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comparison flye.xml @ 2:156e0da5b917 draft

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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
comparison
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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