comparison bowtie2_wrapper.xml @ 31:0d4acadabb04 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit f25b49ba5f2f3e5542e75224948818c32dea920a

30:03e9b2fbc005

<tool id="bowtie2" name="Bowtie2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
    <description>- map reads against reference genome</description>
    <macros>
        <import>bowtie2_macros.xml</import>
    </macros>
    <xrefs>
        <xref type="bio.tools">bowtie2</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">bowtie2</requirement>
        <requirement type="package" version="1.16.1">samtools</requirement>
    </requirements>
    <version_command>bowtie2 --version</version_command>
    <command detect_errors="exit_code"><![CDATA[
## Use pipefail if available to quit with first non-zero exit code
set -o | grep -q pipefail && set -o pipefail;

        #set reads_are_fastq = False
        #set read1 = "input_f.fasta"
    #else:
        #set read1 = "input_f.fastq"
    #end if
    ln -s '${library.input_1.forward}' ${read1} &&

    #if $library.input_1.reverse.is_of_type("fastq.gz", "fastqsanger.gz"):
        #set read2 = "input_r.fastq.gz"
        #set compressed = "GZ"
    #else if $library.input_1.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"):

    #else if $library.input_1.reverse.is_of_type("fasta"):
        #set read2 = "input_r.fasta"
    #else:
        #set read2 = "input_r.fastq"
    #end if
    ln -s '${library.input_1.reverse}' ${read2} &&

#else if str($library.type) == 'paired_interleaved':
    #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
        #set read1 = "input_il.fastq.gz"
        #set compressed = "GZ"

        #set reads_are_fastq = False
        #set read1 = "input_il.fasta"
    #else:
        #set read1 = "input_il.fastq"
    #end if
    ln -s '${library.input_1}' ${read1} &&
#else:
    #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
        #set read1 = "input_f.fastq.gz"
        #set compressed = "GZ"
    #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):

        #set reads_are_fastq = False
        #set read1 = "input_f.fasta"
    #else:
        #set read1 = "input_f.fastq"
    #end if
    ln -s '${library.input_1}' ${read1} &&
#end if

## execute bowtie2

bowtie2

              <option value="single">Single-end</option>
              <option value="paired">Paired-end</option>
              <option value="paired_collection">Paired-end Dataset Collection</option>
              <option value="paired_interleaved">Paired-end data from single interleaved dataset</option>
            </param>

            <when value="single">
                <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="FASTA/Q file" help="Must be of datatype &quot;fastqsanger&quot; or &quot;fasta&quot;" />
                <expand macro="align_unalign" />
            </when>
            <when value="paired">

                <option value="yes">Yes</option>
                <option value="no" selected="true">No</option>
            </param>
            <when value="yes">
                <param name="sam_opt" type="boolean" truevalue="true" falsevalue="false" label="Would you like the output to be a SAM file" help="By default, the output from this Bowtie2 wrapper is a sorted BAM file."/>
                <param name="no_unal" type="boolean" truevalue="--no-unal" falsevalue="" label="Suppress SAM records for reads that failed to align" help="--no-unal; Default=False"/>
                <param name="omit_sec_seq" type="boolean" truevalue="--omit-sec-seq" falsevalue="" label="Suppress SEQ and QUAL strings for secondary alignments" help="--omit-sec-seq; Default=False"/>
                <param name="sam_no_qname_trunc" argument="--sam-no-qname-trunc" type="boolean" truevalue="--sam-no-qname-trunc" falsevalue="" label="Suppress standard behavior of truncating readname at first whitespace at the expense of generating non-standard SAM"/>
                <param argument="--xeq" type="boolean" truevalue="--xeq" falsevalue="" label="Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record."/>
                <param name="soft_clipped_unmapped_tlen" argument="--soft-clipped-unmapped-tlen" type="boolean" truevalue="--soft-clipped-unmapped-tlen" falsevalue="" label=" Exclude soft-clipped bases when reporting TLEN"/>
                <param name="reorder" argument="--reorder" type="boolean" truevalue="--reorder" falsevalue=""
                    label="Reorder output to reflect order of the input file"
                    help="Reorder guarantees that output SAM records are printed in an order corresponding to the order of the reads in the original input file, even when -p is set greater than 1." />
            </when>
            <when value="no"/>
        </conditional>

