Mercurial > repos > iuc > trinity_gene_to_trans_map

comparison macros.xml @ 19:ba460ccf0006 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
author iuc
date Tue, 11 Apr 2023 19:54:25 +0000
parents 318fd1a0646d
children
comparison
equal deleted inserted replaced
18:964b7efe2639 19:ba460ccf0006
1 <?xml version="1.0"?>
2 <macros> 1 <macros>
3 <xml name="requirements"> 2 <xml name="requirements">
4 <requirements> 3 <requirements>
5 <requirement type="package" version="@WRAPPER_VERSION@">trinity</requirement> 4 <requirement type="package" version="@TOOL_VERSION@">trinity</requirement>
6 <yield/> 5 <yield/>
7 </requirements> 6 </requirements>
8 </xml> 7 </xml>
9 <xml name="bio_tools"> 8 <xml name="bio_tools">
10 <xrefs> 9 <xrefs>
11 <xref type="bio.tools">trinity</xref> 10 <xref type="bio.tools">trinity</xref>
12 </xrefs> 11 </xrefs>
13 </xml> 12 </xml>
14 <token name="@WRAPPER_VERSION@">2.9.1</token> 13 <token name="@TOOL_VERSION@">2.15.1</token>
14 <token name="@VERSION_SUFFIX@">0</token>
15 15
16 <token name="@COMMAND_PAIRED_STRAND_JACCARD@"> 16 <token name="@COMMAND_PAIRED_STRAND_JACCARD@">
17 #if $pool.inputs.strand.is_strand_specific: 17 #if $pool.inputs.strand.is_strand_specific == 'true':
18 --SS_lib_type $pool.inputs.strand.library_type 18 --SS_lib_type $pool.inputs.strand.library_type
19 #end if 19 #end if
20 20
21 $pool.inputs.jaccard_clip 21 $pool.inputs.jaccard_clip
22 </token> 22 </token>
23 23
24 <xml name="input_paired_strand_jaccard"> 24 <xml name="input_paired_strand_jaccard">
25 <conditional name="strand"> 25 <conditional name="strand">
26 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/> 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>
27 <when value="false" /> 30 <when value="false" />
28 <when value="true"> 31 <when value="true">
29 <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific library type"> 32 <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific library type">
30 <option value="FR">Forward-Reverse</option> 33 <option value="FR">Forward-Reverse</option>
31 <option value="RF">Reverse-Forward</option> 34 <option value="RF">Reverse-Forward</option>
33 </when> 36 </when>
34 </conditional> 37 </conditional>
35 <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"/> 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"/>
36 </xml> 39 </xml>
37 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
38 <xml name="citation"> 57 <xml name="citation">
39 <citations> 58 <citations>
40 <citation type="doi">10.1038/nbt.1883</citation> 59 <citation type="doi">10.1038/nbt.1883</citation>
41 </citations> 60 </citations>
42 </xml> 61 </xml>