Mercurial > repos > iuc > multiqc
comparison metaphlan_plugin.xml @ 27:7591bce96601 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
| author | iuc |
|---|---|
| date | Tue, 18 Feb 2025 23:18:25 +0000 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| 26:d2aaac19f42f | 27:7591bce96601 |
|---|---|
| 1 <macros> | |
| 2 <token name="@METAPHLAN_COMMAND@"><![CDATA[ | |
| 3 #set $pattern = "#clade_name\tNCBI_tax_id\trelative_abundance\t" | |
| 4 #for $file in $repeat.software_cond.input | |
| 5 @ESCAPE_IDENTIFIER@ | |
| 6 #set file_path = os.path.join($software_dir, str($identifier) + '.txt') | |
| 7 ln -s '$file' '$file_path' && | |
| 8 #end for | |
| 9 ]]></token> | |
| 10 <xml name="metaphlan_form"> | |
| 11 <param name="input" type="data" format="txt" multiple="true" label="Output of MetaPhlAn" help="It should contain '#clade_name\tNCBI_tax_id\trelative_abundance\t'"/> | |
| 12 </xml> | |
| 13 <xml name="metaphlan_test"> | |
| 14 <test expect_num_outputs="3"> | |
| 15 <repeat name="results"> | |
| 16 <conditional name="software_cond"> | |
| 17 <param name="software" value="metaphlan"/> | |
| 18 <param name="input" value="metaphlan.txt"/> | |
| 19 </conditional> | |
| 20 </repeat> | |
| 21 <param name="title" value="Title of the report"/> | |
| 22 <param name="comment" value="Commment for the report"/> | |
| 23 <param name="flat" value="true"/> | |
| 24 <param name="export" value="true"/> | |
| 25 <output name="html_report"> | |
| 26 <assert_contents> | |
| 27 <has_text text="Title of the report"/> | |
| 28 <has_text text="Commment for the report"/> | |
| 29 <has_text text="MetaPhlAn"/> | |
| 30 <has_text text="Top taxa"/> | |
| 31 </assert_contents> | |
| 32 </output> | |
| 33 <output name="stats"> | |
| 34 <assert_contents> | |
| 35 <has_text text="metaphlan-Moraxella_lacunata"/> | |
| 36 <has_text text="metaphlan-Top"/> | |
| 37 <has_text text="22.57968"/> | |
| 38 <has_text text="100.00001000000002"/> | |
| 39 <has_n_lines n="2"/> | |
| 40 <has_n_columns n="3"/> | |
| 41 </assert_contents> | |
| 42 </output> | |
| 43 <output_collection name="plots" type="list" count="7"/> | |
| 44 </test> | |
| 45 </xml> | |
| 46 </macros> |