Mercurial > repos > iuc > flair_correct
comparison flair_macros.xml @ 1:c784170f3b5e draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit 41f4293e4db957a23f3be9ff76874a8619e803a2"
author | iuc |
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date | Fri, 09 Apr 2021 21:15:31 +0000 |
parents | 6927379c9ede |
children |
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0:6927379c9ede | 1:c784170f3b5e |
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11 <version_command>flair.py --version</version_command> | 11 <version_command>flair.py --version</version_command> |
12 </xml> | 12 </xml> |
13 | 13 |
14 <token name="@PREPARE_REF@"><![CDATA[ | 14 <token name="@PREPARE_REF@"><![CDATA[ |
15 #if str($reference_source_genome.ref_selector_genome) == 'history': | 15 #if str($reference_source_genome.ref_selector_genome) == 'history': |
16 ln -s '$reference_source_genome.reffile' reference.fa && | 16 #set reference = $reference_source_genome.reffile |
17 #set ext = $reference.ext | |
17 samtools faidx 'reference.fa' 2>&1 || echo "Error running samtools faidx for indexing fasta reference for flair" >&2 && | 18 samtools faidx 'reference.fa' 2>&1 || echo "Error running samtools faidx for indexing fasta reference for flair" >&2 && |
18 #else | 19 #else |
19 ln -s '${reference_source_genome.reffile.fields.path}' reference.fa && | 20 #set reference = $reference_source_genome.reffile.fields.path |
21 #set ext = $reference_source_genome.reffile.fields.path | |
22 #end if | |
23 #if $ext.endswith(".gz"): | |
24 gunzip -c '$reference' > reference.fa && | |
25 #else: | |
26 ln -sf '$reference' reference.fa && | |
20 #end if | 27 #end if |
21 ]]></token> | 28 ]]></token> |
22 | 29 |
23 <xml name="reference_interface"> | 30 <xml name="reference_interface"> |
24 <conditional name="reference_source_genome"> | 31 <conditional name="reference_source_genome"> |
32 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" /> | 39 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" /> |
33 </options> | 40 </options> |
34 </param> | 41 </param> |
35 </when> | 42 </when> |
36 <when value="history"> | 43 <when value="history"> |
37 <param name="reffile" argument="-g" type="data" format="fasta" label="Reference" help="Reference sequence" /> | 44 <param name="reffile" argument="-g" type="data" format="fasta,fasta.gz" label="Reference" help="Reference sequence" /> |
38 </when> | 45 </when> |
39 </conditional> | 46 </conditional> |
40 </xml> | 47 </xml> |
41 | 48 |
42 <token name="@description@"> | 49 <token name="@description@"> |