Mercurial > repos > bgruening > flye
comparison flye.xml @ 2:156e0da5b917 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit a926a92aed3e22b14fb88af204c8450987c59743
| author | bgruening |
|---|---|
| date | Thu, 29 Nov 2018 04:34:34 -0500 |
| parents | cd256484eb1a |
| children | 1ce9b1d72ec3 |
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| 1:cd256484eb1a | 2:156e0da5b917 |
|---|---|
| 1 <tool id="flye" name="Assembly" version="2.3.5"> | 1 <tool id="flye" name="Assembly" version="2.3.7"> |
| 2 <description>of long and error-prone reads</description> | 2 <description>of long and error-prone reads</description> |
| 3 <macros> | 3 <macros> |
| 4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
| 5 </macros> | 5 </macros> |
| 6 <expand macro="requirements" /> | 6 <expand macro="requirements" /> |
| 23 #end for | 23 #end for |
| 24 | 24 |
| 25 flye | 25 flye |
| 26 $mode | 26 $mode |
| 27 #for $counter, $input in enumerate($inputs): | 27 #for $counter, $input in enumerate($inputs): |
| 28 ./input_${counter}.${input.ext} | 28 ./input_${counter}.$ext |
| 29 #end for | 29 #end for |
| 30 | 30 |
| 31 -o out_dir | 31 -o out_dir |
| 32 -g '$g' | 32 -g '$g' |
| 33 -t \${GALAXY_SLOTS:-4} | 33 -t \${GALAXY_SLOTS:-4} |
| 59 <data name="assembly_graph" format="graph_dot" from_work_dir="out_dir/assembly_graph.dot" label="${tool.name} on ${on_string} (assembly_graph)"/> | 59 <data name="assembly_graph" format="graph_dot" from_work_dir="out_dir/assembly_graph.dot" label="${tool.name} on ${on_string} (assembly_graph)"/> |
| 60 <data name="flye_log" format="txt" from_work_dir="out_dir/flye.log" label="${tool.name} on ${on_string} (log)"/> | 60 <data name="flye_log" format="txt" from_work_dir="out_dir/flye.log" label="${tool.name} on ${on_string} (log)"/> |
| 61 </outputs> | 61 </outputs> |
| 62 <tests> | 62 <tests> |
| 63 <test> | 63 <test> |
| 64 <param name="inputs" ftype="fasta" value="E.coli_PacBio_40x_first_200_reads.fasta"/> | 64 <param name="inputs" ftype="fasta" value="nanopore.fasta"/> |
| 65 <param name="mode" value="--pacbio-raw"/> | 65 <param name="mode" value="--pacbio-raw"/> |
| 66 <param name="g" value="1m"/> | 66 <param name="g" value="10000"/> |
| 67 <output name="contigs" file="result1_contigs.fasta" ftype="fasta"/> | 67 <output name="contigs" file="result1_contigs.fasta" ftype="fasta" compare="sim_size"/> |
| 68 <output name="scaffolds" file="result1_scaffolds.fasta" ftype="fasta"/> | 68 <output name="scaffolds" file="result1_scaffolds.fasta" ftype="fasta" compare="sim_size"/> |
| 69 <output name="assembly_info" file="result1_assembly_info.txt" ftype="tabular"/> | 69 <output name="assembly_info" file="result1_assembly_info.txt" ftype="tabular" compare="sim_size"/> |
| 70 <output name="assembly_graph" file="result1_assembly_graph.dot" ftype="graph_dot" compare="sim_size"/> | 70 <output name="assembly_graph" file="result1_assembly_graph.dot" ftype="graph_dot" compare="sim_size"/> |
| 71 </test> | 71 </test> |
| 72 <test> | 72 <test> |
| 73 <param name="inputs" ftype="fasta" value="Loman_E.coli_MAP006-1_2D_50x_first_500_reads.fasta"/> | 73 <param name="inputs" ftype="fasta" value="nanopore.fasta"/> |
| 74 <param name="mode" value="--nano-raw"/> | 74 <param name="mode" value="--nano-raw"/> |
| 75 <param name="g" value="100000"/> | 75 <param name="g" value="10000"/> |
| 76 <output name="contigs" file="result2_contigs.fasta" ftype="fasta"/> | 76 <output name="contigs" file="result2_contigs.fasta" ftype="fasta" compare="sim_size"/> |
| 77 <output name="scaffolds" file="result2_scaffolds.fasta" ftype="fasta"/> | 77 <output name="scaffolds" file="result2_scaffolds.fasta" ftype="fasta" compare="sim_size"/> |
| 78 <output name="assembly_info" file="result2_assembly_info.txt" ftype="tabular"/> | 78 <output name="assembly_info" file="result2_assembly_info.txt" ftype="tabular" compare="sim_size"/> |
| 79 <output name="assembly_graph" file="result2_assembly_graph.dot" ftype="graph_dot" compare="sim_size"/> | 79 <output name="assembly_graph" file="result2_assembly_graph.dot" ftype="graph_dot" compare="sim_size"/> |
| 80 </test> | 80 </test> |
| 81 <test> | 81 <test> |
| 82 <param name="inputs" ftype="fasta" value="E.coli_PacBio_40x_first_200_reads.fasta"/> | 82 <param name="inputs" ftype="fasta" value="nanopore.fasta"/> |
| 83 <param name="mode" value="--pacbio-raw"/> | 83 <param name="mode" value="--pacbio-raw"/> |
| 84 <param name="g" value="1.1m"/> | 84 <param name="g" value="10000"/> |
| 85 <param name="i" value="2"/> | 85 <param name="i" value="2"/> |
| 86 <output name="contigs" file="result3_contigs.fasta" ftype="fasta"/> | 86 <output name="contigs" file="result3_contigs.fasta" ftype="fasta" compare="sim_size"/> |
| 87 <output name="scaffolds" file="result3_scaffolds.fasta" ftype="fasta"/> | 87 <output name="scaffolds" file="result3_scaffolds.fasta" ftype="fasta" compare="sim_size"/> |
| 88 </test> | 88 </test> |
| 89 </tests> | 89 </tests> |
| 90 <help><![CDATA[ | 90 <help><![CDATA[ |
| 91 | 91 |
| 92 Input reads could be in FASTA or FASTQ format, uncompressed | 92 Input reads could be in FASTA or FASTQ format, uncompressed |