Mercurial > repos > thanhlv > hamronization
view hamronize_summarize.xml @ 0:5fca34360c12 draft default tip
"planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
author | thanhlv |
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date | Tue, 02 Feb 2021 21:18:52 +0000 |
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<tool id="hamronize_summarize" name="hamronize_summarize" version="@VERSION@+galaxy0"> <description> harmorize reports</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <expand macro="version_command" /> <command detect_errors="exit_code"><![CDATA[ #for $counter, $report in enumerate($reports): #if $report.is_of_type('tsv', 'tabular'): #set $ext = 'tsv' #elif $report.is_of_type('json'): #set $ext = 'json' #end if ln -s '$report' ./report_${counter}.${ext} && #end for hamronize summarize --summary_type $summary_type #if $summary_type == "tsv" --output output.tsv #elif $summary_type == "json" --output output.json #else --output output.html #end if *.tsv *.json ]]> </command> <inputs> <param name="reports" type="data" multiple="true" format="tsv,json" label="Report files"/> <param name="summary_type" type="select" label="Output format" multiple="false"> <option value="tsv">tsv</option> <option value="json">json</option> <option value="interactive">interactive</option> </param> </inputs> <outputs> <data format="tsv" name="output_tsv" label="${tool.name} on ${on_string}: Output" from_work_dir="output.tsv"> <filter>summary_type == "tsv"</filter> </data> <data format="json" name="output_json" label="${tool.name} on ${on_string}: Output" from_work_dir="output.json"> <filter>summary_type == "json"</filter> </data> <data format="html" name="output_html" label="${tool.name} on ${on_string}: Output" from_work_dir="output.html"> <filter>summary_type == "interactive"</filter> </data> </outputs> <tests> <!-- tsv output --> <test expect_num_outputs="1"> <param name="reports" value="hamronized_abricate.tsv,hamronized_abricate.json,hamronized_ariba.tsv,hamronized_ariba.json,hamronized_rgi.tsv,hamronized_rgi.json" /> <param name="summary_type" value="tsv" /> <output name="output_tsv" ftype="tsv" file="summary.tsv" /> </test> <!-- json output --> <test expect_num_outputs="1"> <param name="reports" value="hamronized_abricate.tsv,hamronized_abricate.json,hamronized_ariba.tsv,hamronized_ariba.json,hamronized_rgi.tsv,hamronized_rgi.json" /> <param name="summary_type" value="json" /> <output name="output_json" ftype="json"> <assert_contents> <has_text text="GCF_010120755.1_ASM1012075v1_genomic" /> <has_text text="H_NS.3000676.BA000007.3.1737690_1738104.5476" /> <has_text text="NODE_9_length_203843_cov_42.4911_20" /> </assert_contents> </output> </test> </tests> <help> <![CDATA[ ]]> </help> </tool>