name="is_strand_specific" type="select" label="Strand specific data">
44 <option value="false">No</option>
45 <option value="true">Yes</option>
46 </param>
47 <when value="false"/>
48 <when value="true">
49 <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific Library Type">
50 <option value="F">F</option>
51 <option value="R">R</option>
52 </param>
53 </when>
54 </conditional>
55 </xml>
56
57 <xml name="citation">
58 <citations>
59 <citation type="doi">10.1038/nbt.1883</citation>
60 </citations>
61 </xml>
62 </macros>