Mercurial > repos > iuc > flair

annotate flair_macros.xml @ 0:5d17cf201540 draft default tip

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/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
author iuc
date Fri, 27 Nov 2020 18:45:47 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
iuc
parents:
diff changeset
1 <macros>
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
iuc
parents:
diff changeset
2 <token name="@TOOL_VERSION@">1.5</token>
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
iuc
parents:
diff changeset
3 <xml name="requirements">
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
iuc
parents:
diff changeset
4 <requirements>
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
iuc
parents:
diff changeset
5 <requirement type="package" version="@TOOL_VERSION@">flair</requirement>
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
iuc
parents:
diff changeset
6 <yield />
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
iuc
parents:
diff changeset
7 </requirements>
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
iuc
parents:
diff changeset
8 </xml>
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
iuc
parents:
diff changeset
9
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
iuc
parents:
diff changeset
10 <xml name="version_command">
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
iuc
parents:
diff changeset
11 <version_command>flair.py --version</version_command>
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
iuc
parents:
diff changeset
12 </xml>
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
iuc
parents:
diff changeset
13
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
iuc
parents:
diff changeset
14 <token name="@PREPARE_REF@"><![CDATA[
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
iuc
parents:
diff changeset
15 #if str($reference_source_genome.ref_selector_genome) == 'history':
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
iuc
parents:
diff changeset
16 ln -s '$reference_source_genome.reffile' reference.fa &&
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
iuc
parents:
diff changeset
17 samtools faidx 'reference.fa' 2>&1 || echo "Error running samtools faidx for indexing fasta reference for flair" >&2 &&
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
iuc
parents:
diff changeset
18 #else
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
iuc
parents:
diff changeset
19 ln -s '${reference_source_genome.reffile.fields.path}' reference.fa &&
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
iuc
parents:
diff changeset
20 #end if
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
iuc
parents:
diff changeset
21 ]]></token>
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
iuc
parents:
diff changeset
22
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
iuc
parents:
diff changeset
23 <xml name="reference_interface">
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
iuc
parents:
diff changeset
24 <conditional name="reference_source_genome">
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
iuc
parents:
diff changeset
25 <param name="ref_selector_genome" type="select" label="Choose the source for the reference genome">
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
iuc
parents:
diff changeset
26 <option value="cached">Locally cached</option>
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
iuc
parents:
diff changeset
27 <option value="history">History</option>
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
iuc
parents:
diff changeset
28 </param>
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
iuc
parents:
diff changeset
29 <when value="cached">
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
iuc
parents:
diff changeset
30 <param name="reffile" argument="-g" type="select" label="Reference genome">
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
iuc
parents:
diff changeset
31 <options from_data_table="fasta_indexes">
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
iuc
parents:
diff changeset
32 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" />
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
iuc
parents:
diff changeset
33 </options>
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
iuc
parents:
diff changeset
34 </param>
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
iuc
parents:
diff changeset
35 </when>
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
iuc
parents:
diff changeset
36 <when value="history">
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
iuc
parents:
diff changeset
37 <param name="reffile" argument="-g" type="data" format="fasta" label="Reference" help="Reference sequence" />
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
iuc
parents:
diff changeset
38 </when>
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
iuc
parents:
diff changeset
39 </conditional>
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
iuc
parents:
diff changeset
40 </xml>
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
iuc
parents:
diff changeset
41
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
iuc
parents:
diff changeset
42 <token name="@description@">
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
iuc
parents:
diff changeset
43
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
iuc
parents:
diff changeset
44 **FLAIR** FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads. FLAIR has primarily been used for nanopore cDNA, native RNA, and PacBio sequencing reads.
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
iuc
parents:
diff changeset
45 FLAIR can be run optionally with short-read data to help increase splice site accuracy of the long read splice junctions. FLAIR uses multiple alignment steps and splice site filters to increase confidence in the set of isoforms defined from noisy data. FLAIR was designed to be able to sense subtle splicing changes in nanopore data from Tang et al. (2018).
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
iuc
parents:
diff changeset
46 It is recommended to combine all samples together prior to running flair-collapse for isoform assembly by concatenating corrected read psl or bed files together. Following the creation of an isoform reference from flair-collapse, consequent steps will assign reads from each sample individually to isoforms of the combined assembly for downstream analyses.
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
iuc
parents:
diff changeset
47
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
iuc
parents:
diff changeset
48 </token>
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
iuc
parents:
diff changeset
49
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
iuc
parents:
diff changeset
50 <token name="@citation@">
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
iuc
parents:
diff changeset
51
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
iuc
parents:
diff changeset
52 Author: Florian Heyl
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
iuc
parents:
diff changeset
53
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
iuc
parents:
diff changeset
54 </token>
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
iuc
parents:
diff changeset
55 <xml name="citations">
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
iuc
parents:
diff changeset
56 <citations>
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
iuc
parents:
diff changeset
57 <citation type="doi">10.1038/s41467-020-15171-6</citation>
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
iuc
parents:
diff changeset
58 </citations>
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
iuc
parents:
diff changeset
59 </xml>
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
iuc
parents:
diff changeset
60 </macros>