annotate macros.xml @ 15:41db7569b4ba draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
author iuc
date Tue, 11 Apr 2023 19:48:34 +0000
parents 34840e9c79b0
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
1e8a2c87461a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit ed037d83415937b11a45a4611584e71e99ad1da0
iuc
parents:
diff changeset
1 <macros>
1e8a2c87461a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit ed037d83415937b11a45a4611584e71e99ad1da0
iuc
parents:
diff changeset
2 <xml name="requirements">
1e8a2c87461a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit ed037d83415937b11a45a4611584e71e99ad1da0
iuc
parents:
diff changeset
3 <requirements>
15
41db7569b4ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
iuc
parents: 12
diff changeset
4 <requirement type="package" version="@TOOL_VERSION@">trinity</requirement>
0
1e8a2c87461a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit ed037d83415937b11a45a4611584e71e99ad1da0
iuc
parents:
diff changeset
5 <yield/>
1e8a2c87461a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit ed037d83415937b11a45a4611584e71e99ad1da0
iuc
parents:
diff changeset
6 </requirements>
1e8a2c87461a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit ed037d83415937b11a45a4611584e71e99ad1da0
iuc
parents:
diff changeset
7 </xml>
12
34840e9c79b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 33aaad8d6afce20732d8232fbcd777a3aabf09ec"
iuc
parents: 10
diff changeset
8 <xml name="bio_tools">
34840e9c79b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 33aaad8d6afce20732d8232fbcd777a3aabf09ec"
iuc
parents: 10
diff changeset
9 <xrefs>
34840e9c79b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 33aaad8d6afce20732d8232fbcd777a3aabf09ec"
iuc
parents: 10
diff changeset
10 <xref type="bio.tools">trinity</xref>
34840e9c79b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 33aaad8d6afce20732d8232fbcd777a3aabf09ec"
iuc
parents: 10
diff changeset
11 </xrefs>
34840e9c79b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 33aaad8d6afce20732d8232fbcd777a3aabf09ec"
iuc
parents: 10
diff changeset
12 </xml>
15
41db7569b4ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
iuc
parents: 12
diff changeset
13 <token name="@TOOL_VERSION@">2.15.1</token>
41db7569b4ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
iuc
parents: 12
diff changeset
14 <token name="@VERSION_SUFFIX@">0</token>
0
1e8a2c87461a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit ed037d83415937b11a45a4611584e71e99ad1da0
iuc
parents:
diff changeset
15
3
bc4e467da875 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 1
diff changeset
16 <token name="@COMMAND_PAIRED_STRAND_JACCARD@">
15
41db7569b4ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
iuc
parents: 12
diff changeset
17 #if $pool.inputs.strand.is_strand_specific == 'true':
5
afa3a9786339 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
parents: 3
diff changeset
18 --SS_lib_type $pool.inputs.strand.library_type
3
bc4e467da875 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 1
diff changeset
19 #end if
bc4e467da875 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 1
diff changeset
20
5
afa3a9786339 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
parents: 3
diff changeset
21 $pool.inputs.jaccard_clip
3
bc4e467da875 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 1
diff changeset
22 </token>
bc4e467da875 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 1
diff changeset
23
bc4e467da875 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 1
diff changeset
24 <xml name="input_paired_strand_jaccard">
bc4e467da875 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 1
diff changeset
25 <conditional name="strand">
15
41db7569b4ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
iuc
parents: 12
diff changeset
26 <param name="is_strand_specific" type="select" label="Strand specific data">
41db7569b4ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
iuc
parents: 12
diff changeset
27 <option value="false">No</option>
41db7569b4ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
iuc
parents: 12
diff changeset
28 <option value="true">Yes</option>
41db7569b4ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
iuc
parents: 12
diff changeset
29 </param>
3
bc4e467da875 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 1
diff changeset
30 <when value="false" />
bc4e467da875 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 1
diff changeset
31 <when value="true">
bc4e467da875 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 1
diff changeset
32 <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific library type">
bc4e467da875 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 1
diff changeset
33 <option value="FR">Forward-Reverse</option>
bc4e467da875 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 1
diff changeset
34 <option value="RF">Reverse-Forward</option>
bc4e467da875 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 1
diff changeset
35 </param>
bc4e467da875 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 1
diff changeset
36 </when>
bc4e467da875 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 1
diff changeset
37 </conditional>
6
8fed16891aaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 482fb46ba8d588f2294e21829a0904809b0ec3f1
iuc
parents: 5
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"/>
3
bc4e467da875 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 1
diff changeset
39 </xml>
bc4e467da875 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 1
diff changeset
40
15
41db7569b4ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
iuc
parents: 12
diff changeset
41 <xml name="is_strand_specific_f_r">
41db7569b4ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
iuc
parents: 12
diff changeset
42 <conditional name="strand">
41db7569b4ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
iuc
parents: 12
diff changeset
43 <param name="is_strand_specific" type="select" label="Strand specific data">
41db7569b4ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
iuc
parents: 12
diff changeset
44 <option value="false">No</option>
41db7569b4ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
iuc
parents: 12
diff changeset
45 <option value="true">Yes</option>
41db7569b4ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
iuc
parents: 12
diff changeset
46 </param>
41db7569b4ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
iuc
parents: 12
diff changeset
47 <when value="false"/>
41db7569b4ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
iuc
parents: 12
diff changeset
48 <when value="true">
41db7569b4ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
iuc
parents: 12
diff changeset
49 <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific Library Type">
41db7569b4ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
iuc
parents: 12
diff changeset
50 <option value="F">F</option>
41db7569b4ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
iuc
parents: 12
diff changeset
51 <option value="R">R</option>
41db7569b4ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
iuc
parents: 12
diff changeset
52 </param>
41db7569b4ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
iuc
parents: 12
diff changeset
53 </when>
41db7569b4ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
iuc
parents: 12
diff changeset
54 </conditional>
41db7569b4ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
iuc
parents: 12
diff changeset
55 </xml>
41db7569b4ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
iuc
parents: 12
diff changeset
56
0
1e8a2c87461a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit ed037d83415937b11a45a4611584e71e99ad1da0
iuc
parents:
diff changeset
57 <xml name="citation">
1e8a2c87461a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit ed037d83415937b11a45a4611584e71e99ad1da0
iuc
parents:
diff changeset
58 <citations>
1e8a2c87461a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit ed037d83415937b11a45a4611584e71e99ad1da0
iuc
parents:
diff changeset
59 <citation type="doi">10.1038/nbt.1883</citation>
1e8a2c87461a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit ed037d83415937b11a45a4611584e71e99ad1da0
iuc
parents:
diff changeset
60 </citations>
1e8a2c87461a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit ed037d83415937b11a45a4611584e71e99ad1da0
iuc
parents:
diff changeset
61 </xml>
1e8a2c87461a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit ed037d83415937b11a45a4611584e71e99ad1da0
iuc
parents:
diff changeset
62 </macros>