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comparison freyja_boot.xml @ 4:3275124de1b0 draft

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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 11:08:10 +0000
parents 6afb807ede8f
children
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3:945e21ba3066 4:3275124de1b0
10 <expand macro="requirements"/> 10 <expand macro="requirements"/>
11 <expand macro="version"/> 11 <expand macro="version"/>
12 <command detect_errors="exit_code"><![CDATA[ 12 <command detect_errors="exit_code"><![CDATA[
13 @RUN_FREYJA_UPDATE_COMMAND@ 13 @RUN_FREYJA_UPDATE_COMMAND@
14 @PREPROCESS_VCF_INPUT@ 14 @PREPROCESS_VCF_INPUT@
15 @CUSTOM_BARCODES_LINKING@
15 freyja boot 16 freyja boot
16 @STANDARD_INPUT_FOR_BOOT@ 17 @STANDARD_INPUT_FOR_BOOT@
17 --nt \${GALAXY_SLOTS:-4} 18 --nt \${GALAXY_SLOTS:-4}
18 #if $nb 19 #if $nb
19 --nb $nb 20 --nb $nb
99 <assert_contents> 100 <assert_contents>
100 <has_text text="Delta"/> 101 <has_text text="Delta"/>
101 </assert_contents> 102 </assert_contents>
102 </output> 103 </output>
103 </test> 104 </test>
104 </tests> 105
106 <!-- Test 03: Test Custom Usher Barcode file -->
107 <test expect_num_outputs="4">
108 <conditional name="usher_update_option">
109 <param name="choice" value="custom"/>
110 <param name="usher_barcodes" location="https://zenodo.org/records/14888005/files/usher_barcodes.csv"/>
111 </conditional>
112 <param name="variants_file" value="variants.tsv"/>
113 <param name="depth_file" value="depths.tsv"/>
114 <param name="confirmedonly" value="false"/>
115 <param name="nb" value="10"/>
116 <param name="boxplot_pdf" value="true"/>
117 <output name="boot_lineages" ftype="csv">
118 <assert_contents>
119 <has_text text="B.1.617.2"/>
120 </assert_contents>
121 </output>
122 <output name="boot_summarized" ftype="csv">
123 <assert_contents>
124 <has_text text="Del"/>
125 </assert_contents>
126 </output>
127 <output name="boot_lineages_plot" ftype="pdf">
128 <assert_contents>
129 <has_text text="Matplot"/>
130 </assert_contents>
131 </output>
132 <output name="boot_summarized_plot" ftype="pdf">
133 <assert_contents>
134 <has_text text="Matplot"/>
135 </assert_contents>
136 </output>
137 </test>
138 </tests>
105 <help><![CDATA[ 139 <help><![CDATA[
106 @HELP_HEADER@ 140 @HELP_HEADER@
107 141
108 Information about **freyja boot** method 142 Information about **freyja boot** method
109 ======================================== 143 ========================================