comparison hisat2.xml @ 25:3fb01a8c902d draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit b7df8879a0f5d75c8562700fe9b5dc9e8173a652

24:61ee47027bd3

<tool id="hisat2" name="HISAT2" version="2.1.0+galaxy3" profile="17.01">
    <description>A fast and sensitive alignment program</description>
    <macros>
        <import>hisat2_macros.xml</import>
    </macros>
    <requirements>

        -X ${adv.spliced_options.no_spliced_alignment_options.maxins}
    #end if
    --min-intronlen ${adv.spliced_options.min_intron}
    --max-intronlen ${adv.spliced_options.max_intron}
    ${adv.spliced_options.tma}

    #if str($adv.spliced_options.notmplen):
        ${adv.spliced_options.notmplen}
    #end if
#end if

                        <option value="--tmo">Report only those alignments within known transcripts</option>
                        <option value="--dta">Report alignments tailored for transcript assemblers including StringTie</option>
                        <option value="--dta-cufflinks">Report alignments tailored specifically for Cufflinks</option>
                    </param>
                    <param name="notmplen" argument="--no-templatelen-adjustment" type="boolean" truevalue="--no-templatelen-adjustment" falsevalue="" label="Disable automatic template length adjustment for RNA-seq reads" help="Default: false" />
                </when>
            </conditional>

            <conditional name="reporting_options">
                <param name="reporting_options_selector" type="select" label="Reporting options">

        <data name="summary_file"  format="txt" from_work_dir="summary.txt" label="${tool.name} on ${on_string}: Mapping summary" >
          <filter>sum['summary_file'] is True</filter>
          <expand macro="dbKeyActions" />
        </data>

    </outputs>

    <!-- Define tests -->

    <tests>

            <param name="source" value="history" />
            <param name="history_item" ftype="fasta" value="phiX.fa" />
            <param name="input_1" ftype="fastqsanger" value="hisat_input_1_forward.fastq" />
            <param name="input_2" ftype="fastqsanger" value="hisat_input_1_reverse.fastq" />
            <param name="adv|reporting_options|reporting_options_selector" value="advanced"/>
            <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" />
        </test>
        <!-- Ensure advanced scoring options work -->
        <test expect_num_outputs="1" >
            <param name="type" value="paired" />

            <param name="type" value="paired_interleaved" />
            <param name="source" value="history" />
            <param name="history_item" ftype="fasta" value="phiX.fa" />
            <param name="input_1" ftype="fasta" value="hisat_input_1_interleaved.fasta" />
            <output name="output_alignments" file="hisat_output_1_noqual.bam" ftype="bam" lines_diff="2" />
        </test>
    </tests>

    <help><![CDATA[
Introduction

    --dta-cufflinks
            Report alignments tailored specifically for Cufflinks. In addition to what HISAT2 does with the above option (--dta), With this option, HISAT2 looks for novel splice sites with three signals (GT/AG, GC/AG, AT/AC), but all user-provided splice sites are used irrespective of their signals. HISAT2 produces an optional field, XS:A:[+-], for every spliced alignment.

    --no-templatelen-adjustment
            Disables template length adjustment for RNA-seq reads.

-----

**Reporting options**::

25:3fb01a8c902d

<tool id="hisat2" name="HISAT2" version="2.1.0+galaxy4" profile="17.01">
    <description>A fast and sensitive alignment program</description>
    <macros>
        <import>hisat2_macros.xml</import>
    </macros>
    <requirements>

        -X ${adv.spliced_options.no_spliced_alignment_options.maxins}
    #end if
    --min-intronlen ${adv.spliced_options.min_intron}
    --max-intronlen ${adv.spliced_options.max_intron}
    ${adv.spliced_options.tma}
	
    #if str($adv.spliced_options.novel_splicesite_outfile) == "true":
       --novel-splicesite-outfile '$novel_splicesite_output'
    #end if
	
    #if str($adv.spliced_options.notmplen):
        ${adv.spliced_options.notmplen}
    #end if
#end if

