Mercurial > repos > iuc > multiqc
view featurecounts_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 |
line wrap: on
line source
<macros> <token name="@FEATURECOUNTS_COMMAND@"><![CDATA[ #for $file in $repeat.software_cond.input @ESCAPE_IDENTIFIER@ #set file_prefix = os.path.join($software_dir, str($identifier)) if grep -qw Status '$file'; then ln -s '$file' '${file_prefix}.summary'; else echo -e 'Status\t${identifier}' > '${file_prefix}.summary'; cat '$file' >> '${file_prefix}.summary'; fi && #end for ]]></token> <xml name="featurecounts_form"> <param name="input" type="data" format="txt,tabular,tsv,csv" multiple="true" label="Output of FeatureCounts"/> </xml> <!-- add here your test files and tests, the more stringent the better --> <xml name="featurecounts_test"> <test expect_num_outputs="3"> <repeat name="results"> <conditional name="software_cond"> <param name="software" value="featureCounts"/> <param name="input" value="featureCounts.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="featureCounts_assignment_plot"/> </assert_contents> </output> <output name="stats"> <assert_contents> <has_text text="featureCounts_mqc_generalstats_featurecounts_Assigned"/> <has_text text="accepted_hits"/> <has_text text="TopHat"/> <has_text text="featureCounts_mqc_generalstats_featurecounts_percent_assigned"/> <has_n_lines n="7"/> <has_n_columns n="3"/> </assert_contents> </output> <output_collection name="plots" type="list" count="1"/> </test> </xml> </macros>