Mercurial > repos > iuc > freyja_aggregate_plot

comparison macros.xml @ 1:1f89eeba299a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 26266f43c51f3f711ecd3a7dc6aea581a3b57fc5
author iuc
date Fri, 07 Jul 2023 05:51:06 +0000
parents 0ceb9fb0f4ce
children 948903a8555d
comparison
equal deleted inserted replaced
0:0ceb9fb0f4ce 1:1f89eeba299a
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <macros> 2 <macros>
3 <token name="@TOOL_VERSION@">1.3.8</token> 3 <token name="@TOOL_VERSION@">1.4.4</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>
47 ]]></token> 47 ]]></token>
48 <token name="@DASH_COMMAND@"><![CDATA[ 48 <token name="@DASH_COMMAND@"><![CDATA[
49 echo '${plot_format.plot_title}' > plot_title.txt && 49 echo '${plot_format.plot_title}' > plot_title.txt &&
50 echo '${plot_format.plot_intro}' > plot_intro.txt && 50 echo '${plot_format.plot_intro}' > plot_intro.txt &&
51 freyja dash 51 freyja dash
52 --mincov $plot_format.mincov
52 #if $need_aggregation.choice == 'no' 53 #if $need_aggregation.choice == 'no'
53 '$tsv_aggregated' 54 '$tsv_aggregated'
54 #else 55 #else
55 'aggregated.tsv' 56 'aggregated.tsv'
56 #end if 57 #end if
59 plot_intro.txt 60 plot_intro.txt
60 --output abundances_dashboard.html 61 --output abundances_dashboard.html
61 ]]></token> 62 ]]></token>
62 <token name="@PLOT_COMMAND@"><![CDATA[ 63 <token name="@PLOT_COMMAND@"><![CDATA[
63 freyja plot 64 freyja plot
65 $plot_format.lineages
66 --mincov $plot_format.mincov
64 #if $need_aggregation.choice == 'no' 67 #if $need_aggregation.choice == 'no'
65 '$tsv_aggregated' 68 '$tsv_aggregated'
66 #else 69 #else
67 'aggregated.tsv' 70 'aggregated.tsv'
68 #end if 71 #end if
80 <token name="@PLOT_AND_DASH_COMMAND@"><![CDATA[ 83 <token name="@PLOT_AND_DASH_COMMAND@"><![CDATA[
81 #if $plot_format.choice == 'dash' 84 #if $plot_format.choice == 'dash'
82 @DASH_COMMAND@ 85 @DASH_COMMAND@
83 #else if $plot_format.choice == 'plot' 86 #else if $plot_format.choice == 'plot'
84 freyja plot 87 freyja plot
88 $plot_format.lineages
89 --mincov $plot_format.mincov
85 #if $need_aggregation.choice == 'no' 90 #if $need_aggregation.choice == 'no'
86 $tsv_aggregated 91 $tsv_aggregated
87 #else 92 #else
88 aggregated.tsv 93 aggregated.tsv
89 #end if 94 #end if
127 help="e.g. 0.0001."/> 132 help="e.g. 0.0001."/>
128 <param argument="--confirmedonly" type="boolean" truevalue="--confirmedonly" falsevalue="" 133 <param argument="--confirmedonly" type="boolean" truevalue="--confirmedonly" falsevalue=""
129 checked="false" 134 checked="false"
130 label="Remove unconfirmed lineages from the analysis" 135 label="Remove unconfirmed lineages from the analysis"
131 help="If the UShER tree includes proposed lineages, the --confirmedonly flag removes unconfirmed lineages from the analysis."/> 136 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 checked="false"
139 label="Use larger library with non-public lineages"
140 help="Allows to use larger UShER barcodes library extended with GISAID non-public lineages"/>
141 </xml>
142 <xml name="plot_lineages">
143 <param argument="--lineages" type="boolean" truevalue="--lineages" falsevalue=""
144 checked="false" label="Use lineage specific breakdown"/>
145 </xml>
146 <xml name="plot_mincov">
147 <param argument="--mincov" type="float" min="0" max="100" value="60"
148 label="Minimum genome coverage"
149 help="Include in the plot only samples where the 'coverage' value is greater than the specified --mincov parameter. It excludes samples with coverage values below the minimum coverage threshold. By default, the minimum genome coverage is set at 60 percent."/>
132 </xml> 150 </xml>
133 <token name="@HELP_HEADER@"><![CDATA[ 151 <token name="@HELP_HEADER@"><![CDATA[
134 What it does 152 What it does
135 ============ 153 ============
136 154
143 161
144 Freyja is intended as a post-processing step after primer trimming and variant calling in iVar (Grubaugh and Gangavaparu et al., 2019). From measurements of SNV freqency and sequencing depth at each position in the genome, Freyja returns an estimate of the true lineage abundances in the sample. 162 Freyja is intended as a post-processing step after primer trimming and variant calling in iVar (Grubaugh and Gangavaparu et al., 2019). From measurements of SNV freqency and sequencing depth at each position in the genome, Freyja returns an estimate of the true lineage abundances in the sample.
145 ]]></token> 163 ]]></token>
146 <xml name="citations"> 164 <xml name="citations">
147 <citations> 165 <citations>
148 <citation type="doi">10.5281/zenodo.6585067</citation> 166 <citation type="doi">10.1038/s41586-022-05049-6</citation>
149 </citations> 167 </citations>
150 </xml> 168 </xml>
151 </macros> 169 </macros>