Mercurial > repos > iuc > freyja_aggregate_plot

comparison macros.xml @ 4:640c0b8cc8bf draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit cb599a5ca4a1612c5fc8050d6042d52c729a7c06
author iuc
date Wed, 19 Feb 2025 11:09:01 +0000
parents 54acd5139cab
children
comparison
equal deleted inserted replaced
3:54acd5139cab 4:640c0b8cc8bf
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <macros> 2 <macros>
3 <token name="@TOOL_VERSION@">1.5.2</token> 3 <token name="@TOOL_VERSION@">1.5.2</token>
4 <token name="@VERSION_SUFFIX@">0</token> 4 <token name="@VERSION_SUFFIX@">1</token>
5 <token name="@PROFILE@">21.01</token> 5 <token name="@PROFILE@">21.01</token>
6 <xml name="biotools"> 6 <xml name="biotools">
7 <xrefs> 7 <xrefs>
8 <xref type="bio.tools">freyja</xref> 8 <xref type="bio.tools">freyja</xref>
9 </xrefs> 9 </xrefs>
20 <token name="@RUN_FREYJA_UPDATE_COMMAND@"><![CDATA[ 20 <token name="@RUN_FREYJA_UPDATE_COMMAND@"><![CDATA[
21 #if $usher_update_option.choice == 'update' 21 #if $usher_update_option.choice == 'update'
22 freyja update && 22 freyja update &&
23 #end if 23 #end if
24 ]]></token> 24 ]]></token>
25 <token name="@CUSTOM_BARCODES_LINKING@"><![CDATA[
26 #if $usher_update_option.choice == 'custom'
27 ln -s '${usher_update_option.usher_barcodes}' usher_barcodes.csv &&
28 #end if
29 ]]></token>
30 <token name="@CUSTOM_BARCODES_COMMAND@"><![CDATA[
31 #if $usher_update_option.choice == 'custom'
32 --barcodes usher_barcodes.csv
33 #end if
34 ]]></token>
25 <token name="@PREPROCESS_VCF_INPUT@"><![CDATA[ 35 <token name="@PREPROCESS_VCF_INPUT@"><![CDATA[
26 ln -s '$variants_file' 'variants_file.vcf' && 36 ln -s '$variants_file' 'variants_file.vcf' &&
27 ]]></token> 37 ]]></token>
28 <token name="@STANDARD_INPUT_FOR_BOOT@"><![CDATA[ 38 <token name="@STANDARD_INPUT_FOR_BOOT@"><![CDATA[
29 #if $variants_file.ext == 'vcf' 39 #if $variants_file.ext == 'vcf'
38 #if $meta 48 #if $meta
39 --meta '${meta}' 49 --meta '${meta}'
40 #end if 50 #end if
41 $confirmedonly 51 $confirmedonly
42 --pathogen '$pathogen' 52 --pathogen '$pathogen'
43 ]]></token>
44 <token name="@CUSTOM_BARCODES_COMMAND@"><![CDATA[
45 #if $usher_update_option.choice == 'custom'
46 --barcodes '${usher_update_option.usher_barcodes}'
47 #end if
48 ]]></token> 53 ]]></token>
49 <token name="@DASH_COMMAND@"><![CDATA[ 54 <token name="@DASH_COMMAND@"><![CDATA[
50 echo '${plot_format.plot_title}' > plot_title.txt && 55 echo '${plot_format.plot_title}' > plot_title.txt &&
51 echo '${plot_format.plot_intro}' > plot_intro.txt && 56 echo '${plot_format.plot_intro}' > plot_intro.txt &&
52 freyja dash 57 freyja dash