Mercurial > repos > iuc > freyja_aggregate_plot

comparison macros.xml @ 3:54acd5139cab draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 79a21a9a4a63e538f2ba0bc29384593df2c65859
author iuc
date Fri, 15 Nov 2024 16:44:42 +0000
parents 948903a8555d
children
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2:948903a8555d 3:54acd5139cab
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <macros> 2 <macros>
3 <token name="@TOOL_VERSION@">1.5.1</token> 3 <token name="@TOOL_VERSION@">1.5.2</token>
4 <token name="@VERSION_SUFFIX@">0</token> 4 <token name="@VERSION_SUFFIX@">0</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>
37 #end if 37 #end if
38 #if $meta 38 #if $meta
39 --meta '${meta}' 39 --meta '${meta}'
40 #end if 40 #end if
41 $confirmedonly 41 $confirmedonly
42 --pathogen '$pathogen'
42 ]]></token> 43 ]]></token>
43 <token name="@CUSTOM_BARCODES_COMMAND@"><![CDATA[ 44 <token name="@CUSTOM_BARCODES_COMMAND@"><![CDATA[
44 #if $usher_update_option.choice == 'custom' 45 #if $usher_update_option.choice == 'custom'
45 --barcodes '${usher_update_option.usher_barcodes}' 46 --barcodes '${usher_update_option.usher_barcodes}'
46 #end if 47 #end if
136 help="If the UShER tree includes proposed lineages, the --confirmedonly flag removes unconfirmed lineages from the analysis."/> 137 help="If the UShER tree includes proposed lineages, the --confirmedonly flag removes unconfirmed lineages from the analysis."/>
137 <param argument="--wgisaid" type="boolean" truevalue="--wgisaid" falsevalue="" 138 <param argument="--wgisaid" type="boolean" truevalue="--wgisaid" falsevalue=""
138 checked="false" 139 checked="false"
139 label="Use larger library with non-public lineages" 140 label="Use larger library with non-public lineages"
140 help="Allows to use larger UShER barcodes library extended with GISAID non-public lineages"/> 141 help="Allows to use larger UShER barcodes library extended with GISAID non-public lineages"/>
142 <param argument="--pathogen" type="select" label="Pathogen of interest">
143 <option value="SARS-CoV-2" selected="true">SARS-CoV-2</option>
144 <option value="MPXV" selected="true">MPXV</option>
145 <option value="H5NX" selected="true">H5NX</option>
146 <option value="H1N1pdm" selected="true">H1N1pdm</option>
147 <option value="FLU-B-VIC" selected="true">FLU-B-VIC</option>
148 <option value="MEASLESN450" selected="true">MEASLESN450</option>
149 <option value="MEASLES" selected="true">MEASLES</option>
150 <option value="RSVa" selected="true">RSVa</option>
151 <option value="RSVb" selected="true">RSVb</option>
152 </param>
141 </xml> 153 </xml>
142 <xml name="plot_lineages"> 154 <xml name="plot_lineages">
143 <param argument="--lineages" type="boolean" truevalue="--lineages" falsevalue="" 155 <param argument="--lineages" type="boolean" truevalue="--lineages" falsevalue=""
144 checked="false" label="Use lineage specific breakdown"/> 156 checked="false" label="Use lineage specific breakdown"/>
145 </xml> 157 </xml>