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comparison freyja_boot.xml @ 0:4d6fe132443a 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 09:22:45 +0000
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children 6afb807ede8f
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-1:000000000000 0:4d6fe132443a
1 <tool id="freyja_boot" name="Freyja: Bootstrapping" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"
2 profile="@PROFILE@">
3 <description>
4 method
5 </description>
6 <macros>
7 <import>macros.xml</import>
8 </macros>
9 <expand macro="biotools"/>
10 <expand macro="requirements"/>
11 <expand macro="version"/>
12 <command detect_errors="exit_code"><![CDATA[
13 @RUN_FREYJA_UPDATE_COMMAND@
14 @PREPROCESS_VCF_INPUT@
15 freyja boot
16 @STANDARD_INPUT_FOR_BOOT@
17 --nt \${GALAXY_SLOTS:-4}
18 #if $nb
19 --nb $nb
20 #end if
21 --output_base 'boot_output'
22 @CUSTOM_BARCODES_COMMAND@
23 $boxplot_pdf
24 ]]></command>
25 <inputs>
26 <param name="variants_file" type="data" format="tabular" label="Variants file"/>
27 <expand macro="demixing_common_options"/>
28 <param argument="--nb" type="integer" optional="true" label="Number of bootstraps"/>
29 <param name="boxplot_pdf" argument="--boxplot pdf" type="boolean" truevalue="--boxplot pdf"
30 falsevalue=""
31 checked="false" label="Generate boxplot"/>
32 </inputs>
33 <outputs>
34 <data name="boot_lineages" format="csv" label="${tool.name} on ${on_string}: Lineages"
35 from_work_dir="boot_output_lineages.csv"/>
36 <data name="boot_summarized" format="csv" label="${tool.name} on ${on_string}: Summarized"
37 from_work_dir="boot_output_summarized.csv">
38 </data>
39 <data name="boot_lineages_plot" format="pdf"
40 label="${tool.name} on ${on_string}: Lineages boxplot"
41 from_work_dir="boot_output_lineages.pdf">
42 <filter>boxplot_pdf</filter>
43 </data>
44 <data name="boot_summarized_plot" format="pdf"
45 label="${tool.name} on ${on_string}: Summarized boxplot"
46 from_work_dir="boot_output_summarized.pdf">
47 <filter>boxplot_pdf</filter>
48 </data>
49 </outputs>
50 <tests>
51 <!-- Test 01: test tsv input files and plots -->
52 <test expect_num_outputs="4">
53 <conditional name="usher_update_option">
54 <param name="choice" value="repo"/>
55 </conditional>
56 <param name="variants_file" value="variants.tsv"/>
57 <param name="depth_file" value="depths.tsv"/>
58 <param name="confirmedonly" value="false"/>
59 <param name="nb" value="10"/>
60 <param name="boxplot_pdf" value="true"/>
61 <output name="boot_lineages" ftype="csv">
62 <assert_contents>
63 <has_text text="B.1.617.2"/>
64 </assert_contents>
65 </output>
66 <output name="boot_summarized" ftype="csv">
67 <assert_contents>
68 <has_text text="Delta"/>
69 </assert_contents>
70 </output>
71 <output name="boot_lineages_plot" ftype="pdf">
72 <assert_contents>
73 <has_text text="Matplotlib"/>
74 </assert_contents>
75 </output>
76 <output name="boot_summarized_plot" ftype="pdf">
77 <assert_contents>
78 <has_text text="Matplotlib"/>
79 </assert_contents>
80 </output>
81 </test>
82 <!-- Test 02: test VCF input file -->
83 <test expect_num_outputs="2">
84 <conditional name="usher_update_option">
85 <param name="choice" value="repo"/>
86 </conditional>
87 <param name="variants_file" value="test.vcf"/>
88 <param name="depth_file" value="depths.tsv"/>
89 <param name="confirmedonly" value="false"/>
90 <param name="nb" value="10"/>
91 <param name="boxplot_pdf" value="false"/>
92 <output name="boot_lineages" ftype="csv">
93 <assert_contents>
94 <has_text text="B.1.617.2"/>
95 </assert_contents>
96 </output>
97 <output name="boot_summarized" ftype="csv">
98 <assert_contents>
99 <has_text text="Delta"/>
100 </assert_contents>
101 </output>
102 </test>
103 </tests>
104 <help><![CDATA[
105 @HELP_HEADER@
106
107 Information about **freyja boot** method
108 ========================================
109
110 A fast bootstrapping method for freyja.
111
112 Outputs
113 =======
114
115 Bootstrapping method results:
116
117 1. Bootstrap lineages: the 0.025, 0.05,0.25,0.5 (median),0.75, 0.95, and 0.975 percentiles for each lineage;
118 2. Bootstrap summarized: WHO designated VOI/VOC
119
120 ]]></help>
121 <expand macro="citations"/>
122 </tool>