Mercurial > repos > bgruening > flye
diff flye.xml @ 4:3ee0ef312022 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 1143ac8397d6fefb3f18d33bb752ee3f13c072d6"
author | bgruening |
---|---|
date | Wed, 05 Feb 2020 19:37:18 -0500 |
parents | 1ce9b1d72ec3 |
children | de24438c9988 |
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--- a/flye.xml Sun Dec 02 12:53:28 2018 -0500 +++ b/flye.xml Wed Feb 05 19:37:18 2020 -0500 @@ -1,4 +1,4 @@ -<tool id="flye" name="Assembly" version="2.3.7"> +<tool id="flye" name="Flye assembly" version="2.6"> <description>of long and error-prone reads</description> <macros> <import>macros.xml</import> @@ -35,6 +35,12 @@ #if $m: -m '$m' #end if + #if $asm: + --asm-coverage '$asm' + #end if + ${plasmids} + ${meta} + ${no_trestle} 2>&1 ]]></command> <inputs> @@ -51,12 +57,16 @@ </param> <param argument="-i" type="integer" value="1" label="number of polishing iterations" /> <param argument="-m" type="integer" optional="true" label="minimum overlap between reads (default: auto)" /> + <param name="asm" argument="--asm-coverage" type="integer" optional="true" label="reduced coverage for initial disjointing assembly" /> + <param argument="--plasmids" type="boolean" truevalue="--plasmids" falsevalue="" checked="False" label="rescue short unassembled plasmids" /> + <param argument="--meta" type="boolean" truevalue="--meta" falsevalue="" checked="False" label="perform metagenomic assembly" /> + <param name="no_trestle" argument="--no-trestle" type="boolean" truevalue="--no-trestle" falsevalue="" checked="False" label="skip trestle stage" /> </inputs> <outputs> - <data name="scaffolds" format="fasta" from_work_dir="out_dir/scaffolds.fasta" label="${tool.name} on ${on_string} (scaffolds)"/> - <data name="assembly_info" format="tabular" from_work_dir="out_dir/assembly_info.txt" label="${tool.name} on ${on_string} (assembly_info)"/> + <data name="consensus" format="fasta" from_work_dir="out_dir/assembly.fasta" label="${tool.name} on ${on_string} (consensus)"/> <data name="assembly_graph" format="graph_dot" from_work_dir="out_dir/assembly_graph.gv" label="${tool.name} on ${on_string} (assembly_graph)"/> <data name="assembly_gfa" format="txt" from_work_dir="out_dir/assembly_graph.gfa" label="${tool.name} on ${on_string} (Graphical Fragment Assembly)"/> + <data name="assembly_info" format="tabular" from_work_dir="out_dir/assembly_info.txt" label="${tool.name} on ${on_string} (assembly_info)"/> <data name="flye_log" format="txt" from_work_dir="out_dir/flye.log" label="${tool.name} on ${on_string} (log)"/> </outputs> <tests> @@ -64,27 +74,43 @@ <param name="inputs" ftype="fasta" value="nanopore.fasta"/> <param name="mode" value="--pacbio-raw"/> <param name="g" value="10000"/> - <output name="scaffolds" file="result1_scaffolds.fasta" ftype="fasta" compare="sim_size"/> <output name="assembly_info" file="result1_assembly_info.txt" ftype="tabular" compare="sim_size"/> <output name="assembly_graph" file="result1_assembly_graph.dot" ftype="graph_dot" compare="sim_size"/> <output name="assembly_gfa" file="result1_assembly_graph.gfa" ftype="txt" compare="sim_size"/> + <output name="consensus" file="result1_assembly.fasta" ftype="fasta" compare="sim_size"/> </test> <test> <param name="inputs" ftype="fasta" value="nanopore.fasta"/> <param name="mode" value="--nano-raw"/> <param name="g" value="10000"/> - <output name="scaffolds" file="result2_scaffolds.fasta" ftype="fasta" compare="sim_size"/> <output name="assembly_info" file="result2_assembly_info.txt" ftype="tabular" compare="sim_size"/> <output name="assembly_graph" file="result2_assembly_graph.dot" ftype="graph_dot" compare="sim_size"/> <output name="assembly_gfa" file="result2_assembly_graph.gfa" ftype="txt" compare="sim_size"/> + <output name="consensus" file="result2_assembly.fasta" ftype="fasta" compare="sim_size"/> + </test> + <test> + <param name="inputs" ftype="fasta" value="nanopore.fasta"/> + <param name="mode" value="--nano-corr"/> + <param name="g" value="10000"/> + <param name="i" value="2"/> + <param name="asm" value="40"/> + <output name="assembly_info" file="result3_assembly_info.txt" ftype="tabular" compare="sim_size"/> + <output name="assembly_graph" file="result3_assembly_graph.dot" ftype="graph_dot" compare="sim_size"/> + <output name="assembly_gfa" file="result3_assembly_graph.gfa" ftype="txt" compare="sim_size"/> + <output name="consensus" file="result3_assembly.fasta" ftype="fasta" compare="sim_size"/> </test> <test> <param name="inputs" ftype="fasta" value="nanopore.fasta"/> <param name="mode" value="--pacbio-raw"/> <param name="g" value="10000"/> - <param name="i" value="2"/> - <output name="scaffolds" file="result3_scaffolds.fasta" ftype="fasta" compare="sim_size"/> - <output name="assembly_gfa" file="result2_assembly_graph.gfa" ftype="txt" compare="sim_size"/> + <param name="i" value="1"/> + <param name="meta" value="true"/> + <param name="plasmids" value="true"/> + <param name="no-trestle" value="true"/> + <output name="assembly_info" file="result4_assembly_info.txt" ftype="tabular" compare="sim_size"/> + <output name="assembly_graph" file="result4_assembly_graph.dot" ftype="graph_dot" compare="sim_size"/> + <output name="assembly_gfa" file="result4_assembly_graph.gfa" ftype="txt" compare="sim_size"/> + <output name="consensus" file="result4_assembly.fasta" ftype="fasta" compare="sim_size"/> </test> </tests> <help><![CDATA[