comparison flye.xml @ 10:75b2cf8c5aa4 draft

"planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/flye commit 2d9005e9f7366f761369b4ad7ddda383ff80a47f-dirty"

9:2a79279b6ff6

<tool id="flye" name="Flye assembler" version="@VERSION@">
    <description>of long and error-prone reads</description>
    <macros>
        <token name="@VERSION@">2.7</token>
    </macros>
    <requirements>
    <requirement type="package" version="@VERSION@">flye</requirement>
    </requirements>
    <version_command>flye --version</version_command>
    <command detect_errors="exit_code">
        <![CDATA[

    #for $counter, $input in enumerate($inputs):

        #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('fastq'):

        #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:

    '$keep_haplotypes'
    '$trestle'
    2>&1
    ]]>    </command>
    <inputs>
        <param name="inputs" type="data" format="fasta,fasta.gz,fastq,fastq.gz,fastqsanger.gz,fastqsanger" multiple="true" label="Input reads">
            <help><![CDATA[

    Input reads could be in FASTA or FASTQ format, uncompressed
    or compressed with gz. Currenlty, raw and corrected reads
    from PacBio and ONT are supported. The expected error rates are

10:75b2cf8c5aa4

<tool id="flye" name="Flye assembler" version="@VERSION@+galaxy1">
    <description>of long and error-prone reads</description>
    <macros>
        <token name="@VERSION@">2.7</token>
    </macros>
    <requirements>
    <requirement type="package" version="@VERSION@">flye</requirement>
    </requirements>
    <version_command>flye --version</version_command>
    <command detect_errors="exit_code">
        <![CDATA[
        #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('fastq'):

        #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.${ext} &&
    flye
    $mode
    ./input.$ext
    -o out_dir
    -g '$g'
    -t \${GALAXY_SLOTS:-4}
    -i $i
    #if $m:

    '$keep_haplotypes'
    '$trestle'
    2>&1
    ]]>    </command>
    <inputs>
        <param name="input" type="data" format="fasta,fasta.gz,fastq,fastq.gz,fastqsanger.gz,fastqsanger" multiple="false" label="Input reads">
            <help><![CDATA[

    Input reads could be in FASTA or FASTQ format, uncompressed
    or compressed with gz. Currenlty, raw and corrected reads
    from PacBio and ONT are supported. The expected error rates are