Mercurial > repos > iuc > multiqc
diff bismark_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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bismark_plugin.xml Mon Sep 02 14:22:54 2024 +0000 @@ -0,0 +1,83 @@ +<macros> + <token name="@BISMARK_COMMAND@"><![CDATA[ + #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) + @CREATE_REPEAT_DIR_1@ + #if str($repeat2.type) == "align" + #for $file in $repeat2.input + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($repeat_dir, str($identifier) + '_SE_report.txt') + ln -s '$file' '$file_path' && + #end for + #elif str($repeat2.type) == "dedup" + #for $file in $repeat2.input + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($repeat_dir, str($identifier) + '_deduplication_report.txt') + ln -s '$file' '$file_path' && + #end for + #elif str($repeat2.type) == "meth_extract" + #for $file in $repeat2.input + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($repeat_dir, str($identifier) + '_splitting_report.txt') + ln -s '$file' '$file_path' && + #end for + #elif str($repeat2.type) == "m_bias" + #for $file in $repeat2.input + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($repeat_dir, str($identifier) + '_M-bias.txt') + ln -s '$file' '$file_path' && + #end for + #elif str($repeat2.type) == "bam2nuc" + #for $file in $repeat2.input + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($repeat_dir, str($identifier) + '.nucleotide_stats.txt') + ln -s '$file' '$file_path' && + #end for + #end if + #end for + ]]></token> + <xml name="bismark_form"> + <repeat name="output" title="Bismark output" min="1"> + <param name="type" type="select" label="Type of Bismark output?"> + <option value="align">Alignment file</option> + <option value="dedup">Deduplication file</option> + <option value="meth_extract">Methylation file</option> + <option value="m_bias">m_bias file</option> + <option value="bam2nuc">bam2nuc file</option> + </param> + <param name="input" type="data" format="txt" multiple="true" label="Bismark output"/> + </repeat> + </xml> + <!-- add here your test files and tests, the more stringent the better --> + <xml name="bismark_test"> + <test expect_num_outputs="3"> + <repeat name="results"> + <conditional name="software_cond"> + <param name="software" value="bismark"/> + <repeat name="output"> + <param name="type" value="align"/> + <param name="input" value="bismark.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="bismark-alignment"/> + </assert_contents> + </output> + <output name="stats"> + <assert_contents> + <has_text text="bismark_txt_SE_report"/> + <has_n_lines n="2"/> + <has_n_columns n="3"/> + </assert_contents> + </output> + <output_collection name="plots" type="list" count="0"/> + </test> + </xml> +</macros>