Mercurial > repos > iuc > multiqc
diff vcftools_plugin.xml @ 24:f7e2f1eb3a16 draft
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/vcftools_plugin.xml Mon Sep 02 14:22:54 2024 +0000 @@ -0,0 +1,94 @@ +<macros> + <token name="@VCFTOOLS_COMMAND@"><![CDATA[ + #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) + @CREATE_REPEAT_DIR_2@ + #if str($repeat2.type.type) == "relatedness2" + #for $file in $repeat2.type.input + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($repeat_dir, str($identifier) + '.relatedness2') + ln -s '$file' '$file_path' && + #end for + #elif str($repeat2.type) == "tstv_by_count" + #for $file in $repeat2.type.input + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($repeat_dir, str($identifier) + '.TsTv.count') + ln -s '$file' '$file_path' && + #end for + #elif str($repeat2.type) == "tstv_by_qual" + #for $file in $repeat2.type.input + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($repeat_dir, str($identifier) + '.TsTv.qual') + ln -s '$file' '$file_path' && + #end for + #elif str($repeat2.type) == "tstv_summary" + #for $file in $repeat2.type.input + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($repeat_dir, str($identifier) + '.TsTv.summary') + ln -s '$file' '$file_path' && + #end for + #end if + #end for + ]]></token> + <xml name="vcftools_form"> + <repeat name="output" title="VCFTools output" min="1"> + <conditional name="type"> + <param name="type" type="select" label="Type of VCFTools output?"> + <option value="relatedness2">relatedness2</option> + <option value="tstv_by_count">tstv_by_count</option> + <option value="tstv_by_qual">tstv_by_qual</option> + <option value="tstv_summary">tstv_summary</option> + </param> + <when value="relatedness2"> + <param name="input" type="data" format="txt" label="VCFTools relatedness2 output" multiple="true"/> + </when> + <when value="tstv_by_count"> + <param name="input" type="data" format="tabular,tsv" label="VCFTools TsTV count output" multiple="true"/> + </when> + <when value="tstv_by_qual"> + <param name="input" type="data" format="tabular" label="VCFTools TsTV qual output" multiple="true"/> + </when> + <when value="tstv_summary"> + <param name="input" type="data" format="txt" label="VCFTools TsTV summary output" multiple="true"/> + </when> + </conditional> + </repeat> + </xml> + <xml name="vcftools_test"> + <test expect_num_outputs="2"> + <repeat name="results"> + <conditional name="software_cond"> + <param name="software" value="vcftools"/> + <repeat name="output"> + <conditional name="type"> + <param name="type" value="tstv_by_qual"/> + <param name="input" value="vcftools.txt"/> + </conditional> + </repeat> + </conditional> + </repeat> + <param name="title" value="Title of the report"/> + <param name="comment" value="Commment for the report"/> + <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"/> + <has_text text="All-in-one FASTQ preprocessor"/> + <has_text text="trimmomatic_plot"/> + </assert_contents> + </output> + <output name="stats"> + <assert_contents> + <has_text text="dataset_33"/> + <has_text text="R1_fq"/> + <has_text text="result_right"/> + <has_text text="25839_merged"/> + <has_text text="C2"/> + <has_n_lines n="11"/> + <has_n_columns n="22"/> + </assert_contents> + </output> + <output_collection name="plots" type="list" count="29"/> + </test> + </xml> +</macros>