Mercurial > repos > bgruening > agat
annotate macros.xml @ 5:e7449b2c14bf draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 28a6a1644ff8ffd8c3a47ccaaad0cb2da2aa87e3
author | bgruening |
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date | Wed, 07 Aug 2024 20:54:27 +0000 |
parents | abba05ead5d7 |
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rev | line source |
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0
f7c0a0030254
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 0851e9e6d46223a8233c56f3b0bcf14e19d63916
bgruening
parents:
diff
changeset
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1 <macros> |
5
e7449b2c14bf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 28a6a1644ff8ffd8c3a47ccaaad0cb2da2aa87e3
bgruening
parents:
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diff
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2 <token name="@TOOL_VERSION@">1.4.0</token> |
e7449b2c14bf
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 28a6a1644ff8ffd8c3a47ccaaad0cb2da2aa87e3
bgruening
parents:
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3 <token name="@VERSION_SUFFIX@">0</token> |
0
f7c0a0030254
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 0851e9e6d46223a8233c56f3b0bcf14e19d63916
bgruening
parents:
diff
changeset
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4 <xml name="requirements"> |
f7c0a0030254
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 0851e9e6d46223a8233c56f3b0bcf14e19d63916
bgruening
parents:
diff
changeset
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5 <requirements> |
f7c0a0030254
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 0851e9e6d46223a8233c56f3b0bcf14e19d63916
bgruening
parents:
diff
changeset
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6 <requirement type="package" version="@TOOL_VERSION@">agat</requirement> |
f7c0a0030254
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 0851e9e6d46223a8233c56f3b0bcf14e19d63916
bgruening
parents:
diff
changeset
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7 </requirements> |
f7c0a0030254
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 0851e9e6d46223a8233c56f3b0bcf14e19d63916
bgruening
parents:
diff
changeset
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8 </xml> |
f7c0a0030254
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 0851e9e6d46223a8233c56f3b0bcf14e19d63916
bgruening
parents:
diff
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9 <xml name="biotools"> |
f7c0a0030254
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 0851e9e6d46223a8233c56f3b0bcf14e19d63916
bgruening
parents:
diff
changeset
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10 <xrefs> |
f7c0a0030254
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 0851e9e6d46223a8233c56f3b0bcf14e19d63916
bgruening
parents:
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changeset
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11 <xref type="bio.tools">agat</xref> |
f7c0a0030254
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 0851e9e6d46223a8233c56f3b0bcf14e19d63916
bgruening
parents:
diff
changeset
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12 </xrefs> |
f7c0a0030254
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 0851e9e6d46223a8233c56f3b0bcf14e19d63916
bgruening
parents:
diff
changeset
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13 </xml> |
f7c0a0030254
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 0851e9e6d46223a8233c56f3b0bcf14e19d63916
bgruening
parents:
diff
changeset
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14 <xml name="citations"> |
f7c0a0030254
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 0851e9e6d46223a8233c56f3b0bcf14e19d63916
bgruening
parents:
diff
changeset
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15 <citations> |
f7c0a0030254
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 0851e9e6d46223a8233c56f3b0bcf14e19d63916
bgruening
parents:
diff
changeset
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16 <citation type="doi">10.5281/zenodo.3552717</citation> |
f7c0a0030254
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 0851e9e6d46223a8233c56f3b0bcf14e19d63916
bgruening
parents:
diff
changeset
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17 </citations> |
f7c0a0030254
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 0851e9e6d46223a8233c56f3b0bcf14e19d63916
bgruening
parents:
diff
changeset
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18 </xml> |
f7c0a0030254
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 0851e9e6d46223a8233c56f3b0bcf14e19d63916
bgruening
parents:
diff
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19 <xml name="ANNOTATION_INPUT" token_format="gff,gtf,gff3,gff3.gz"> |
f7c0a0030254
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 0851e9e6d46223a8233c56f3b0bcf14e19d63916
bgruening
parents:
diff
changeset
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20 <param argument="--gff" type="data" format="@FORMAT@" label="Annotation file" help="Input GTF/GFF file" /> |
f7c0a0030254
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 0851e9e6d46223a8233c56f3b0bcf14e19d63916
bgruening
parents:
diff
changeset
