Mercurial > repos > iuc > freyja_variants

comparison macros.xml @ 0:08c2d81e7942 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
author iuc
date Thu, 28 Jul 2022 09:26:32 +0000
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children 1f467ed22412
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-1:000000000000 0:08c2d81e7942
1 <?xml version="1.0"?>
2 <macros>
3 <token name="@TOOL_VERSION@">1.3.8</token>
4 <token name="@VERSION_SUFFIX@">0</token>
5 <token name="@PROFILE@">21.01</token>
6 <xml name="biotools">
7 <xrefs>
8 <xref type="bio.tools">freyja</xref>
9 </xrefs>
10 </xml>
11 <xml name="requirements">
12 <requirements>
13 <requirement type="package" version="@TOOL_VERSION@">freyja</requirement>
14 <yield/>
15 </requirements>
16 </xml>
17 <xml name="version">
18 <version_command>freyja --version</version_command>
19 </xml>
20 <token name="@RUN_FREYJA_UPDATE_COMMAND@"><![CDATA[
21 #if $usher_update_option.choice == 'update'
22 freyja update &&
23 #end if
24 ]]></token>
25 <token name="@PREPROCESS_VCF_INPUT@"><![CDATA[
26 ln -s '$variants_file' 'variants_file.vcf' &&
27 ]]></token>
28 <token name="@STANDARD_INPUT_FOR_BOOT@"><![CDATA[
29 #if $variants_file.ext == 'vcf'
30 'variants_file.vcf'
31 #else
32 '$variants_file'
33 #end if
34 '$depth_file'
35 #if $eps
36 --eps '${eps}'
37 #end if
38 #if $meta
39 --meta '${meta}'
40 #end if
41 $confirmedonly
42 ]]></token>
43 <token name="@CUSTOM_BARCODES_COMMAND@"><![CDATA[
44 #if $usher_update_option.choice == 'custom'
45 --barcodes '${usher_update_option.usher_barcodes}'
46 #end if
47 ]]></token>
48 <token name="@DASH_COMMAND@"><![CDATA[
49 echo '${plot_format.plot_title}' > plot_title.txt &&
50 echo '${plot_format.plot_intro}' > plot_intro.txt &&
51 freyja dash
52 #if $need_aggregation.choice == 'no'
53 '$tsv_aggregated'
54 #else
55 'aggregated.tsv'
56 #end if
57 '$plot_format.csv_meta'
58 plot_title.txt
59 plot_intro.txt
60 --output abundances_dashboard.html
61 ]]></token>
62 <token name="@PLOT_COMMAND@"><![CDATA[
63 freyja plot
64 #if $need_aggregation.choice == 'no'
65 '$tsv_aggregated'
66 #else
67 'aggregated.tsv'
68 #end if
69 --output abundances_plot.pdf
70 #if $plot_format.csv_meta
71 --times '${plot_format.csv_meta}'
72 #end if
73 #if $plot_format.interval == 'MS'
74 --interval MS
75 #else
76 --interval D
77 --windowsize 70
78 #end if
79 ]]></token>
80 <token name="@PLOT_AND_DASH_COMMAND@"><![CDATA[
81 #if $plot_format.choice == 'dash'
82 @DASH_COMMAND@
83 #else if $plot_format.choice == 'plot'
84 freyja plot
85 #if $need_aggregation.choice == 'no'
86 $tsv_aggregated
87 #else
88 aggregated.tsv
89 #end if
90 --output abundances_plot.pdf
91 #if $plot_format.need_metadata.choice == 'yes'
92 --times '${plot_format.need_metadata.csv_meta}'
93 #if $plot_format.need_metadata.interval == 'MS'
94 --interval MS
95 #else
96 --interval D
97 --windowsize 70
98 #end if
99 #end if
100 #else if $plot_format.choice == 'plot_and_dash'
101 @DASH_COMMAND@ &&
102 @PLOT_COMMAND@
103 #end if
104 ]]></token>
105 <xml name="demixing_common_options">
106 <param name="depth_file" type="data" format="tabular" label="Sequencing depth file"/>
107 <conditional name="usher_update_option">
108 <param name="choice" type="select" label="Source of UShER barcodes data"
109 help="Freyja ships with an usher_barcodes.csv file, which the tool can access internally. Since this file gets updated rather frequently, you can also download the latest version of the file from https://github.com/andersen-lab/Freyja/raw/main/freyja/data/usher_barcodes.csv, set the dataset's datatype to csv and use it as a custom barcodes file.">
110 <option value="repo" selected="true">Use data shipped with the tool (can be
111 outdated)
112 </option>
113 <option value="custom">Provide a custom barcodes file</option>
114 <!--<option value="update">Get updated versions of the curated lineage file as well as the UShER global phylogenetic tree (can cause tool to run slowly)</option>-->
115 </param>
116 <when value="repo"/>
117 <when value="custom">
118 <param name="usher_barcodes" type="data" format="csv" label="UShER barcodes file"/>
119 </when>
120 <!--<when value="update" />-->
121 </conditional>
122 <param argument="--meta" type="data" format="json" optional="true"
123 label="Custom lineage metadata file"
124 help="For additional flexibility and reproducibility of analyses, a custom lineage-to-contellation mapping metadata file can be provided."/>
125 <param argument="--eps" type="float" optional="true"
126 label="Minimum lineage abundance tp include"
127 help="e.g. 0.0001."/>
128 <param argument="--confirmedonly" type="boolean" truevalue="--confirmedonly" falsevalue=""
129 checked="false"
130 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."/>
132 </xml>
133 <token name="@HELP_HEADER@"><![CDATA[
134 What it does
135 ============
136
137 Freyja is a tool to recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset (BAM aligned to the Hu-1 reference).
138
139 General information
140 ===================
141
142 Freyja is a tool to recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset (BAM aligned to the Hu-1 reference). The method uses lineage-determining mutational "barcodes" derived from the UShER global phylogenetic tree as a basis set to solve the constrained (unit sum, non-negative) de-mixing problem.
143
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.
145 ]]></token>
146 <xml name="citations">
147 <citations>
148 <citation type="doi">10.5281/zenodo.6585067</citation>
149 </citations>
150 </xml>
151 </macros>