Mercurial > repos > iuc > multiqc
diff 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 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/metaphlan_plugin.xml Tue Feb 18 23:18:25 2025 +0000 @@ -0,0 +1,46 @@ +<macros> + <token name="@METAPHLAN_COMMAND@"><![CDATA[ + #set $pattern = "#clade_name\tNCBI_tax_id\trelative_abundance\t" + #for $file in $repeat.software_cond.input + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($software_dir, str($identifier) + '.txt') + ln -s '$file' '$file_path' && + #end for + ]]></token> + <xml name="metaphlan_form"> + <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'"/> + </xml> + <xml name="metaphlan_test"> + <test expect_num_outputs="3"> + <repeat name="results"> + <conditional name="software_cond"> + <param name="software" value="metaphlan"/> + <param name="input" value="metaphlan.txt"/> + </conditional> + </repeat> + <param name="title" value="Title of the report"/> + <param name="comment" value="Commment for the report"/> + <param name="flat" value="true"/> + <param name="export" value="true"/> + <output name="html_report"> + <assert_contents> + <has_text text="Title of the report"/> + <has_text text="Commment for the report"/> + <has_text text="MetaPhlAn"/> + <has_text text="Top taxa"/> + </assert_contents> + </output> + <output name="stats"> + <assert_contents> + <has_text text="metaphlan-Moraxella_lacunata"/> + <has_text text="metaphlan-Top"/> + <has_text text="22.57968"/> + <has_text text="100.00001000000002"/> + <has_n_lines n="2"/> + <has_n_columns n="3"/> + </assert_contents> + </output> + <output_collection name="plots" type="list" count="7"/> + </test> + </xml> +</macros>