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21 </xml> |
2
e009d8260be2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 8eb20f601bc1d2a50c8877b7d0ade057e8f86eae
bgruening
parents:
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22 <xml name="AGAT_CONFIG"> |
e009d8260be2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 8eb20f601bc1d2a50c8877b7d0ade057e8f86eae
bgruening
parents:
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23 <conditional name="output_format"> |
e009d8260be2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 8eb20f601bc1d2a50c8877b7d0ade057e8f86eae
bgruening
parents:
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24 <param name="selector" type="select" label="Output format"> |
e009d8260be2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 8eb20f601bc1d2a50c8877b7d0ade057e8f86eae
bgruening
parents:
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changeset
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25 <option value="GFF">GFF</option> |
e009d8260be2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 8eb20f601bc1d2a50c8877b7d0ade057e8f86eae
bgruening
parents:
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changeset
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26 <option value="GTF">GTF</option> |
e009d8260be2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 8eb20f601bc1d2a50c8877b7d0ade057e8f86eae
bgruening
parents:
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changeset
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27 </param> |
e009d8260be2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 8eb20f601bc1d2a50c8877b7d0ade057e8f86eae
bgruening
parents:
1
diff
changeset
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28 <when value="GFF"> |
e009d8260be2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 8eb20f601bc1d2a50c8877b7d0ade057e8f86eae
bgruening
parents:
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29 <param name="version" type="select" label="Format version"> |
e009d8260be2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 8eb20f601bc1d2a50c8877b7d0ade057e8f86eae
bgruening
parents:
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30 <option value="1">1</option> |
e009d8260be2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 8eb20f601bc1d2a50c8877b7d0ade057e8f86eae
bgruening
parents:
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31 <option value="2">2</option> |
e009d8260be2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 8eb20f601bc1d2a50c8877b7d0ade057e8f86eae
bgruening
parents:
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32 <option value="2.5">2.5</option> |
e009d8260be2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 8eb20f601bc1d2a50c8877b7d0ade057e8f86eae
bgruening
parents:
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33 <option value="3" selected="true">3</option> |
e009d8260be2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 8eb20f601bc1d2a50c8877b7d0ade057e8f86eae
bgruening
parents:
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34 </param> |
e009d8260be2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 8eb20f601bc1d2a50c8877b7d0ade057e8f86eae
bgruening
parents:
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35 </when> |
e009d8260be2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 8eb20f601bc1d2a50c8877b7d0ade057e8f86eae
bgruening
parents:
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36 <when value="GTF"> |
e009d8260be2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 8eb20f601bc1d2a50c8877b7d0ade057e8f86eae
bgruening
parents:
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37 <param name="version" type="select" label="Format version"> |
e009d8260be2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 8eb20f601bc1d2a50c8877b7d0ade057e8f86eae
bgruening
parents:
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38 <option value="1">1 = ("CDS", "start_codon", "stop_codon", "exon", "intron")</option> |
e009d8260be2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 8eb20f601bc1d2a50c8877b7d0ade057e8f86eae
bgruening
parents:
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39 <option value="2">2 = ("CDS", "start_codon", "stop_codon", "exon")</option> |
e009d8260be2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 8eb20f601bc1d2a50c8877b7d0ade057e8f86eae
bgruening
parents:
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40 <option value="2.1">2.1 = ("CDS", "start_codon", "stop_codon", "exon", "5UTR", "3UTR")</option> |
e009d8260be2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 8eb20f601bc1d2a50c8877b7d0ade057e8f86eae
bgruening
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41 <option value="2.2">2.2 = ("CDS", "start_codon", "stop_codon", "5UTR", "3UTR", "inter", "inter_CNS", "intron_CNS", "exon")</option> |
e009d8260be2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 8eb20f601bc1d2a50c8877b7d0ade057e8f86eae
bgruening
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42 <option value="2.5">2.5 = ("gene", "transcript", "exon", "CDS", "UTR", "start_codon", "stop_codon", "Selenocysteine")</option> |
e009d8260be2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 8eb20f601bc1d2a50c8877b7d0ade057e8f86eae
