comparison hisat2.xml @ 10:da8d655e2154 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890

9:2dbb7f0ea66f

<?xml version="1.0"?>
<tool id="hisat2" name="HISAT2" version="2.0.5">
    <description>A fast and sensitive alignment program</description>
    <macros>
        <import>hisat2_macros.xml</import>
    </macros>
    <requirements>

    <command><![CDATA[
        #if str($spliced_options.spliced_options_selector) == "advanced" and str($spliced_options.known_splice_gtf) != 'None':
            ln -s '${spliced_options.known_splice_gtf}' splice_sites.gtf &&
            hisat2_extract_splice_sites.py splice_sites.gtf > splice_sites.txt &&
        #end if
        #if $reference_genome.reference_genome_source == "history":
            ln -s '$reference_genome.history_item' genome.fa &&
            hisat2-build -p \${GALAXY_SLOTS:-1} genome.fa genome &&
            #set index_path = 'genome'
        #else:
            #set index_path = $reference_genome.index.fields.path
        #end if
        hisat2 -p \${GALAXY_SLOTS:-1} -x '${index_path}'
        #if str($input_format.paired.paired_selector) == 'paired':
            -1 '${input_format.paired.reads_f}' -2 '${input_format.paired.reads_r}'
            @paired_end_options@
        #else if str($input_format.paired.paired_selector) == 'paired_collection':
            -1 '${input_format.paired.reads.forward}' -2 '${input_format.paired.reads.reverse}'
            @paired_end_options@
        #else:
            -U '${input_format.paired.reads}'
            #if str( $input_format.paired.unaligned_file ) == "true":
                --un '$output_unaligned_reads_l'
            #end if
            #if str( $input_format.paired.aligned_file ) == "true":
                --al '$output_aligned_reads_l'
            #end if
        #end if
        #if $input_format.input_format_selector == 'fasta':
            -f
        #end if

            </param>
            <when value="fasta">
                <expand macro="paired_input_conditional" ftype="fasta" />
            </when>
            <when value="fastq">
                <expand macro="paired_input_conditional" ftype="fastq" />
            </when>
        </conditional>
        <conditional name="reference_genome">
            <param name="reference_genome_source" type="select" label="Source for the reference genome to align against" help="Built-in references were created using default options">
                <option value="indexed" selected="True">Use a built-in genome</option>

            <param name="reads_f" value="test_unaligned_reads.fasta" ftype="fasta" />
            <param name="reads_r" value="test_unaligned_reads.fasta" ftype="fasta" />
            <output name="output_unaligned_reads_l" file="test_unaligned_reads.fasta" />
            <output name="output_unaligned_reads_r" file="test_unaligned_reads.fasta" />
        </test>
    </tests>
    <help>
        <![CDATA[
Introduction
============

10:da8d655e2154

<?xml version="1.0"?>
<tool id="hisat2" name="HISAT2" version="2.0.5" profile="17.01">
    <description>A fast and sensitive alignment program</description>
    <macros>
        <import>hisat2_macros.xml</import>
    </macros>
    <requirements>

    <command><![CDATA[
        #if str($spliced_options.spliced_options_selector) == "advanced" and str($spliced_options.known_splice_gtf) != 'None':
            ln -s '${spliced_options.known_splice_gtf}' splice_sites.gtf &&
            hisat2_extract_splice_sites.py splice_sites.gtf > splice_sites.txt &&
        #end if

        @FASTQGZ_SETUP@

        #if $reference_genome.reference_genome_source == "history":
            ln -s '$reference_genome.history_item' genome.fa &&
            hisat2-build -p \${GALAXY_SLOTS:-1} genome.fa genome &&
            #set index_path = 'genome'
        #else:
            #set index_path = $reference_genome.index.fields.path
        #end if
        hisat2 -p \${GALAXY_SLOTS:-1} -x '${index_path}'
        #if str($input_format.paired.paired_selector) != 'single':
            -1 '${read1}' -2 '${read2}'
            @paired_end_options@
        #else:
            -U '${read1}'
            #if str( $input_format.paired.unaligned_file ) == "true":
                #if $compressed == "GZ":
                    --un-gz '$output_unaligned_reads_l'
                #else if $compressed == "BZ2":
                    --un-gz '$output_unaligned_reads_l'
                #else:
                    --un '$output_unaligned_reads_l'
                #end if
            #end if
            #if str( $input_format.paired.aligned_file ) == "true":
                #if $compressed == "GZ":
                    --al-gz '$output_aligned_reads_l'
                #else if $compressed == "BZ2":
                    --al-bz2 '$output_aligned_reads_l'
                #else:
                    --al '$output_aligned_reads_l'
                #end if
            #end if
        #end if
        #if $input_format.input_format_selector == 'fasta':
            -f
        #end if

            </param>
            <when value="fasta">
                <expand macro="paired_input_conditional" ftype="fasta" />
            </when>
            <when value="fastq">
                <expand macro="paired_input_conditional" ftype="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" />
            </when>
        </conditional>
        <conditional name="reference_genome">
            <param name="reference_genome_source" type="select" label="Source for the reference genome to align against" help="Built-in references were created using default options">
                <option value="indexed" selected="True">Use a built-in genome</option>

            <param name="reads_f" value="test_unaligned_reads.fasta" ftype="fasta" />
            <param name="reads_r" value="test_unaligned_reads.fasta" ftype="fasta" />
            <output name="output_unaligned_reads_l" file="test_unaligned_reads.fasta" />
            <output name="output_unaligned_reads_r" file="test_unaligned_reads.fasta" />
        </test>
        <test><!-- Ensure fastqsanger.gz works -->
            <param name="input_format_selector" value="fastq" />
            <param name="paired_selector" value="paired" />
            <param name="reference_genome_source" value="history" />
            <param name="history_item" value="phiX.fa" ftype="fasta" />
            <param name="input_options_selector" value="advanced" />
            <param name="trim_three" value="15" />
            <param name="trim_five" value="15" />
            <param name="reads_f" ftype="fastqsanger.gz" value="hisat_input_2_forward.fastq.gz" />
            <param name="reads_r" ftype="fastqsanger.gz" value="hisat_input_2_reverse.fastq.gz" />
            <param name="paired_end_options_selector" value="advanced" />
            <param name="no_mixed" value="True" />
            <param name="no_discordant" value="True" />
            <output name="output_alignments" ftype="bam" file="hisat_output_3.bam" lines_diff="2" />
        </test>
        <test><!-- Ensure fastqsanger.bz2 works -->
            <param name="input_format_selector" value="fastq" />
            <param name="paired_selector" value="paired" />
            <param name="reference_genome_source" value="history" />
            <param name="history_item" value="phiX.fa" ftype="fasta" />
            <param name="input_options_selector" value="advanced" />
            <param name="trim_three" value="15" />
            <param name="trim_five" value="15" />
            <param name="reads_f" ftype="fastqsanger.bz2" value="hisat_input_2_forward.fastq.bz2" />
            <param name="reads_r" ftype="fastqsanger.bz2" value="hisat_input_2_reverse.fastq.bz2" />
            <param name="paired_end_options_selector" value="advanced" />
            <param name="no_mixed" value="True" />
            <param name="no_discordant" value="True" />
            <output name="output_alignments" ftype="bam" file="hisat_output_3.bam" lines_diff="2" />
        </test>
    </tests>
    <help>
        <![CDATA[
Introduction
============