Mercurial > repos > iuc > multiqc
comparison gatk_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="@GATK_COMMAND@"><![CDATA[ | |
| 3 #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) | |
| 4 #if str($repeat2.type) == "varianteval" | |
| 5 #set $pattern = "#:GATKTable:TiTvVariantEvaluator" | |
| 6 @LN_2_FILES@ | |
| 7 #elif str($repeat2.type) == "base_recalibrator" | |
| 8 #set $pattern = "#:GATKTable:Arguments:Recalibration" | |
| 9 @LN_2_FILES@ | |
| 10 #end if | |
| 11 #end for | |
| 12 ]]></token> | |
| 13 <xml name="gatk_form"> | |
| 14 <repeat name="output" title="GATK output" min="1"> | |
| 15 <param name="type" type="select" label="Type of GATK output?"> | |
| 16 <option value="varianteval">Variant eval file</option> | |
| 17 <option value="base_recalibrator">Base recalibrator file</option> | |
| 18 </param> | |
| 19 <param name="input" type="data" format="txt" multiple="true" label="GATK output"/> | |
| 20 </repeat> | |
| 21 </xml> | |
| 22 <!-- add here your test files and tests, the more stringent the better --> | |
| 23 <xml name="gatk_test"> | |
| 24 <test expect_num_outputs="3"> | |
| 25 <repeat name="results"> | |
| 26 <conditional name="software_cond"> | |
| 27 <param name="software" value="gatk"/> | |
| 28 <repeat name="output"> | |
| 29 <param name="type" value="base_recalibrator"/> | |
| 30 <param name="input" value="gatk_BaseRecalibrator.txt"/> | |
| 31 </repeat> | |
| 32 <repeat name="output"> | |
| 33 <param name="type" value="varianteval"/> | |
| 34 <param name="input" value="gatk_varianteval.txt"/> | |
| 35 </repeat> | |
| 36 </conditional> | |
| 37 </repeat> | |
| 38 <param name="title" value="Title of the report"/> | |
| 39 <param name="comment" value="Commment for the report"/> | |
| 40 <param name="flat" value="true"/> | |
| 41 <param name="export" value="true"/> | |
| 42 <output name="html_report"> | |
| 43 <assert_contents> | |
| 44 <has_text text="Title of the report"/> | |
| 45 <has_text text="Commment for the report"/> | |
| 46 <has_text text="gatk_varianteval_variant_plot"/> | |
| 47 </assert_contents> | |
| 48 </output> | |
| 49 <output name="stats"> | |
| 50 <assert_contents> | |
| 51 <has_text text="gatk_varianteval_txt"/> | |
| 52 <has_n_lines n="2"/> | |
| 53 <has_n_columns n="3"/> | |
| 54 </assert_contents> | |
| 55 </output> | |
| 56 <output_collection name="plots" type="list" count="4"/> | |
| 57 </test> | |
| 58 </xml> | |
| 59 </macros> |