Mercurial > repos > sanbi-uwc > summarize_poliovirus_alignment
diff summarize_poliovirus_alignment.xml @ 0:7e49c6b19f5e draft
planemo upload commit a99e10fec2fac5aae70974c977eb3b362a1a8429
author | sanbi-uwc |
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date | Tue, 19 Jul 2022 11:47:08 +0000 |
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children | f2a7aaf93a1d |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/summarize_poliovirus_alignment.xml Tue Jul 19 11:47:08 2022 +0000 @@ -0,0 +1,60 @@ +<tool id="summarize_poliovirus_alignment" name="Summarize poliovirus alignment" version="0.1.0+galaxy0" profile="21.05"> + <requirements> + <requirement type="package" version="3.9">python</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + python $__tool_directory__/summarize_alignment.py + --summary_output_filename '$output1' + --variant_list_outputs + #for $key in $variant_list.keys() + '$variant_list[$key]' + #end for + --datasets + #for $dataset in $alignment_assessments + '$dataset' + #end for + + ]]></command> + <inputs> + <!-- input is list of reports for poliovirus sabin 1, 2 and 3 --> + <param name="alignment_assessments" format="json" type="data_collection" collection_type="list" label="Poliovius alignment assessments" help="Input is a list of JSON reports from the assess_poliovirus_alignment tool" /> + </inputs> + <outputs> + <data name="output1" format="tabular" label="Poliovirus variant summary on ${on_string}" /> + <collection name="variant_list" type="list" label="Poliovirus variant lists on ${on_string}" structured_like="alignment_assessments" format="tabular"> + <!-- todo - find a way to set the metadata columns for the tabular datasets --> + </collection> + </outputs> + <tests> + <test expect_num_outputs="3"> + <param name="alignment_assessments" ftype="json"> + <collection type="list"> + <element name="sample1" value="sample1_output.json" /> + </collection> + </param> + <output name="output1" ftype="tabular"> + <assert_contents> + <has_text text="23:G:A;26:G:A;38:A:G;40:T:C;59:C:T;65:T:C;72:A:G;" /> + </assert_contents> + </output> + <output_collection name="variant_list"> + <element name="sample1" file="sample1_variants.tabular" ftype="tabular" /> + </output_collection> + </test> + </tests> + <help><![CDATA[ + Given a list of outputs of the assess_poliovirus_alignment tool, make a final summary. + ]]></help> + <citations> + <citation type="bibtex"><![CDATA[ + @software{van_Heusden_Poliovirus_variation_reporting_2022, + author = {van Heusden, Peter}, + month = {7}, + title = {{Poliovirus variation reporting scripts}}, + url = {https://github.com/pvanheus/polio_report}, + version = {0.1.0}, + year = {2022} + } + ]]></citation> + </citations> +</tool> \ No newline at end of file