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view fastqc_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 |
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date | Mon, 02 Sep 2024 14:22:54 +0000 |
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<macros> <token name="@FASTQC_COMMAND@"><![CDATA[ #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) @CREATE_REPEAT_DIR_1@ #if str($repeat2.type) == "data" #for $k, $file in enumerate($repeat2.input) #set file_dir = os.path.join($repeat_dir, 'file_' + str($k)) #set file_path = os.path.join($file_dir, 'fastqc_data.txt') mkdir '$file_dir' && ln -s '$file' '$file_path' && #end for #elif str($repeat2.type) == "theoretical_gc" #for $file in $repeat2.input @ESCAPE_IDENTIFIER@ #set file_path = os.path.join($repeat_dir, str($identifier) + '_fastqc_theoretical_gc') ln -s '$file' '$file_path' && #end for #end if #end for ]]></token> <xml name="fastqc_form"> <repeat name="output" title="FastQC output" min="1"> <param name="type" type="select" label="Type of FastQC output?"> <option value="data">Raw data</option> <option value="theoretical_gc">Theorectical GC</option> </param> <param name="input" type="data" format="txt" multiple="true" label="FastQC output"> <validator type="expression" message="MultiQC does not accept the HTML report generated by FastQC, only the Raw Data">value is not None and value.extension != "html"</validator> </param> </repeat> </xml> <!-- add here your test files and tests, the more stringent the better --> <xml name="fastqc_test"> <test expect_num_outputs="3"> <repeat name="results"> <conditional name="software_cond"> <param name="software" value="fastqc" /> <repeat name="output"> <param name="type" value="data"/> <param name="input" value="fastqc_1.txt,fastqc_2.txt"/> </repeat> </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="fastqc_seq_heatmap_key_t" /> </assert_contents> </output> <output name="stats"> <assert_contents> <has_text text="poulet5_1"/> <has_text text="poulet5_2"/> <has_text text="FastQC_mqc_generalstats_fastqc_median_sequence_length"/> <has_n_lines n="3"/> <has_n_columns n="7"/> </assert_contents> </output> <output_collection name="plots" type="list" count="7"/> </test> </xml> </macros>