Mercurial > repos > iuc > trinity_define_clusters_by_cutting_tree
comparison macros.xml @ 18:ae501908a17f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
author | iuc |
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date | Tue, 11 Apr 2023 19:50:15 +0000 |
parents | 718a5b66395e |
children |
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17:5192f657f305 | 18:ae501908a17f |
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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> |