view hicFindRestrictionSites.xml @ 9:6c5097f6d41e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9

<tool id="hicexplorer_hicfindrestrictionsites" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>identify restriction enzyme sites</description>
    <macros>
        <token name="@BINARY@">hicFindRestSite</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        @BINARY@
            --fasta '$fasta'
            #set $searchPatternList = ' '.join([ '\'%s\'' % $pattern for $pattern in str($searchPattern).split(' ') ])

            --searchPattern '$searchPatternList'
            --outFile restriction_site.bed

    ]]>    </command>
    <inputs>
        <param argument="--fasta" type="data" format="fasta,fasta.gz" label="Fasta file for the organism genome." 
            help="The organism genome fasta file to compute the restriction enzyme position." />
        <param argument="--searchPattern" type="text" value="" label="Restriction enzyme sequence" help='Search pattern. For example, for HindIII this pattern is \"AAGCTT\".
            Both, forward and reverse strand are searched for a match. The pattern
            is a regexp and can contain regexp specif syntax
            (see https://docs.python.org/2/library/re.html). For example the pattern
            CG..GC will find all occurrence of CG followed by any two bases and then GC.'>
            <validator type="expression" message="Only ASCII characters are allowed."><![CDATA[all(ord(c) < 128 for c in value)]]></validator>
        </param>
    </inputs>
    <outputs>
        <data name="restrictionSites" from_work_dir="restriction_site.bed" format="bed" label="${tool.name} on ${fasta.name} ${searchPattern} [${on_string}]: Restriction sites" />
    </outputs>
    <tests>
        <test>
            <param name="fasta" value="hicFindRestrictionSites/reference_genome.fasta" />
            <param name="searchPattern" value="GTAC" />
            <output name="restrictionSites" file="hicFindRestrictionSites/restriction_sites.bed" ftype="bed" />
        </test>
    </tests>
    <help><![CDATA[

Find restriction sites
======================

This scripts find the locations of a given restriction enzyme sequence. This file can be used to build an Hi-C interaction matrix with restriction enzyme resolution by hicBuildMatrix.


For more information about HiCExplorer please consider our documentation on readthedocs.io_

.. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
]]>    </help>
    <expand macro="citations" />
</tool>