Mercurial > repos > iuc > flair_correct

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit 41f4293e4db957a23f3be9ff76874a8619e803a2"
author iuc
date Fri, 09 Apr 2021 21:15:31 +0000
parents 6927379c9ede
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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1 <macros>
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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2 <token name="@TOOL_VERSION@">1.5</token>
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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3 <xml name="requirements">
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4 <requirements>
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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5 <requirement type="package" version="@TOOL_VERSION@">flair</requirement>
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6 <yield />
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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7 </requirements>
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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8 </xml>
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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10 <xml name="version_command">
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11 <version_command>flair.py --version</version_command>
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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12 </xml>
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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13
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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14 <token name="@PREPARE_REF@"><![CDATA[
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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15 #if str($reference_source_genome.ref_selector_genome) == 'history':
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c784170f3b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit 41f4293e4db957a23f3be9ff76874a8619e803a2"
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16 #set reference = $reference_source_genome.reffile
c784170f3b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit 41f4293e4db957a23f3be9ff76874a8619e803a2"
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17 #set ext = $reference.ext
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18 samtools faidx 'reference.fa' 2>&1 || echo "Error running samtools faidx for indexing fasta reference for flair" >&2 &&
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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19 #else
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20 #set reference = $reference_source_genome.reffile.fields.path
c784170f3b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit 41f4293e4db957a23f3be9ff76874a8619e803a2"
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21 #set ext = $reference_source_genome.reffile.fields.path
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22 #end if
c784170f3b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit 41f4293e4db957a23f3be9ff76874a8619e803a2"
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23 #if $ext.endswith(".gz"):
c784170f3b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit 41f4293e4db957a23f3be9ff76874a8619e803a2"
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24 gunzip -c '$reference' > reference.fa &&
c784170f3b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit 41f4293e4db957a23f3be9ff76874a8619e803a2"
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25 #else:
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26 ln -sf '$reference' reference.fa &&
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27 #end if
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28 ]]></token>
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29
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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30 <xml name="reference_interface">
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31 <conditional name="reference_source_genome">
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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32 <param name="ref_selector_genome" type="select" label="Choose the source for the reference genome">
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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33 <option value="cached">Locally cached</option>
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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34 <option value="history">History</option>
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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35 </param>
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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36 <when value="cached">
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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37 <param name="reffile" argument="-g" type="select" label="Reference genome">
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38 <options from_data_table="fasta_indexes">
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39 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" />
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40 </options>
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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41 </param>
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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42 </when>
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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43 <when value="history">
1
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44 <param name="reffile" argument="-g" type="data" format="fasta,fasta.gz" label="Reference" help="Reference sequence" />
0
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45 </when>
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46 </conditional>
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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47 </xml>
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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48
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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49 <token name="@description@">
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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50
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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51 **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.
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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52 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).
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53 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.
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54
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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55 </token>
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56
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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57 <token name="@citation@">
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58
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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59 Author: Florian Heyl
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60
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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61 </token>
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62 <xml name="citations">
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63 <citations>
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64 <citation type="doi">10.1038/s41467-020-15171-6</citation>
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65 </citations>
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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66 </xml>
6927379c9ede "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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67 </macros>