Mercurial > repos > iuc > trinity

annotate macros.xml @ 29:e8aca4d11bc0 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 33aaad8d6afce20732d8232fbcd777a3aabf09ec"
author iuc
date Fri, 10 Sep 2021 22:33:00 +0000
parents 3fba0b2671c8
children cfd83bfe5fa9
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
11
80c6d1ec9cd7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit baff3f60cf4a039a74091e24b3453f4499cfaf02
iuc
parents:
diff changeset
1 <?xml version="1.0"?>
80c6d1ec9cd7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit baff3f60cf4a039a74091e24b3453f4499cfaf02
iuc
parents:
diff changeset
2 <macros>
80c6d1ec9cd7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit baff3f60cf4a039a74091e24b3453f4499cfaf02
iuc
parents:
diff changeset
3 <xml name="requirements">
80c6d1ec9cd7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit baff3f60cf4a039a74091e24b3453f4499cfaf02
iuc
parents:
diff changeset
4 <requirements>
22
35520c1c0940 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 482fb46ba8d588f2294e21829a0904809b0ec3f1
iuc
parents: 21
diff changeset
5 <requirement type="package" version="@WRAPPER_VERSION@">trinity</requirement>
11
80c6d1ec9cd7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit baff3f60cf4a039a74091e24b3453f4499cfaf02
iuc
parents:
diff changeset
6 <yield/>
80c6d1ec9cd7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit baff3f60cf4a039a74091e24b3453f4499cfaf02
iuc
parents:
diff changeset
7 </requirements>
80c6d1ec9cd7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit baff3f60cf4a039a74091e24b3453f4499cfaf02
iuc
parents:
diff changeset
8 </xml>
29
e8aca4d11bc0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 33aaad8d6afce20732d8232fbcd777a3aabf09ec"
iuc
parents: 26
diff changeset
9 <xml name="bio_tools">
e8aca4d11bc0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 33aaad8d6afce20732d8232fbcd777a3aabf09ec"
iuc
parents: 26
diff changeset
10 <xrefs>
e8aca4d11bc0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 33aaad8d6afce20732d8232fbcd777a3aabf09ec"
iuc
parents: 26
diff changeset
11 <xref type="bio.tools">trinity</xref>
e8aca4d11bc0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 33aaad8d6afce20732d8232fbcd777a3aabf09ec"
iuc
parents: 26
diff changeset
12 </xrefs>
e8aca4d11bc0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 33aaad8d6afce20732d8232fbcd777a3aabf09ec"
iuc
parents: 26
diff changeset
13 </xml>
26
3fba0b2671c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit f5736e63d4d4210c33eea4a1985508466c3c168d"
iuc
parents: 24
diff changeset
14 <token name="@WRAPPER_VERSION@">2.9.1</token>
11
80c6d1ec9cd7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit baff3f60cf4a039a74091e24b3453f4499cfaf02
iuc
parents:
diff changeset
15
18
87ab70ffdf1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 16
diff changeset
16 <token name="@COMMAND_PAIRED_STRAND_JACCARD@">
21
3867ecd957f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
parents: 18
diff changeset
17 #if $pool.inputs.strand.is_strand_specific:
3867ecd957f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
parents: 18
diff changeset
18 --SS_lib_type $pool.inputs.strand.library_type
18
87ab70ffdf1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 16
diff changeset
19 #end if
87ab70ffdf1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 16
diff changeset
20
21
3867ecd957f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
parents: 18
diff changeset
21 $pool.inputs.jaccard_clip
18
87ab70ffdf1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 16
diff changeset
22 </token>
87ab70ffdf1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 16
diff changeset
23
87ab70ffdf1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 16
diff changeset
24 <xml name="input_paired_strand_jaccard">
87ab70ffdf1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 16
diff changeset
25 <conditional name="strand">
87ab70ffdf1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 16
diff changeset
26 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
87ab70ffdf1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 16
diff changeset
27 <when value="false" />
87ab70ffdf1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 16
diff changeset
28 <when value="true">
87ab70ffdf1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 16
diff changeset
29 <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific library type">
87ab70ffdf1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 16
diff changeset
30 <option value="FR">Forward-Reverse</option>
87ab70ffdf1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 16
diff changeset
31 <option value="RF">Reverse-Forward</option>
87ab70ffdf1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 16
diff changeset
32 </param>
87ab70ffdf1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 16
diff changeset
33 </when>
87ab70ffdf1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 16
diff changeset
34 </conditional>
22
35520c1c0940 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 482fb46ba8d588f2294e21829a0904809b0ec3f1
iuc
parents: 21
diff changeset
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"/>
18
87ab70ffdf1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 16
diff changeset
36 </xml>
87ab70ffdf1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
parents: 16
diff changeset
37
11
80c6d1ec9cd7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit baff3f60cf4a039a74091e24b3453f4499cfaf02
iuc
parents:
diff changeset
38 <xml name="citation">
80c6d1ec9cd7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit baff3f60cf4a039a74091e24b3453f4499cfaf02
iuc
parents:
diff changeset
39 <citations>
80c6d1ec9cd7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit baff3f60cf4a039a74091e24b3453f4499cfaf02
iuc
parents:
diff changeset
40 <citation type="doi">10.1038/nbt.1883</citation>
80c6d1ec9cd7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit baff3f60cf4a039a74091e24b3453f4499cfaf02
iuc
parents:
diff changeset
41 </citations>
80c6d1ec9cd7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit baff3f60cf4a039a74091e24b3453f4499cfaf02
iuc
parents:
diff changeset
42 </xml>
80c6d1ec9cd7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit baff3f60cf4a039a74091e24b3453f4499cfaf02
iuc
parents:
diff changeset
43 </macros>