Mercurial > repos > iuc > flair_collapse

comparison flair_macros.xml @ 1:03b7b7811ea6 draft

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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 21:15:09 +0000
parents 57dc46adf2da
children
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0:57dc46adf2da 1:03b7b7811ea6
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@">