annotate flair_macros.xml @ 2:1fdcbfcca71c draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit 116d8aa50dda2eb771b71fa5e3ed8f0f35e2821c"
author iuc
date Sat, 27 Nov 2021 09:37:51 +0000
parents 03b7b7811ea6
children
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57dc46adf2da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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1 <macros>
57dc46adf2da "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>
57dc46adf2da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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3 <xml name="requirements">
57dc46adf2da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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4 <requirements>
57dc46adf2da "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 />
57dc46adf2da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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7 </requirements>
57dc46adf2da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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8 </xml>
57dc46adf2da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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9
57dc46adf2da "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>
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12 </xml>
57dc46adf2da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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13
57dc46adf2da "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[
57dc46adf2da "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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16 #set reference = $reference_source_genome.reffile
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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 &&
57dc46adf2da "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
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21 #set ext = $reference_source_genome.reffile.fields.path
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22 #end if
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23 #if $ext.endswith(".gz"):
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24 gunzip -c '$reference' > reference.fa &&
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25 #else:
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26 ln -sf '$reference' reference.fa &&
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27 #end if
57dc46adf2da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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28 ]]></token>
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29
57dc46adf2da "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">
57dc46adf2da "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">
57dc46adf2da "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>
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34 <option value="history">History</option>
57dc46adf2da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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35 </param>
57dc46adf2da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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36 <when value="cached">
57dc46adf2da "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" />
57dc46adf2da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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40 </options>
57dc46adf2da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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41 </param>
57dc46adf2da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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42 </when>
57dc46adf2da "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>
57dc46adf2da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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46 </conditional>
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47 </xml>
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48
57dc46adf2da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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49 <token name="@description@">
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50
57dc46adf2da "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.
57dc46adf2da "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
57dc46adf2da "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
57dc46adf2da "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
57dc46adf2da "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
57dc46adf2da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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61 </token>
57dc46adf2da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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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>
57dc46adf2da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit e6e3295a4e0168d80b7966684bc21d2863bed108"
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66 </xml>
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67 </macros>