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comparison macros.xml @ 1:d4d05a202bc3 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/jasminesv/ commit 600a9e3c1d884e5cf106e4477c7b8223ef105cdb"
author iuc
date Thu, 29 Apr 2021 12:23:33 +0000
parents a4962f14d05d
children
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0:a4962f14d05d 1:d4d05a202bc3
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <macros> 2 <macros>
3 <token name="@TOOL_VERSION@">1.0.11</token> 3 <token name="@TOOL_VERSION@">1.0.11</token>
4 <token name="@VERSION_SUFFIX@">0</token> 4 <token name="@VERSION_SUFFIX@">1</token>
5 <token name="@PROFILE@">20.01</token> 5 <token name="@PROFILE@">20.01</token>
6 <xml name="requirements"> 6 <xml name="requirements">
7 <requirements> 7 <requirements>
8 <requirement type="package" version="@TOOL_VERSION@">jasminesv</requirement> 8 <requirement type="package" version="@TOOL_VERSION@">jasminesv</requirement>
9 </requirements> 9 </requirements>
25 <!-- 25 <!--
26 Command 26 Command
27 --> 27 -->
28 <token name="@REF_FASTA@"><![CDATA[ 28 <token name="@REF_FASTA@"><![CDATA[
29 #if $dup_to_ins.reference_source.reference_source_selector == 'history': 29 #if $dup_to_ins.reference_source.reference_source_selector == 'history':
30 ln -f -s '$dup_to_ins.reference_source.ref_file' reference.fa && 30 #set reference = $dup_to_ins.reference_source.ref_file
31 #set ext = $reference.ext
31 #else: 32 #else:
32 ln -f -s '$dup_to_ins.reference_source.ref_file.fields.path' reference.fa && 33 #set reference = $dup_to_ins.reference_source.ref_file.fields.path
34 #set ext = $dup_to_ins.reference_source.ref_file.fields.path
35 #end if
36 #if $ext.endswith(".gz"):
37 gunzip -c '$reference' > reference &&
38 #else:
39 ln -sf '$reference' reference &&
33 #end if 40 #end if
34 ]]></token> 41 ]]></token>
35 42
36 <xml name="reference"> 43 <xml name="reference">
37 <conditional name="reference_source"> 44 <conditional name="reference_source">
47 </options> 54 </options>
48 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> 55 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
49 </param> 56 </param>
50 </when> 57 </when>
51 <when value="history"> 58 <when value="history">
52 <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"/> 59 <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"/>
53 </when> 60 </when>
54 </conditional> 61 </conditional>
55 </xml> 62 </xml>
56 <!-- 63 <!--
57 Help 64 Help
62 ]]></token> 69 ]]></token>
63 <token name="@REFERENCES@"><![CDATA[ 70 <token name="@REFERENCES@"><![CDATA[
64 More information is available in the `github <https://github.com/mkirsche/Jasmine>`_. 71 More information is available in the `github <https://github.com/mkirsche/Jasmine>`_.
65 ]]></token> 72 ]]></token>
66 </macros> 73 </macros>
74