comparison sRbowtie.xml @ 4:615d2550977f draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit b6de14061c479f0418cd89e26d6f5ac26e565a07

3:68b71bd388eb

    <description>for FASTA small reads</description>
    <requirements>
        <requirement type="package" version="1.1.2">bowtie</requirement>
        <requirement type="package" version="1.2">samtools</requirement>
    </requirements>
    <command interpreter="python"> sRbowtie.py --input $input
                                             --input-format $input.extension
                                             --method $method
                                             --v-mismatches $v_mismatches
                                             --output-format $output_format
                                             --output $output
                                             --index-from $refGenomeSource.genomeSource
                                             ## the very source of the index (indexed or fasta file)
                                             --index-source
                                             #if $refGenomeSource.genomeSource == "history":
                                                 $refGenomeSource.ownFile
                                             #else:
                                                 $refGenomeSource.index.fields.path
                                             #end if
                                             --aligned $aligned
                                             --unaligned $unaligned
                                             --num-threads \${GALAXY_SLOTS:-4} ## number of processors to be handled by bowtie
  </command>
    <inputs>
        <param format="fasta, fastq" help="Only with clipped, raw fasta files" label="Input fasta file: reads clipped from their adapter" name="input" type="data" />
        <param help="bowtie parameters adjusted to the type of matching. RNA option match to only one strand" label="What kind of matching do you want to do?" name="method" type="select">
            <option value="RNA">Match on sense strand RNA reference index, multiple mappers randomly matched at a single position</option>
            <option value="unique">Match unique mappers on DNA reference index</option>

4:615d2550977f

    <description>for FASTA small reads</description>
    <requirements>
        <requirement type="package" version="1.1.2">bowtie</requirement>
        <requirement type="package" version="1.2">samtools</requirement>
    </requirements>
    <command><![CDATA[
        python '$__tool_directory__'/sRbowtie.py
        --input '$input'
        --input-format '$input.extension'
        --method '$method'
        --v-mismatches $v_mismatches
        --output-format $output_format
        --output '$output'
        --index-from '$refGenomeSource.genomeSource'
        ## the very source of the index (indexed or fasta file)
        --index-source
        #if $refGenomeSource.genomeSource == "history":
            '$refGenomeSource.ownFile'
        #else:
            '$refGenomeSource.index.fields.path'
        #end if
        --aligned '$aligned'
        --unaligned '$unaligned'
        --num-threads \${GALAXY_SLOTS:-4} ## number of processors to be handled by bowtie
        ]]></command>
    <inputs>
        <param format="fasta, fastq" help="Only with clipped, raw fasta files" label="Input fasta file: reads clipped from their adapter" name="input" type="data" />
        <param help="bowtie parameters adjusted to the type of matching. RNA option match to only one strand" label="What kind of matching do you want to do?" name="method" type="select">
            <option value="RNA">Match on sense strand RNA reference index, multiple mappers randomly matched at a single position</option>
            <option value="unique">Match unique mappers on DNA reference index</option>