| Previous changeset 5:de24438c9988 (2020-11-02) Next changeset 7:8d4f03b5fe9d (2021-06-21) |
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Commit message:
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit d2767c87b1cc7459fd0d51c5c87f8e51d88d7f48" |
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modified:
flye.xml macros.xml |
| b |
| diff -r de24438c9988 -r 0284be52bfcf flye.xml --- a/flye.xml Mon Nov 02 17:54:14 2020 +0000 +++ b/flye.xml Thu Jan 14 11:19:21 2021 +0000 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="flye" name="Flye assembly" version="2.6+galaxy0"> +<tool id="flye" name="Flye assembly" version="2.8.2+galaxy0"> <description>of long and error-prone reads</description> <macros> <import>macros.xml</import> @@ -29,14 +29,14 @@ #end for -o out_dir - -g '$g' -t \${GALAXY_SLOTS:-4} -i $i #if $m: -m '$m' #end if - #if $asm: - --asm-coverage '$asm' + #if str($asm.asm_select) == "true": + --asm-coverage '$asm.asm' + -g '$asm.g' #end if ${plasmids} ${meta} @@ -52,12 +52,23 @@ <option value="--pacbio-corr">PacBio corrected</option> <option value="--subassemblies">high-quality contig-like input</option> </param> - <param argument="-g" type="text" label="estimated genome size (for example, 5m or 2.6g)"> - <validator type="regex" message="Genome size must be a float or integer, optionally followed by the a unit prefix (kmg)">^([0-9]*[.])?[0-9]+[kmg]?$</validator> - </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" /> + + <conditional name="asm"> + <param name="asm_select" type="select" label="description" help=""> + <option value="true">Enable reduced coverage for initial disjointing assembly</option> + <option value="false" selected="true">Disable reduced coverage for initial disjointing assembly</option> + </param> + <when value="true"> + <param name="asm" argument="--asm-coverage" type="integer" label="reduced coverage for initial disjointing assembly" /> + <param argument="-g" type="text" label="estimated genome size (for example, 5m or 2.6g)"> + <validator type="regex" message="Genome size must be a float or integer, optionally followed by the a unit prefix (kmg)">^([0-9]*[.])?[0-9]+[kmg]?$</validator> + </param> + </when> + <when value="false" /> + </conditional> + <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" /> @@ -73,7 +84,6 @@ <test> <param name="inputs" ftype="fasta" value="nanopore.fasta"/> <param name="mode" value="--pacbio-raw"/> - <param name="g" value="10000"/> <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"/> @@ -82,7 +92,6 @@ <test> <param name="inputs" ftype="fasta" value="nanopore.fasta"/> <param name="mode" value="--nano-raw"/> - <param name="g" value="10000"/> <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"/> @@ -91,9 +100,12 @@ <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"/> + <conditional name="asm"> + <param name="asm_select" value="true" /> + <param name="asm" value="40"/> + <param name="g" value="10000"/> + </conditional> <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"/> @@ -102,7 +114,6 @@ <test> <param name="inputs" ftype="fasta" value="nanopore.fasta"/> <param name="mode" value="--pacbio-raw"/> - <param name="g" value="10000"/> <param name="i" value="1"/> <param name="meta" value="true"/> <param name="plasmids" value="true"/> |
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| diff -r de24438c9988 -r 0284be52bfcf macros.xml --- a/macros.xml Mon Nov 02 17:54:14 2020 +0000 +++ b/macros.xml Thu Jan 14 11:19:21 2021 +0000 |
| b |
| @@ -1,7 +1,7 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="2.6">flye</requirement> + <requirement type="package" version="2.8.2">flye</requirement> <yield/> </requirements> </xml> |