comparison convert/ob_convert.xml @ 2:125da3a296ca draft default tip

Uploaded

1:b52872a1755a

    -->
    <requirements>
        <requirement type="package" version="2.3.2">openbabel</requirement>
    </requirements>
    <command>
## The command is a Cheetah template which allows some Python based syntax.
## Lines starting hash hash are comments. Galaxy will turn newlines into spaces

#set $format = $oformat.oformat_opts_selector

    #if $format == "fs":
        ## For the fastsearch index we need to copy the original molecule files to the composite datatype of obfs.
        ## Because openbabel likes file extensions, we give the molecule file a proper file extension.
        mkdir $outfile.extra_files_path;
        cp "${infile}" ${os.path.join($outfile.extra_files_path, 'molecule.%s' % $infile.ext )};
    #end if

obabel -i "${infile.ext}"

    #if $format == "fs":
        ## the fs filetype need his own symlink path, all others can take the original ones
        ${os.path.join($outfile.extra_files_path, 'molecule.%s' % $infile.ext )}
        -o "$format" -e
        -O ${os.path.join($outfile.extra_files_path,'molecule.fs')}
        #if int($oformat.fs_fold) > 0:
            -xN$oformat.fs_fold
        #end if
        ${oformat.fs_fptype}
    #else:

    #if int($ph) >= 0:
        -p $ph
    #end if

    2>&1
    </command>
    <inputs>
        <param name="infile" type="data" format="sdf,mol2,cml,inchi,smi" label="Select input file with molecules"/>
        <conditional name="oformat">
            <param name="oformat_opts_selector" type="select" label="Output format">

                <option value="cacint">Cacao Internal format</option>
                <option value="can" selected="True">Canonical SMILES format (can)</option>
                <option value="cdxml">ChemDraw CDXML format</option>
                <option value="cht">Chemtool format</option>
                <option value="cif">Crystallographic Information File</option>
                <option value="cml">Chemical Markup Language</option>
                <option value="cmlr">CML Reaction format</option>
                <option value="com">Gaussian 98/03 Cartesian Input</option>
                <option value="copy">Copies raw text</option>
                <option value="crk2d">Chemical Resource Kit 2D diagram format</option>
                <option value="crk3d">Chemical Resource Kit 3D format</option>

                <when input="oformat.oformat_opts_selector" value="fs" format="obfs"/>
            </change_format>
        </data>
    </outputs>
    <help>

.. class:: infomark

**What this tool does**

The compound converter joins several `Open Babel`_ command prompt converters in an easy to use tool. It converts various chemistry and moleculare modeling data files. 
The output format can be specified as well as several parameters. Some parameters are available for all tools (e.g. protonation state and pH) 
others are specific for a given output format (e.g. exclude isotopes for conversion to canSMI).

-----

.. class:: infomark

`Open Babel`_

.. _`Open Babel`: http://openbabel.org/wiki/Main_Page


  </help>
</tool>

2:125da3a296ca

    -->
    <requirements>
        <requirement type="package" version="2.3.2">openbabel</requirement>
    </requirements>
    <command>
<![CDATA[
## The command is a Cheetah template which allows some Python based syntax.
## Lines starting hash hash are comments. Galaxy will turn newlines into spaces

#set $format = $oformat.oformat_opts_selector

    #if $format == "fs":
        ## For the fastsearch index we need to copy the original molecule files to the composite datatype of obfs.
        ## Because openbabel likes file extensions, we give the molecule file a proper file extension.
        mkdir $outfile.files_path;
        cp "${infile}" ${os.path.join($outfile.files_path, 'molecule.%s' % $infile.ext )};
    #end if

obabel -i "${infile.ext}"

    #if $format == "fs":
        ## the fs filetype need his own symlink path, all others can take the original ones
        ${os.path.join($outfile.files_path, 'molecule.%s' % $infile.ext )}
        -o "$format" -e
        -O ${os.path.join($outfile.files_path,'molecule.fs')}
        #if int($oformat.fs_fold) > 0:
            -xN$oformat.fs_fold
        #end if
        ${oformat.fs_fptype}
    #else:

    #if int($ph) >= 0:
        -p $ph
    #end if

    2>&1
]]>
    </command>
    <inputs>
        <param name="infile" type="data" format="sdf,mol2,cml,inchi,smi" label="Select input file with molecules"/>
        <conditional name="oformat">
            <param name="oformat_opts_selector" type="select" label="Output format">

                <option value="cacint">Cacao Internal format</option>
                <option value="can" selected="True">Canonical SMILES format (can)</option>
                <option value="cdxml">ChemDraw CDXML format</option>
                <option value="cht">Chemtool format</option>
                <option value="cif">Crystallographic Information File</option>
                <option value="cml">Chemical Markup Language (CML)</option>
                <option value="cmlr">CML Reaction format</option>
                <option value="com">Gaussian 98/03 Cartesian Input</option>
                <option value="copy">Copies raw text</option>
                <option value="crk2d">Chemical Resource Kit 2D diagram format</option>
                <option value="crk3d">Chemical Resource Kit 3D format</option>

                <when input="oformat.oformat_opts_selector" value="fs" format="obfs"/>
            </change_format>
        </data>
    </outputs>
    <help>
<![CDATA[

.. class:: infomark

**What this tool does**

The compound converter joins several `Open Babel`_ command prompt converters in an easy to use tool. It converts various chemistry and moleculare modeling data files.
The output format can be specified as well as several parameters. Some parameters are available for all tools (e.g. protonation state and pH)
others are specific for a given output format (e.g. exclude isotopes for conversion to canSMI).

-----

.. class:: infomark

`Open Babel`_

.. _`Open Babel`: http://openbabel.org/wiki/Main_Page


]]>
  </help>
</tool>