                        <option value="--tmo">Report only those alignments within known transcripts</option>
                        <option value="--dta">Report alignments tailored for transcript assemblers including StringTie</option>
                        <option value="--dta-cufflinks">Report alignments tailored specifically for Cufflinks</option>
                    </param>
                    <param name="notmplen" argument="--no-templatelen-adjustment" type="boolean" truevalue="--no-templatelen-adjustment" falsevalue="" label="Disable automatic template length adjustment for RNA-seq reads" help="Default: false" />
                    <param name="novel_splicesite_outfile" type="boolean" checked="false" label="reports a list of novel splice sites" help="Default: false" />
                </when>
            </conditional>

            <conditional name="reporting_options">
                <param name="reporting_options_selector" type="select" label="Reporting options">

        <data name="summary_file"  format="txt" from_work_dir="summary.txt" label="${tool.name} on ${on_string}: Mapping summary" >
          <filter>sum['summary_file'] is True</filter>
          <expand macro="dbKeyActions" />
        </data>

        <!-- Novel Splice file -->
        <data name="novel_splicesite_output"  format="tabular" label="${tool.name} on ${on_string}: Novel Splice Sites" >
          <filter>adv['spliced_options']['spliced_options_selector'] == 'advanced' and adv['spliced_options']['novel_splicesite_outfile'] is True</filter>
          <expand macro="dbKeyActions" />
        </data>


    </outputs>

    <!-- Define tests -->

    <tests>

            <param name="source" value="history" />
            <param name="history_item" ftype="fasta" value="phiX.fa" />
            <param name="input_1" ftype="fastqsanger" value="hisat_input_1_forward.fastq" />
            <param name="input_2" ftype="fastqsanger" value="hisat_input_1_reverse.fastq" />
            <param name="adv|reporting_options|reporting_options_selector" value="advanced"/>
            <param name="novel_splicesite_outfile" value="false" />
            <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" />
        </test>
        <!-- Ensure advanced scoring options work -->
        <test expect_num_outputs="1" >
            <param name="type" value="paired" />

            <param name="type" value="paired_interleaved" />
            <param name="source" value="history" />
            <param name="history_item" ftype="fasta" value="phiX.fa" />
            <param name="input_1" ftype="fasta" value="hisat_input_1_interleaved.fasta" />
            <output name="output_alignments" file="hisat_output_1_noqual.bam" ftype="bam" lines_diff="2" />
        </test>
        <!-- Ensure novel splicesite file output works -->
        <test>
            <param name="type" value="single" />
            <param name="source" value="history" />
            <param name="history_item" ftype="fasta" value="phiX.fa" />
            <param name="input_1" ftype="fastqsanger" value="hisat_input_1_split_forward.fastq" />
            <param name="rna_strandness" value="R" />
            <param name="adv|spliced_options|spliced_options_selector" value="advanced"/>
            <param name="adv|spliced_options|novel_splicesite_outfile" value="true" />
            <output name="output_alignments" file="hisat_output_spliced_1.bam" ftype="bam" lines_diff="2" />
            <output name="novel_splicesite_output" file="novel_splicesite_out.tab" ftype="tabular" />
        </test>
    </tests>

    <help><![CDATA[
Introduction

    --dta-cufflinks
            Report alignments tailored specifically for Cufflinks. In addition to what HISAT2 does with the above option (--dta), With this option, HISAT2 looks for novel splice sites with three signals (GT/AG, GC/AG, AT/AC), but all user-provided splice sites are used irrespective of their signals. HISAT2 produces an optional field, XS:A:[+-], for every spliced alignment.

    --no-templatelen-adjustment
            Disables template length adjustment for RNA-seq reads.
    
    --novel-splicesite-outfile
			In this mode, HISAT2 reports a list of splice sites in the file :
				chromosome name <tab> genomic position of the flanking base on the left side of an intron <tab> genomic position of the flanking base on the right <tab> strand (+, -, and .) '.' indicates an unknown strand for non-canonical splice sites.

-----

**Reporting options**::