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comparison macros.xml @ 1:1d4f065fa0ef draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit e3ffd8ae7c25536658ff3ee76389f0c2a9894b4c"
author iuc
date Mon, 17 May 2021 17:29:39 +0000
parents 30fc9f2bcbe4
children 3242dbeea69c
comparison
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0:30fc9f2bcbe4 1:1d4f065fa0ef
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <macros> 2 <macros>
3 <token name="@TOOL_VERSION@">1.0.4</token> 3 <token name="@TOOL_VERSION@">1.0.4</token>
4 <token name="@PROFILE@">18.01</token> 4 <token name="@PROFILE@">20.01</token>
5 <xml name="requirements"> 5 <xml name="requirements">
6 <requirements> 6 <requirements>
7 <requirement type="package" version="1.9">samtools</requirement> 7 <requirement type="package" version="1.9">samtools</requirement>
8 <requirement type="package" version="@TOOL_VERSION@">irissv</requirement> 8 <requirement type="package" version="@TOOL_VERSION@">irissv</requirement>
9 </requirements> 9 </requirements>
27 command 27 command
28 --> 28 -->
29 29
30 <token name="@REF_FASTA@"><![CDATA[ 30 <token name="@REF_FASTA@"><![CDATA[
31 #if $reference_source.reference_source_selector == 'history': 31 #if $reference_source.reference_source_selector == 'history':
32 ln -f -s '$reference_source.ref_file' reference.fa && 32 #set reference = $reference_source.ref_file
33 #set ext = $reference.ext
33 #else: 34 #else:
34 ln -f -s '$reference_source.ref_file.fields.path' reference.fa && 35 #set reference = $reference_source.ref_file.fields.path
36 #set ext = $reference_source.ref_file.fields.path
37 #end if
38 #if $ext.endswith('.gz'):
39 gunzip -c '$reference' > reference &&
40 #else:
41 ln -sf '$reference' reference &&
35 #end if 42 #end if
36 ]]></token> 43 ]]></token>
37 44
38 <xml name="reference"> 45 <xml name="reference">
39 <conditional name="reference_source"> 46 <conditional name="reference_source">
49 </options> 56 </options>
50 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> 57 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
51 </param> 58 </param>
52 </when> 59 </when>
53 <when value="history"> 60 <when value="history">
54 <param name="ref_file" type="data" format="fasta,fastq" label="Use the following dataset as the reference sequence" help="You can upload a FASTA or FASTQ sequence to the history and use it as reference"/> 61 <param name="ref_file" type="data" format="fasta,fasta.gz,fastq,fastq.gz" label="Use the following dataset as the reference sequence" help="You can upload a FASTA or FASTQ sequence to the history and use it as reference"/>
55 </when> 62 </when>
56 </conditional> 63 </conditional>
57 </xml> 64 </xml>
58 <!-- 65 <!--
59 Help 66 Help