Mercurial > repos > iuc > multiqc
diff cutadapt_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 (3 months ago) |
parents | |
children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cutadapt_plugin.xml Mon Sep 02 14:22:54 2024 +0000 @@ -0,0 +1,48 @@ +<macros> + <token name="@CUTADAPT_COMMAND@"><![CDATA[ + #set $pattern = "This is cutadapt" + #for $file in $repeat.software_cond.input + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($software_dir, str($identifier) + '.txt') + ln -s '$file' '$file_path' && + ## replace header for old cutadapt release + sed -i.old 's/You are running/This is/' '$file_path' && + grep -q "$pattern" '$file_path' || die "'$pattern' or 'You are running cutadapt' not found in the file" && + #end for + ]]></token> + <xml name="cutadapt_form"> + <param name="input" type="data" format="txt,tabular,tsv,csv" multiple="true" label="Output of Cutadapt" help="It should contain 'This is cutadapt' or 'You are running cutadapt'"/> + </xml> + <xml name="cutadapt_test"> + <test expect_num_outputs="3"> + <repeat name="results"> + <conditional name="software_cond"> + <param name="software" value="cutadapt"/> + <param name="input" value="cutadapt.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="cutadapt_trimmed_sequences_plot"/> + </assert_contents> + </output> + <output name="stats"> + <assert_contents> + <has_text text="Cutadapt"/> + <has_text text="Cutadapt_mqc_generalstats_cutadapt_percent_trimmed"/> + <has_text text="10"/> + <has_text text="Cutadapt_mqc_generalstats_cutadapt_percent_trimmed"/> + <has_n_lines n="2"/> + <has_n_columns n="2"/> + </assert_contents> + </output> + <output_collection name="plots" type="list" count="2"/> + </test> + </xml> +</macros>