<tool id="homer_scanMotifGenomeWide" name="scanMotifGenomeWide" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
    <description/>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="xrefs"/>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
scanMotifGenomeWide.pl
'$motif'
#if str( $genome.source ) == "installed":
    '$genome.all_fasta_source.fields.path'
#elif str( $genome.source ) == "history":
    '$genome.fasta'
#end if
$bed
$keepAll
$mask
$Fivep
$homer1
> 
#if $bed:
    '${output_bed}'
#else
    '${output_text}'
#end if
        ]]></command>
    <inputs>
        <param name="motif" type="data" format="txt" label="Motif file"/>
        <conditional name="genome">
            <param name="source" type="select" label="Will you select a reference genome from your history or use a installed genome?">
                <option value="installed">Installed</option>
                <option value="history">From History</option>
            </param>
            <when value="installed">
                <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
                    <options from_data_table="all_fasta">
                        <filter type="sort_by" column="2"/>
                        <validator type="no_options" message="No references are available"/>
                    </options>
                </param>
            </when>
            <when value="history">
                <param name="fasta" type="data" format="fasta" label="Select reference genome"/>
            </when>
        </conditional>
        <param argument="-bed" type="boolean" truevalue="-bed" falsevalue="" checked="false" label="Output bed format"/>
        <param argument="-keepAll" type="boolean" truevalue="-keepAll" falsevalue="" checked="false" label="Report all motifs even if overlap"
        help="By default, HOMER will remove a motif that overlaps itself, useful for palindromes. To report all, specify this option."/>
        <param argument="-mask" type="boolean" truevalue="-mask" falsevalue="" checked="false"
        label="Do not look for motifs in RepeatMasked sequence (lower case sequence in FASTA files)"/>
        <param argument="-5p" name="Fivep" type="boolean" truevalue="-5p" falsevalue="" checked="false"
        label="Report motif positions based on the 5' end of the motif sequence"/>
        <param argument="-homer1" type="boolean" truevalue="-homer1" falsevalue="" checked="false"
        label="Use homer1 instead of homer2"/>
    </inputs>
    <outputs>
        <data format="tabular" name="output_text" label="motif occurrences from ${tool.name} on ${on_string}">
            <filter>bed is False</filter>
        </data>
        <data format="bed" name="output_bed" label="motif occurrences from ${tool.name} on ${on_string} as bed">
            <filter>bed is True</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="motif" value="motif_test1/homerResults/motif1.motif"/>
            <conditional name="genome">
                <param name="source" value="installed"/>
                <param name="all_fasta_source" value="phiX174"/>
            </conditional>
            <output name="output_text" file="scanMotif_res1.txt" ftype="tabular"/>
        </test>
        <test expect_num_outputs="1">
            <param name="motif" value="motif_test1/homerResults/motif1.motif"/>
            <conditional name="genome">
                <param name="source" value="history"/>
                <param name="fasta" value="phiX174.fasta"/>
            </conditional>
            <param name="bed" value="-bed"/>
            <output name="output_bed" file="scanMotif_res1.bed" ftype="bed"/>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark

    This is a wrapper for scanMotifGenomeWide.pl from HOMER but not all options are included.

    The scanMotifGenomeWide.pl script will take a motif file (may contain multiple motifs) and look for instances across the genome. 

    ]]></help>
    <expand macro="citation"/>
</tool>