31:0d4acadabb04

<tool id="bowtie2" name="Bowtie2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
    <description>- map reads against reference genome</description>
    <macros>
        <import>bowtie2_macros.xml</import>
    </macros>
    <xrefs>
        <xref type="bio.tools">bowtie2</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">bowtie2</requirement>
        <requirement type="package" version="1.19.2">samtools</requirement>
    </requirements>
    <version_command>bowtie2 --version</version_command>
    <command detect_errors="exit_code"><![CDATA[
## Use pipefail if available to quit with first non-zero exit code
set -o | grep -q pipefail && set -o pipefail;

        #set reads_are_fastq = False
        #set read1 = "input_f.fasta"
    #else:
        #set read1 = "input_f.fastq"
    #end if
    ln -f -s '${library.input_1.forward}' ${read1} &&

    #if $library.input_1.reverse.is_of_type("fastq.gz", "fastqsanger.gz"):
        #set read2 = "input_r.fastq.gz"
        #set compressed = "GZ"
    #else if $library.input_1.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"):

    #else if $library.input_1.reverse.is_of_type("fasta"):
        #set read2 = "input_r.fasta"
    #else:
        #set read2 = "input_r.fastq"
    #end if
    ln -f -s '${library.input_1.reverse}' ${read2} &&

#else if str($library.type) == 'paired_interleaved':
    #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
        #set read1 = "input_il.fastq.gz"
        #set compressed = "GZ"

        #set reads_are_fastq = False
        #set read1 = "input_il.fasta"
    #else:
        #set read1 = "input_il.fastq"
    #end if
    ln -f -s '${library.input_1}' ${read1} &&
#else:
    #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
        #set read1 = "input_f.fastq.gz"
        #set compressed = "GZ"
    #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):

        #set reads_are_fastq = False
        #set read1 = "input_f.fasta"
    #else:
        #set read1 = "input_f.fastq"
    #end if
    ln -f -s '${library.input_1}' ${read1} &&
#end if

## execute bowtie2

bowtie2

              <option value="single">Single-end</option>
              <option value="paired">Paired-end</option>
              <option value="paired_collection">Paired-end Dataset Collection</option>
              <option value="paired_interleaved">Paired-end data from single interleaved dataset</option>
            </param>
            <when value="single">
                <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="FASTA/Q file" help="Must be of datatype &quot;fastqsanger&quot; or &quot;fasta&quot;" />
                <expand macro="align_unalign" />
            </when>
            <when value="paired">

                <option value="yes">Yes</option>
                <option value="no" selected="true">No</option>
            </param>
            <when value="yes">
                <param name="sam_opt" type="boolean" truevalue="true" falsevalue="false" label="Would you like the output to be a SAM file" help="By default, the output from this Bowtie2 wrapper is a sorted BAM file."/>
                <param argument="--no-unal" type="boolean" truevalue="--no-unal" falsevalue="" label="Suppress SAM records for reads that failed to align" help="--no-unal; Default=False"/>
                <param argument="--omit-sec-seq" type="boolean" truevalue="--omit-sec-seq" falsevalue="" label="Suppress SEQ and QUAL strings for secondary alignments" help="--omit-sec-seq; Default=False"/>
                <param argument="--sam-no-qname-trunc" type="boolean" truevalue="--sam-no-qname-trunc" falsevalue="" label="Suppress standard behavior of truncating readname at first whitespace at the expense of generating non-standard SAM"/>
                <param argument="--xeq" type="boolean" truevalue="--xeq" falsevalue="" label="Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record."/>
                <param argument="--soft-clipped-unmapped-tlen" type="boolean" truevalue="--soft-clipped-unmapped-tlen" falsevalue="" label=" Exclude soft-clipped bases when reporting TLEN"/>
                <param argument="--reorder" type="boolean" truevalue="--reorder" falsevalue=""
                    label="Reorder output to reflect order of the input file"
                    help="Reorder guarantees that output SAM records are printed in an order corresponding to the order of the reads in the original input file, even when -p is set greater than 1." />
            </when>
            <when value="no"/>
        </conditional>