Mercurial > repos > iuc > multiqc
comparison busco_plugin.xml @ 24:f7e2f1eb3a16 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
| author | iuc |
|---|---|
| date | Mon, 02 Sep 2024 14:22:54 +0000 |
| parents | |
| children |
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| 23:abfd8a6544d7 | 24:f7e2f1eb3a16 |
|---|---|
| 1 <macros> | |
| 2 <token name="@BUSCO_COMMAND@"><![CDATA[ | |
| 3 ## Searches for files "short_summary_[samplename].txt" | |
| 4 #for $file in $repeat.software_cond.input | |
| 5 @ESCAPE_IDENTIFIER@ | |
| 6 #set file_path = os.path.join($software_dir, 'short_summary_' + str($identifier)) | |
| 7 ln -s '$file' '$file_path' && | |
| 8 #end for | |
| 9 ]]></token> | |
| 10 <xml name="busco_form"> | |
| 11 <param name="input" type="data" format="txt" multiple="true" label="Output of BUSCO"/> | |
| 12 </xml> | |
| 13 <!-- add here your test files and tests, the more stringent the better --> | |
| 14 <xml name="busco_test"> | |
| 15 <test expect_num_outputs="3"> | |
| 16 <repeat name="results"> | |
| 17 <conditional name="software_cond"> | |
| 18 <param name="software" value="busco"/> | |
| 19 <param name="input" value="busco.txt"/> | |
| 20 </conditional> | |
| 21 </repeat> | |
| 22 <param name="title" value="Title of the report"/> | |
| 23 <param name="comment" value="Commment for the report"/> | |
| 24 <param name="flat" value="true"/> | |
| 25 <param name="export" value="true"/> | |
| 26 <output name="html_report"> | |
| 27 <assert_contents> | |
| 28 <has_text text="Title of the report"/> | |
| 29 <has_text text="Commment for the report"/> | |
| 30 <has_text text="busco-lineage-fungi_odb9"/> | |
| 31 </assert_contents> | |
| 32 </output> | |
| 33 <!-- Not sure why this is empty | |
| 34 <output name="stats"> | |
| 35 <assert_contents> | |
| 36 <has_text text="R1_fq"/> | |
| 37 <has_text text="result_right"/> | |
| 38 <has_text text="25839_merged"/> | |
| 39 <has_text text="C2"/> | |
| 40 <has_n_lines n="11"/> | |
| 41 <has_n_columns n="22"/> | |
| 42 </assert_contents> | |
| 43 </output> | |
| 44 --> | |
| 45 <output_collection name="plots" type="list" count="1"/> | |
| 46 </test> | |
| 47 </xml> | |
| 48 </macros> |