annotate macros.xml @ 20:04bb8bb7c198 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c6eab3b60743dfa415dc135d657267cc8a0a31ce
author iuc
date Tue, 08 Aug 2023 09:11:17 +0000
parents 1b1a25f93f80
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
7e6f53726329 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
1 <macros>
7e6f53726329 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
2 <xml name="requirements">
7e6f53726329 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
3 <requirements>
19
1b1a25f93f80 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
iuc
parents: 16
diff changeset
4 <requirement type="package" version="@TOOL_VERSION@">trinity</requirement>
0
7e6f53726329 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
5 <yield/>
7e6f53726329 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
6 </requirements>
7e6f53726329 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
7 </xml>
16
b58468eb4e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 33aaad8d6afce20732d8232fbcd777a3aabf09ec"
iuc
parents: 14
diff changeset
8 <xml name="bio_tools">
b58468eb4e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 33aaad8d6afce20732d8232fbcd777a3aabf09ec"
iuc
parents: 14
diff changeset
9 <xrefs>
b58468eb4e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 33aaad8d6afce20732d8232fbcd777a3aabf09ec"
iuc
parents: 14
diff changeset
10 <xref type="bio.tools">trinity</xref>
b58468eb4e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 33aaad8d6afce20732d8232fbcd777a3aabf09ec"
iuc
parents: 14
diff changeset
11 </xrefs>
b58468eb4e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 33aaad8d6afce20732d8232fbcd777a3aabf09ec"
iuc
parents: 14
diff changeset
12 </xml>
19
1b1a25f93f80 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
iuc
parents: 16
diff changeset
13 <token name="@TOOL_VERSION@">2.15.1</token>
1b1a25f93f80 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
iuc
parents: 16
diff changeset
14 <token name="@VERSION_SUFFIX@">0</token>
0
7e6f53726329 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
15
7
77983b40ffb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 5
diff changeset
16 <token name="@COMMAND_PAIRED_STRAND_JACCARD@">
19
1b1a25f93f80 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
iuc
parents: 16
diff changeset
17 #if $pool.inputs.strand.is_strand_specific == 'true':
9
226663afe49c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
parents: 7
diff changeset
18 --SS_lib_type $pool.inputs.strand.library_type
7
77983b40ffb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 5
diff changeset
19 #end if
77983b40ffb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 5
diff changeset
20
9
226663afe49c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
parents: 7
diff changeset
21 $pool.inputs.jaccard_clip
7
77983b40ffb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 5
diff changeset
22 </token>
77983b40ffb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 5
diff changeset
23
77983b40ffb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 5
diff changeset
24 <xml name="input_paired_strand_jaccard">
77983b40ffb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 5
diff changeset
25 <conditional name="strand">
19
1b1a25f93f80 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
iuc
parents: 16
diff changeset
26 <param name="is_strand_specific" type="select" label="Strand specific data">
1b1a25f93f80 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
iuc
parents: 16
diff changeset
27 <option value="false">No</option>
1b1a25f93f80 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
iuc
parents: 16
diff changeset
28 <option value="true">Yes</option>
1b1a25f93f80 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
iuc
parents: 16
diff changeset
29 </param>
7
77983b40ffb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 5
diff changeset
30 <when value="false" />
77983b40ffb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 5
diff changeset
31 <when value="true">
77983b40ffb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 5
diff changeset
32 <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific library type">
77983b40ffb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 5
diff changeset
33 <option value="FR">Forward-Reverse</option>
77983b40ffb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 5
diff changeset
34 <option value="RF">Reverse-Forward</option>
77983b40ffb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 5
diff changeset
35 </param>
77983b40ffb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 5
diff changeset
36 </when>
77983b40ffb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 5
diff changeset
37 </conditional>
10
44971c7016b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 482fb46ba8d588f2294e21829a0904809b0ec3f1
iuc
parents: 9
diff changeset
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"/>
7
77983b40ffb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 5
diff changeset
39 </xml>
77983b40ffb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 5
diff changeset
40
19
1b1a25f93f80 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
iuc
parents: 16
diff changeset
41 <xml name="is_strand_specific_f_r">
1b1a25f93f80 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
iuc
parents: 16
diff changeset
42 <conditional name="strand">
1b1a25f93f80 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
iuc
parents: 16
diff changeset
43 <param name="is_strand_specific" type="select" label="Strand specific data">
1b1a25f93f80 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
iuc
parents: 16
diff changeset
44 <option value="false">No</option>
1b1a25f93f80 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
iuc
parents: 16
diff changeset
45 <option value="true">Yes</option>
1b1a25f93f80 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
iuc
parents: 16
diff changeset
46 </param>
1b1a25f93f80 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
iuc
parents: 16
diff changeset
47 <when value="false"/>
1b1a25f93f80 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
iuc
parents: 16
diff changeset
48 <when value="true">
1b1a25f93f80 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
iuc
parents: 16
diff changeset
49 <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific Library Type">
1b1a25f93f80 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
iuc
parents: 16
diff changeset
50 <option value="F">F</option>
1b1a25f93f80 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
iuc
parents: 16
diff changeset
51 <option value="R">R</option>
1b1a25f93f80 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
iuc
parents: 16
diff changeset
52 </param>
1b1a25f93f80 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
iuc
parents: 16
diff changeset
53 </when>
1b1a25f93f80 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
iuc
parents: 16
diff changeset
54 </conditional>
1b1a25f93f80 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
iuc
parents: 16
diff changeset
55 </xml>
1b1a25f93f80 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
iuc
parents: 16
diff changeset
56
0
7e6f53726329 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
57 <xml name="citation">
7e6f53726329 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
58 <citations>
7e6f53726329 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
59 <citation type="doi">10.1038/nbt.1883</citation>
7e6f53726329 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
60 </citations>
7e6f53726329 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
61 </xml>
7e6f53726329 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
62 </macros>