bgruening
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43 <option value="3">3 = ("gene", "transcript", "exon", "CDS", "Selenocysteine", "start_codon", "stop_codon", "three_prime_utr", "five_prime_utr")</option> |
e009d8260be2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 8eb20f601bc1d2a50c8877b7d0ade057e8f86eae
bgruening
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44 <option value="relax" selected="true">Relax = All feature types will be accepted</option> |
e009d8260be2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 8eb20f601bc1d2a50c8877b7d0ade057e8f86eae
bgruening
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45 </param> |
e009d8260be2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 8eb20f601bc1d2a50c8877b7d0ade057e8f86eae
bgruening
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46 </when> |
e009d8260be2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 8eb20f601bc1d2a50c8877b7d0ade057e8f86eae
bgruening
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47 </conditional> |
e009d8260be2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 8eb20f601bc1d2a50c8877b7d0ade057e8f86eae
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48 <param name="merge_loci" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Merge loci" help="Should overlapping loci (at CDS level) be merged in a single locus. Only one gene is kept, and the mRNA features become isoforms." /> |
e009d8260be2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 8eb20f601bc1d2a50c8877b7d0ade057e8f86eae
bgruening
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49 <param name="create_exon" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Create exon when l2 do not have children"/> |
e009d8260be2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 8eb20f601bc1d2a50c8877b7d0ade057e8f86eae
bgruening
parents:
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50 </xml> |
e009d8260be2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 8eb20f601bc1d2a50c8877b7d0ade057e8f86eae
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51 |
0
f7c0a0030254
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 0851e9e6d46223a8233c56f3b0bcf14e19d63916
bgruening
parents:
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52 <xml name="REFERENCE_FASTA"> |
f7c0a0030254
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 0851e9e6d46223a8233c56f3b0bcf14e19d63916
bgruening
parents:
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53 <conditional name="reference_genome"> |
f7c0a0030254
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 0851e9e6d46223a8233c56f3b0bcf14e19d63916
bgruening
parents:
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54 <param name="source" type="select" label="Source for the reference genome" help="Built-in references were created using default options."> |
f7c0a0030254
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 0851e9e6d46223a8233c56f3b0bcf14e19d63916
bgruening
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55 <option value="indexed" selected="true">Use a built-in genome</option> |
f7c0a0030254
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 0851e9e6d46223a8233c56f3b0bcf14e19d63916
bgruening
parents:
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56 <option value="history" selected="true">Use a genome from history</option> |
f7c0a0030254
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 0851e9e6d46223a8233c56f3b0bcf14e19d63916
bgruening
parents:
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57 </param> |
f7c0a0030254
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 0851e9e6d46223a8233c56f3b0bcf14e19d63916
bgruening
parents:
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58 <when value="indexed"> |
f7c0a0030254
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 0851e9e6d46223a8233c56f3b0bcf14e19d63916
bgruening
parents:
diff
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59 <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team."> |
f7c0a0030254
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 0851e9e6d46223a8233c56f3b0bcf14e19d63916
bgruening
parents:
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60 <options from_data_table="fasta_indexes"> |
f7c0a0030254
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 0851e9e6d46223a8233c56f3b0bcf14e19d63916
bgruening
parents:
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61 <filter type="sort_by" column="2" /> |
f7c0a0030254
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 0851e9e6d46223a8233c56f3b0bcf14e19d63916
bgruening
parents:
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62 <validator type="no_options" message="No genomes are available for the selected input dataset" /> |
f7c0a0030254
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 0851e9e6d46223a8233c56f3b0bcf14e19d63916
bgruening
parents:
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63 </options> |
f7c0a0030254
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 0851e9e6d46223a8233c56f3b0bcf14e19d63916
bgruening
parents:
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64 </param> |
f7c0a0030254
