view hal_halAlignmentDepth.xml @ 0:25489f7c4cff draft default tip

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

<tool id="hal_halalignmentdepth" name="halAlignmentDepth" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>makes a alignment depth wiggle plot for a genome</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/> 
    <expand macro="stdio"/>
    <command detect_errors="aggressive"><![CDATA[
        halAlignmentDepth
            #if $genome.reference == 'custom':
                $genome.noAncestors
            #end if 
            #if $mode.export == 'sequence':
                --refSequence '$mode.sequence'
            #end if
            --start $start
            --length $length
            ## --step $step ## Has a known bug https://github.com/ComparativeGenomicsToolkit/hal/issues/326
            #if $filter.option == '--targetGenomes':
                --targetGenomes '$filter.targetGenomes'
            #else if $filter.option == '--rootGenome':
                --rootGenome '$filter.rootGenome'
            #end if 
            $countDupes
            '$input_hal' 
            #if $genome.reference == 'custom':
                '$genome.refGenome'
            #else
                "\"\""  ## Defaults to input HAL file's tree root
            #end if 
            > '$out_file'
    ]]></command>
    <inputs>        
        <expand macro="input_hal"/>
        <expand macro="params_conditional_refGenome"/>
        <conditional name="mode">
            <param name="export" type="select" label="Convert options">
                <option value="default" selected="true">Convert full reference genome (default)</option>
                <option value="sequence">Convert a reference sequence (--refSequence)</option>
            </param>
            <when value="default"/>
            <when value="sequence">
                <expand macro="params_sequence"/>
            </when>
        </conditional>
        <expand macro="params_start"/>
        <expand macro="params_length"/>
        <conditional name="filter">
            <param name="option" type="select" label="Genomes to include in the output">
                <option value="" selected="true">All genomes (default)</option>
                <option value="--targetGenomes">Specific target genomes (--targetGenomes)</option>
                <option value="--rootGenome">Only genomes in the subtree to a root (--rootGenome)</option>
            </param>
            <when value=""/>
            <when value="--targetGenomes">
                <expand macro="params_targetGenomes"/>
            </when>
            <when value="--rootGenome">
                <expand macro="params_rootGenome"/>
            </when>
        </conditional>
        <param argument="--countDupes" type="boolean" truevalue="--countDupes" falsevalue="" checked="false" label="Count duplicates" help="Count every aligned position instead of counting unique genomes. This includes paralogous matches, so a genome can be counted multiple times. This will give the height of the MAF column created with hal2maf"/>
    </inputs>
    <outputs>
        <data name="out_file" format="wig" label="${tool.name} on ${on_string}"/>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="input_hal" value="halTest.hal"/>
            <output name="out_file" ftype="wig">
                <assert_contents>
                    <has_line line="fixedStep chrom=Genome_0_seq start=1 step=1"/>
                    <has_line line="3"/>
                    <has_line line="0"/>
                    <has_n_lines n="1759"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <param name="input_hal" value="halTest.hal"/>
            <conditional name="mode">
                <param name="export" value="sequence"/>
                <param name="sequence" value="Genome_0_seq"/>
            </conditional>
            <param name="start" value="10"/>
            <param name="length" value="50"/>
            <output name="out_file" ftype="wig">
                <assert_contents>
                    <has_line line="fixedStep chrom=Genome_0_seq start=11 step=1"/>
                    <has_line line="3"/>
                    <has_n_lines n="51"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <param name="input_hal" value="halTest.hal"/>
            <param name="countDupes" value="true"/>
            <output name="out_file" ftype="wig">
                <assert_contents>
                    <has_line line="fixedStep chrom=Genome_0_seq start=1 step=1"/>
                    <has_line line="5"/>
                    <has_line line="10"/>
                    <has_line line="0"/>
                    <has_n_lines n="1759"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <param name="input_hal" value="halTest.hal"/>
            <conditional name="filter">
                <param name="option" value="--targetGenomes"/>
                <param name="targetGenomes" value="Genome_1,Genome_2"/>
            </conditional>
            <output name="out_file" ftype="wig">
                <assert_contents>
                    <has_line line="fixedStep chrom=Genome_0_seq start=1 step=1"/>
                    <has_line line="2"/>
                    <has_line line="0"/>
                    <has_n_lines n="1759"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <param name="input_hal" value="halTest.hal"/>
            <conditional name="genome">
                <param name="reference" value="custom"/>
                <param name="refGenome" value="Genome_1"/>
                <param name="noAncestors" value="true"/>
            </conditional>
            <output name="out_file" ftype="wig">
                <assert_contents>
                    <has_line line="fixedStep chrom=Genome_1_seq start=1 step=1"/>
                    <has_line line="2"/>
                    <has_line line="0"/>
                    <has_n_lines n="5473"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
halAlignmentDepth computes alignment depth across a reference genome from a HAL alignment. 
The tool reports, for each base, how many genomes it aligns to. 
By default, each genome is counted once per position, including ancestral genomes. 
The result is written as a wiggle track.
    ]]></help>
    <expand macro="citation"/>
    <expand macro="creator"/>
</tool>