Mercurial > repos > thanhlv > flye
comparison flye.xml @ 2:e57e2c2952ff draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 0b1a602e21fbf8cfeba1294b6b985f1fba75afe9-dirty
| author | thanhlv |
|---|---|
| date | Thu, 04 Apr 2019 11:48:36 -0400 |
| parents | 5e8958350b97 |
| children | 09d56997363f |
comparison
equal
deleted
inserted
replaced
| 1:5e8958350b97 | 2:e57e2c2952ff |
|---|---|
| 42 '$plasmid' | 42 '$plasmid' |
| 43 #end if | 43 #end if |
| 44 #if $meta: | 44 #if $meta: |
| 45 '$meta' | 45 '$meta' |
| 46 #end if | 46 #end if |
| 47 #if $no-trestle: | 47 #if $no_trestle: |
| 48 '$no-trestle' | 48 '$no_trestle' |
| 49 #end if | 49 #end if |
| 50 2>&1 | 50 2>&1 |
| 51 ]]></command> | 51 ]]></command> |
| 52 <inputs> | 52 <inputs> |
| 53 <param name="inputs" type="data" format="fasta,fasta.gz,fastq,fastq.gz,fastqsanger.gz,fastqsanger" multiple="true" label="Input reads" /> | 53 <param name="inputs" type="data" format="fasta,fasta.gz,fastq,fastq.gz,fastqsanger.gz,fastqsanger" multiple="true" label="Input reads" /> |
| 64 <param argument="-i" type="integer" value="1" label="number of polishing iterations" /> | 64 <param argument="-i" type="integer" value="1" label="number of polishing iterations" /> |
| 65 <param argument="-m" type="integer" optional="true" label="minimum overlap between reads (default: auto)" /> | 65 <param argument="-m" type="integer" optional="true" label="minimum overlap between reads (default: auto)" /> |
| 66 <param argument="--asm_coverage" type="integer" optional="true" label="reduced coverage for initial contig assembly (default: not set)" /> | 66 <param argument="--asm_coverage" type="integer" optional="true" label="reduced coverage for initial contig assembly (default: not set)" /> |
| 67 <param argument="--plasmid" type="boolean" truevalue="--plasmid" falsevalue="" checked="False" label="rescue short unassmebled plasmids" /> | 67 <param argument="--plasmid" type="boolean" truevalue="--plasmid" falsevalue="" checked="False" label="rescue short unassmebled plasmids" /> |
| 68 <param argument="--meta" type="boolean" truevalue="--meta" falsevalue="" checked="False" label="metagenome / uneven coverage mode" /> | 68 <param argument="--meta" type="boolean" truevalue="--meta" falsevalue="" checked="False" label="metagenome / uneven coverage mode" /> |
| 69 <param argument="--no-trestle" type="boolean" truevalue="--no-trestle" falsevalue="" checked="False" label="skip Trestle stage" /> | 69 <param argument="--no_trestle" type="boolean" truevalue="--no-trestle" falsevalue="" checked="False" label="skip Trestle stage" /> |
| 70 </inputs> | 70 </inputs> |
| 71 <outputs> | 71 <outputs> |
| 72 <data name="scaffolds" format="fasta" from_work_dir="out_dir/scaffolds.fasta" label="${tool.name} on ${on_string} (scaffolds)"/> | 72 <data name="scaffolds" format="fasta" from_work_dir="out_dir/scaffolds.fasta" label="${tool.name} on ${on_string} (scaffolds)"/> |
| 73 <data name="assembly_info" format="tabular" from_work_dir="out_dir/assembly_info.txt" label="${tool.name} on ${on_string} (assembly_info)"/> | 73 <data name="assembly_info" format="tabular" from_work_dir="out_dir/assembly_info.txt" label="${tool.name} on ${on_string} (assembly_info)"/> |
| 74 <data name="assembly_graph" format="graph_dot" from_work_dir="out_dir/assembly_graph.gv" label="${tool.name} on ${on_string} (assembly_graph)"/> | 74 <data name="assembly_graph" format="graph_dot" from_work_dir="out_dir/assembly_graph.gv" label="${tool.name} on ${on_string} (assembly_graph)"/> |