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comparison lotus2.xml @ 7:692832801d70 draft

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"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 81334bedc488edc36581c015b5a4c06926ec236c"
author earlhaminst
date Sun, 06 Jun 2021 17:55:32 +0000
parents fc78d02657a9
children 0fddee8b1f7e
comparison
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6:fc78d02657a9 7:692832801d70
1 <tool id="lotus2" name="LotuS2" version="@VERSION@" profile="20.01"> 1 <tool id="lotus2" name="LotuS2" version="@VERSION@+galaxy1" profile="20.01">
2 <description>fast OTU processing pipeline</description> 2 <description>fast OTU processing pipeline</description>
3 <macros> 3 <macros>
4 <token name="@VERSION@">2.07</token> 4 <token name="@VERSION@">2.07</token>
5 <xml name="refDB_macro" token_ref_fasta_formats="fasta,fasta.gz"> 5 <xml name="refDB_macro" token_ref_fasta_formats="fasta,fasta.gz">
6 <conditional name="refDB_cond"> 6 <conditional name="refDB_cond">
177 -lulu $tax_args.lulu 177 -lulu $tax_args.lulu
178 -buildPhylo $tax_args.buildPhylo 178 -buildPhylo $tax_args.buildPhylo
179 179
180 ; EXIT_VALUE=\$? ; 180 ; EXIT_VALUE=\$? ;
181 181
182 tar -cvzf output.tar.gz output/ 182 zip -8 -r -v output.zip output/
183 && 183 &&
184 exit \$EXIT_VALUE 184 exit \$EXIT_VALUE
185 ]]></command> 185 ]]></command>
186 186
187 <inputs> 187 <inputs>
327 </param> 327 </param>
328 </section> 328 </section>
329 </inputs> 329 </inputs>
330 330
331 <outputs> 331 <outputs>
332 <data name="outputs" format="zip" label="${tool.name} on ${on_string}: Complete LotuS2 output" from_work_dir="output.zip" />
332 <data name="otu" format="tabular" label="${tool.name} on ${on_string}: OTU abundance matrix" from_work_dir="output/OTU.txt" /> 333 <data name="otu" format="tabular" label="${tool.name} on ${on_string}: OTU abundance matrix" from_work_dir="output/OTU.txt" />
333 <data name="otu_biom" format="biom1" label="${tool.name} on ${on_string}: biom-formatted OTU abundance matrix" from_work_dir="output/OTU.biom" />
334 <data name="otu_fna" format="fasta" label="${tool.name} on ${on_string}: FASTA-formatted extended OTU seed sequences" from_work_dir="output/OTU.fna" /> 334 <data name="otu_fna" format="fasta" label="${tool.name} on ${on_string}: FASTA-formatted extended OTU seed sequences" from_work_dir="output/OTU.fna" />
335 <data name="OTUphylo_nwk" format="newick" label="${tool.name} on ${on_string}: Newick-formatted phylogenetic tree between sequences" from_work_dir="output/OTUphylo.nwk" /> 335 <data name="OTUphylo_nwk" format="newick" label="${tool.name} on ${on_string}: Newick-formatted phylogenetic tree between sequences" from_work_dir="output/OTUphylo.nwk" />
336 <data name="mapping" format="tabular" label="${tool.name} on ${on_string}: mapping file" from_work_dir="output/primary/in.map" /> 336 <data name="mapping" format="tabular" label="${tool.name} on ${on_string}: mapping file" from_work_dir="output/primary/in.map" />
337 <data name="runlog" format="txt" label="${tool.name} on ${on_string}: main log file" from_work_dir="output/LotuSLogS/LotuS_run.log" /> 337 <data name="runlog" format="txt" label="${tool.name} on ${on_string}: main log file" from_work_dir="output/LotuSLogS/LotuS_run.log" />
338 <data name="outputs" format="tar" label="${tool.name} on ${on_string}: All output files" from_work_dir="output.tar.gz" />
339 </outputs> 338 </outputs>
340 339
341 <tests> 340 <tests>
342 <test> 341 <test>
343 <param name="paired_or_single" value="single"/> 342 <param name="paired_or_single" value="single"/>