view hal_hal2fasta.xml @ 0:90503ee992eb draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/haltools commit 6244b9d15a5ad97ae20191e2f8fbafe2050c3cac

<tool id="hal_hal2fasta" name="hal2fasta" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>exports sequences from HAL to FASTA</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/> 
    <expand macro="stdio"/>
    <command detect_errors="aggressive"><![CDATA[
        hal2fasta
            #if $mode.export == 'default':
                --start $mode.start
                --length $mode.length
            #else if $mode.export == '--sequence':
                --sequence '$mode.sequence'
                --start $mode.start
                --length $mode.length
            #else if $mode.export == '--subtree':
                --subtree
            #end if
            --lineWidth $lineWidth
            $upper
            $ucscSequenceNames
            '$input_hal' '$refGenome' > temp.fasta
            #if $compression.type == 'gz':
                && gzip -c temp.fasta > '$out_file'
            #else if $compression.type == 'bz2':
                && bzip2 -c temp.fasta > '$out_file'
            #else:
                && mv temp.fasta '$out_file'
            #end if
    ]]></command>
    <inputs>
        <expand macro="input_hal"/>
        <expand macro="params_refGenome"/>
        <conditional name="mode">
            <param name="export" type="select" label="Export options">
                <option value="default" selected="true">Export full reference genome (default)</option>
                <option value="--sequence">Export a reference sequence (--sequence)</option>
                <option value="--subtree">Export all genomes in the reference genome subtree (--subtree)</option>
            </param>
            <when value="default">
                <expand macro="params_start"/>
                <expand macro="params_length"/>
            </when>
            <when value="--subtree"/>
            <when value="--sequence">
                <expand macro="params_sequence"/>
                <expand macro="params_start"/>
                <expand macro="params_length"/>
            </when>
        </conditional>
        <param argument="--upper" type="boolean" truevalue="--upper" falsevalue="" checked="false" label="Uppercase bases" help="Convert all bases to uppercase"/>
        <param argument="--ucscSequenceNames" type="boolean" truevalue="--ucscSequenceNames" falsevalue="" checked="false" label="Use UCSC convention" help="Use the UCSC convention of Genome.Sequence for names. By default, only sequence names are used"/>
        <param argument="--lineWidth" type="integer" min="1" value="80" label="Line width" help="Line width for output"/>
        <expand macro="params_conditional_compression"/>
    </inputs>
    <outputs>
        <data name="out_file" format="fasta" label="${tool.name} on ${on_string}: Genome FASTA">
            <change_format>
                <when input="compression.type" value="gz" format="fasta.gz"/>
                <when input="compression.type" value="bz2" format="fasta.bz2"/>
            </change_format>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="input_hal" value="halTest.hal"/>
            <param name="refGenome" value="Genome_0"/>
            <output name="out_file" ftype="fasta">
                <assert_contents>
                    <has_line line=">Genome_0_seq"/>
                    <has_line line="CCCGTAACCCAATCCACGGTGCCGGCGGCGAGATGTATTGTCTGGGCGCAAAGCCATTTCGCCACCACATGCTGCGCGAC"/>
                    <has_n_lines n="23"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <param name="input_hal" value="halTest.hal"/>
            <param name="refGenome" value="Genome_0"/>
             <conditional name="compression">
                <param name="type" value="gz"/>
            </conditional>
            <output name="out_file" ftype="fasta.gz" file="hal2fasta_output.fasta.gz"/>
        </test>
        <test expect_num_outputs="1">
            <param name="input_hal" value="halTest.hal"/>
            <param name="refGenome" value="Genome_0"/>
             <conditional name="compression">
                <param name="type" value="bz2"/>
            </conditional>
            <output name="out_file" ftype="fasta.bz2" file="hal2fasta_output.fasta.bz2"/>
        </test>
        <test expect_num_outputs="1">
            <param name="input_hal" value="halTest.hal"/>
            <param name="refGenome" value="Genome_0"/>
            <param name="lineWidth" value="40"/>
            <param name="upper" value="true"/>
            <output name="out_file" ftype="fasta">
                <assert_contents>
                    <has_line line=">Genome_0_seq"/>
                    <has_line line="TGCCGCGCGTGAGGTTGACACTCCGTTCGTGTTACATGTC"/>
                    <has_n_lines n="45"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <param name="input_hal" value="halTest.hal"/>
            <param name="refGenome" value="Genome_0"/>
            <conditional name="mode">
                <param name="export" value="--sequence"/>
                <param name="sequence" value="Genome_0_seq"/>
            </conditional>
            <output name="out_file" ftype="fasta">
                <assert_contents>
                    <has_line line=">Genome_0_seq"/>
                    <has_line line="CCCGTAACCCAATCCACGGTGCCGGCGGCGAGATGTATTGTCTGGGCGCAAAGCCATTTCGCCACCACATGCTGCGCGAC"/>
                    <has_n_lines n="23"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <param name="input_hal" value="halTest.hal"/>
            <param name="refGenome" value="Genome_0"/>
            <conditional name="mode">
                <param name="export" value="--subtree"/>
            </conditional>
            <output name="out_file" ftype="fasta">
                <assert_contents>
                    <has_line line=">Genome_0_seq"/>
                    <has_line line=">Genome_1_seq"/>
                    <has_line line=">Genome_2_seq"/>
                    <has_line line=">Genome_3_seq"/>
                    <has_line line="CCCGTAACCCAATCCACGGTGCCGGCGGCGAGATGTATTGTCTGGGCGCAAAGCCATTTCGCCACCACATGCTGCGCGAC"/>
                    <has_n_lines n="226"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <param name="input_hal" value="halTest.hal"/>
            <param name="refGenome" value="Genome_2"/>
            <conditional name="mode">
                <param name="export" value="--sequence"/>
                <param name="sequence" value="Genome_2_seq"/>
                <param name="start" value="50"/>
                <param name="length" value="10"/>
            </conditional>
            <param name="ucscSequenceNames" value="true"/>
            <output name="out_file" ftype="fasta">
                <assert_contents>
                    <has_line line=">Genome_2.Genome_2_seq"/>
                    <has_line line="GAGGTTGACA"/>
                    <has_n_lines n="2"/>
                </assert_contents>
            </output>
        </test>
        <!-- 
        Does not pass currently due to a bug - that was fixed but not avalaible as release yet (16.12.2025)
        https://github.com/ComparativeGenomicsToolkit/hal/issues/324

        <test expect_num_outputs="1">
            <param name="input_hal" value="halTest.hal"/>
            <param name="genome" value="Genome_0"/>
            <conditional name="mode">
                <param name="export" value="default"/>
                <param name="start" value="50"/>
                <param name="length" value="10"/>
            </conditional>
            <param name="ucscSequenceNames" value="true"/>
            <output name="out_file" ftype="fasta">
                <assert_contents>
                    <has_line line=">Genome_0.Genome_0_seq"/>
                    <has_line line="GAGGTTGACA"/>
                </assert_contents>
            </output>
        </test>
        -->
    </tests>
    <help><![CDATA[
hal2fasta exports sequence data from an input HAL file to an output FASTA file. 
It can export a full genome, a single sequence of that genome, or all genomes in the entire subtree rooted of that genome.
When exporting the full genome or a single sequence of that genome, the exported range can be limited using start and length.
    ]]></help>
    <expand macro="citation"/>
    <expand macro="creator"/>
</tool>