comparison sRbowtie.xml @ 40:cdf2ffe2f8be draft default tip

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 0d4bc357e7f0b13488806ebdab71090411d9b430

39:97f256cbdaf6

<tool id="bowtieForSmallRNA" name="sRbowtie" version="1.2">
    <description>for FASTA small reads</description>
    <requirements>
        <requirement type="package" version="1.1.2=py27_2">bowtie</requirement>
        <requirement type="package" version="1.2">samtools</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        #if $refGenomeSource.genomeSource == "history":
            bowtie-build -f $refGenomeSource.ownFile local_index &&
        #else:
            ln -f -s $refGenomeSource.index.fields.path local_index &&
        #end if
        #if $input.extension == "fasta":
            #set format = "-f"
        #elif $input.extension == "fastq":
            #set format = "-q"

       
        #set $method_postfix = " %s %s " % ($method_prefix, $extra_output)

        ## run the bowtie alignement
        #if $output_format == "tabular":
            bowtie -p \${GALAXY_SLOTS:-4} $method_postfix --suppress 6,7,8 local_index $format '$input' > $output
        #elif $output_format == "sam":
            bowtie -p \${GALAXY_SLOTS:-4} $method_postfix -S local_index $format '$input' > '$output'
        #elif $output_format == "bam":
            bowtie -p \${GALAXY_SLOTS:-4} $method_postfix -S local_index $format '$input' | samtools view -u - | samtools sort -@ "\${GALAXY_SLOTS:-4}" -T tmp -O bam -o $output
        #end if
        ##### | samtools view -uS
        ]]></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>
            <option selected="true" value="multiple">Match on DNA, multiple mappers randomly matched at a single position</option>
            <option value="k_option">Match on DNA as fast as possible, without taking care of mapping issues (for raw annotation of reads)</option>

A generic "Map with Bowtie for Illumina" Galaxy tool is available in the main Galaxy distribution.

However, this Bowtie wrapper tool only takes FASTQ files as inputs.

The sRbowtie wrapper specifically works with short reads FASTA inputs (-v bowtie mode)

------

**OPTIONS**

**Input formats**

.. class:: warningmark

*The only accepted format for the script is a raw fasta list of reads, clipped from their adapter*

-----

**OUTPUTS**

If you choose tabular as the output format, you will obtain the matched reads in standard bowtie output format, having the following columns::

    Column    Description
  --------    --------------------------------------------------------
   1 FastaID  fasta identifier
   2 polarity + or - depending whether the match was reported on the forward or reverse strand

40:cdf2ffe2f8be

<tool id="bowtieForSmallRNA" name="sRbowtie" version="1.3">
    <description>for FASTA small reads</description>
    <requirements>
        <requirement type="package" version="1.1.2=py27_2">bowtie</requirement>
        <requirement type="package" version="1.2">samtools</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        #if $refGenomeSource.genomeSource == "history":
            bowtie-build -f $refGenomeSource.ownFile genome &&
            ln -s -f '$refGenomeSource.ownFile' genome.fa &&
            #set index_path = 'genome'
        #else:
            #set index_path = $refGenomeSource.index.fields.path
        #end if
        #if $input.extension == "fasta":
            #set format = "-f"
        #elif $input.extension == "fastq":
            #set format = "-q"

       
        #set $method_postfix = " %s %s " % ($method_prefix, $extra_output)

        ## run the bowtie alignement
        #if $output_format == "tabular":
            bowtie -p \${GALAXY_SLOTS:-4} $method_postfix --suppress 6,7,8 $index_path $format '$input' > $output
        #elif $output_format == "sam":
            bowtie -p \${GALAXY_SLOTS:-4} $method_postfix -S $index_path $format '$input' > '$output'
        #elif $output_format == "bam":
            bowtie -p \${GALAXY_SLOTS:-4} $method_postfix -S $index_path $format '$input' | samtools view -u - | samtools sort -@ "\${GALAXY_SLOTS:-4}" -T tmp -O bam -o $output
        #end if
        ##### | samtools view -uS
        ]]></command>
    <inputs>
        <param format="fasta, fastq" help="Only with clipped, fasta or fastq read files" label="Input fasta or fastq 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>
            <option selected="true" value="multiple">Match on DNA, multiple mappers randomly matched at a single position</option>
            <option value="k_option">Match on DNA as fast as possible, without taking care of mapping issues (for raw annotation of reads)</option>

A generic "Map with Bowtie for Illumina" Galaxy tool is available in the main Galaxy distribution.

However, this Bowtie wrapper tool only takes FASTQ files as inputs.

The sRbowtie wrapper works with short (-v bowtie mode) reads inputs, in fasta or fastq format, and proposes a simplified set of configurations suited to small RNA analysis.

------

**OPTIONS**

**Input formats**

.. class:: warningmark

*Lists of reads, in fasta or fastq format, clipped from their adapter sequence*

-----

**OUTPUTS**

If you choose tabular as the output format, you will obtain the matched reads in tabular bowtie output format, having the following columns::

    Column    Description
  --------    --------------------------------------------------------
   1 FastaID  fasta identifier
   2 polarity + or - depending whether the match was reported on the forward or reverse strand