comparison flye.xml @ 3:c5417aa9eb4f draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 9de56f311ae694ec8c636b24be7815f92521ca96

2:792735cc7ddb

        #if $input.is_of_type('fastqsanger', 'fastq'):
            #set $ext = 'fastq'
        #elif $input.is_of_type('fastqsanger.gz'):
            #set $ext = 'fastq.gz'
        #elif $input.is_of_type('fasta.gz'):        
            #set $ext = 'fasta.gz'
        #elif $input.is_of_type('fasta'):        
            #set $ext = 'fasta'
        #end if
        ln -s '$input' ./input_${counter}.${ext} &&
    #end for
    
    flye
    $mode
    #for $counter, $input in enumerate($inputs):
        ./input_${counter}.$ext
    #end for

    -o out_dir 
    -g '$g'
    -t \${GALAXY_SLOTS:-4}
    -i $i
    #if $m:
        -m '$m'
    #end if    
    2>&1
    ]]></command>
    <inputs>
        <param name="inputs" type="data" format="fasta,fasta.gz,fastq,fastq.gz,fastqsanger.gz,fastqsanger" multiple="true" label="Input reads" />
        <param name="mode" type="select" label="Mode">

            <option value="--pacbio-raw">PacBio raw</option>
            <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]?$</validator> 
        </param>
        <param argument="-i" type="integer" value="1" label="number of polishing iterations" />
        <param argument="-m" type="integer" optional="true" label="minimum overlap between reads (default: auto)" />
    </inputs>
    <outputs>
        <data name="contigs" format="fasta" from_work_dir="out_dir/contigs.fasta" label="${tool.name} on ${on_string} (contigs)"/>
        <data name="scaffolds" format="fasta" from_work_dir="out_dir/scaffolds.fasta" label="${tool.name} on ${on_string} (scaffolds)"/>
        <data name="assembly_info" format="tabular" from_work_dir="out_dir/assembly_info.txt" label="${tool.name} on ${on_string} (assembly_info)"/>
        <data name="assembly_graph" format="graph_dot" from_work_dir="out_dir/assembly_graph.dot" label="${tool.name} on ${on_string} (assembly_graph)"/>
        <data name="flye_log" format="txt" from_work_dir="out_dir/flye.log" label="${tool.name} on ${on_string} (log)"/>
    </outputs>
    <tests>
        <test>            
            <param name="inputs" ftype="fasta" value="nanopore.fasta"/>
            <param name="mode" value="--pacbio-raw"/>
            <param name="g" value="10000"/>
            <output name="contigs" file="result1_contigs.fasta" ftype="fasta" compare="sim_size"/>
            <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"/>    
        </test>
        <test>            
            <param name="inputs" ftype="fasta" value="nanopore.fasta"/>
            <param name="mode" value="--nano-raw"/>
            <param name="g" value="10000"/>
            <output name="contigs" file="result2_contigs.fasta" ftype="fasta" compare="sim_size"/>
            <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"/>    
        </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="contigs" file="result3_contigs.fasta" ftype="fasta" compare="sim_size"/>
            <output name="scaffolds" file="result3_scaffolds.fasta" ftype="fasta" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[

Input reads could be in FASTA or FASTQ format, uncompressed

3:c5417aa9eb4f

        #if $input.is_of_type('fastqsanger', 'fastq'):
            #set $ext = 'fastq'
        #elif $input.is_of_type('fastqsanger.gz'):
            #set $ext = 'fastq.gz'
        #elif $input.is_of_type('fasta.gz'):
            #set $ext = 'fasta.gz'
        #elif $input.is_of_type('fasta'):
            #set $ext = 'fasta'
        #end if
        ln -s '$input' ./input_${counter}.${ext} &&
    #end for

    flye
    $mode
    #for $counter, $input in enumerate($inputs):
        ./input_${counter}.$ext
    #end for

    -o out_dir
    -g '$g'
    -t \${GALAXY_SLOTS:-4}
    -i $i
    #if $m:
        -m '$m'
    #end if
    2>&1
    ]]></command>
    <inputs>
        <param name="inputs" type="data" format="fasta,fasta.gz,fastq,fastq.gz,fastqsanger.gz,fastqsanger" multiple="true" label="Input reads" />
        <param name="mode" type="select" label="Mode">

            <option value="--pacbio-raw">PacBio raw</option>
            <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]?$</validator>
        </param>
        <param argument="-i" type="integer" value="1" label="number of polishing iterations" />
        <param argument="-m" type="integer" optional="true" label="minimum overlap between reads (default: auto)" />
    </inputs>
    <outputs>
        <data name="scaffolds" format="fasta" from_work_dir="out_dir/scaffolds.fasta" label="${tool.name} on ${on_string} (scaffolds)"/>
        <data name="assembly_info" format="tabular" from_work_dir="out_dir/assembly_info.txt" label="${tool.name} on ${on_string} (assembly_info)"/>
        <data name="assembly_graph" format="graph_dot" from_work_dir="out_dir/assembly_graph.gv" label="${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 ${on_string} (Graphical Fragment Assembly)"/>
        <data name="flye_log" format="txt" from_work_dir="out_dir/flye.log" label="${tool.name} on ${on_string} (log)"/>
    </outputs>
    <tests>
        <test>
            <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"/>
        </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"/>
        </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"/>
        </test>
    </tests>
    <help><![CDATA[

Input reads could be in FASTA or FASTQ format, uncompressed