Mercurial > repos > iuc > freyja_boot
comparison freyja_boot.xml @ 4:cd5d77d118f2 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit cb599a5ca4a1612c5fc8050d6042d52c729a7c06
| author | iuc |
|---|---|
| date | Wed, 19 Feb 2025 11:08:52 +0000 |
| parents | a09398bc953a |
| children |
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| 3:16331f8cff98 | 4:cd5d77d118f2 |
|---|---|
| 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 ======================================== |