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 0851e9e6d46223a8233c56f3b0bcf14e19d63916
bgruening
parents:
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65 </when> |
f7c0a0030254
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 0851e9e6d46223a8233c56f3b0bcf14e19d63916
bgruening
parents:
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66 <when value="history"> |
f7c0a0030254
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 0851e9e6d46223a8233c56f3b0bcf14e19d63916
bgruening
parents:
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67 <param name="history_item" type="data" format="fasta" label="Reference genome" help="A reference genome in FASTA format" /> |
f7c0a0030254
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 0851e9e6d46223a8233c56f3b0bcf14e19d63916
bgruening
parents:
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68 </when> |
f7c0a0030254
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 0851e9e6d46223a8233c56f3b0bcf14e19d63916
bgruening
parents:
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69 </conditional> |
f7c0a0030254
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 0851e9e6d46223a8233c56f3b0bcf14e19d63916
bgruening
parents:
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70 </xml> |
f7c0a0030254
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 0851e9e6d46223a8233c56f3b0bcf14e19d63916
bgruening
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71 <token name="@input_annotation_single@"><![CDATA[ |
f7c0a0030254
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 0851e9e6d46223a8233c56f3b0bcf14e19d63916
bgruening
parents:
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72 #set $input_annotation = 'annotation.' + str($tool.gff.ext) |
f7c0a0030254
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 0851e9e6d46223a8233c56f3b0bcf14e19d63916
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73 ln -s '${tool.gff}' $input_annotation && |
f7c0a0030254
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 0851e9e6d46223a8233c56f3b0bcf14e19d63916
bgruening
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74 ]]></token> |
f7c0a0030254
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 0851e9e6d46223a8233c56f3b0bcf14e19d63916
bgruening
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75 <token name="@input_reference@"><![CDATA[ |
f7c0a0030254
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 0851e9e6d46223a8233c56f3b0bcf14e19d63916
bgruening
parents:
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76 #if $tool.reference_genome.source == 'history': |
f7c0a0030254
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 0851e9e6d46223a8233c56f3b0bcf14e19d63916
bgruening
parents:
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77 #set $ref_genome = 'reference.fasta' |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
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78 ln -s -f '${tool.reference_genome.history_item}' '$ref_genome' && |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 0851e9e6d46223a8233c56f3b0bcf14e19d63916
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79 #else: |
f7c0a0030254
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 0851e9e6d46223a8233c56f3b0bcf14e19d63916
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80 #set $ref_genome = $tool.reference_genome.index.fields.path |
f7c0a0030254
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 0851e9e6d46223a8233c56f3b0bcf14e19d63916
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81 #end if |
f7c0a0030254
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 0851e9e6d46223a8233c56f3b0bcf14e19d63916
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82 ]]></token> |
f7c0a0030254
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 0851e9e6d46223a8233c56f3b0bcf14e19d63916
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83 <token name="@input_annotation_double@"><![CDATA[ |
f7c0a0030254
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 0851e9e6d46223a8233c56f3b0bcf14e19d63916
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84 #set $input1 = 'annotation1.' + str($tool.input_annotation1.ext) |
f7c0a0030254
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 0851e9e6d46223a8233c56f3b0bcf14e19d63916
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85 #set $input2 = 'annotation2.' + str($tool.input_annotation2.ext) |
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a6318f87f2cd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
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86 ln -s '${tool.input_annotation1}' '$input1' && |
a6318f87f2cd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
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2
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87 ln -s '${tool.input_annotation2}' '$input2' && |
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f7c0a0030254
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 0851e9e6d46223a8233c56f3b0bcf14e19d63916
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88 ]]></token> |
f7c0a0030254
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 0851e9e6d46223a8233c56f3b0bcf14e19d63916
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89 </macros> |