annotate sdf2fps.xml @ 7:0d88631bb7de draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e

<tool id="ctb_sdf2fps" name="SDF to Fingerprint" version="1.5">
    <description>- extract fingerprints from sdf file metadata</description>
    <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism-->
    <requirements>
        <requirement type="package" version="1.5">chemfp</requirement>
        <requirement type="package" version="2.4.1">openbabel</requirement>
    </requirements>
    <command>
<![CDATA[
        sdf2fps --pubchem '${infile}' > '${outfile}'
]]>
    </command>
    <inputs>
        <param name="infile" type='data' format="sdf" label="SD-file with fingerprints as metadata"/>
    </inputs>
    <outputs>
        <data name="outfile" format="fps"/>
    </outputs>
    <tests>
        <test>
            <param name="infile" ftype="sdf" value="CID_2244.sdf" />
            <output name="outfile" file='sdf2fps_result1.fps' ftype="fps" lines_diff="4" />
        </test>
    </tests>
    <help>
<![CDATA[

.. class:: infomark

**What this tool does**

Read an input SD file, extract the fingerprints and store them in a FPS-file.

-----

.. class:: infomark

**Input**

`SD-Format`_, storing the atom types, together with the Cartesian coordinates.

.. _`SD-Format`: http://en.wikipedia.org/wiki/Chemical_table_file

* Example::

		28434379
		  -OEChem-02031205132D

		 37 39  0     0  0  0  0  0  0999 V2000
		    8.1648   -1.8842    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
		    6.0812   -0.2134    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
		    6.0812   -1.8229    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
		    2.5369   -2.0182    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
		    6.3919    0.7371    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
		    7.3704    0.9433    0.0000 C   0  0  0  0
		    ......
		  1 15  1  0  0  0  0
		  1 35  1  0  0  0  0
		  2  5  1  0  0  0  0
		  2 11  1  0  0  0  0
		  2 12  1  0  0  0  0
		  3 12  2  0  0  0  0
		  3 13  1  0  0  0  0
		  4 18  1  0  0  0  0
		  ......

			>PUBCHEM_COMPOUND_CID<
			28434379

			> <PUBCHEM_COMPOUND_CANONICALIZED>
			1

			> <PUBCHEM_CACTVS_COMPLEXITY>
			280

			> <PUBCHEM_CACTVS_HBOND_ACCEPTOR>
			2

			> <PUBCHEM_CACTVS_HBOND_DONOR>
			2

			> <PUBCHEM_CACTVS_ROTATABLE_BOND>
			2

			> <PUBCHEM_CACTVS_SUBSKEYS>
			AAADceBzIAAAAAAAAAAAAAAAAAAAAWAAAAAwYAAAAAAAAFgB8AAAHgAQCAAACCjhlwYx0LdMEgCgASZiZASCgC0hEqAJ2CA4dJiKeKLA2dGUJAhokALYyCcQAAAAAACAAAQAACAAAQAACAAAQAAAAAAAAA==

			>

-----

.. class:: infomark

**Output**

After the first few lines, starting with a hash symbol, which contain generic information, the fingerprints are listed as hexadecimal strings.

* Example::

	#FPS1
	#num_bits=881
	#type=CACTVS-E_SCREEN/1.0 extended=2
	#software=CACTVS/unknown
	#source=/home/mohammed/galaxy-central/database/files/000/dataset_409.dat
	#date=2012-02-03T10:44:12
	07ce04000000000000000000000000000080060000000c0600
	00000000001a800f0000780008100000101487e9608c0bed32
	48000580644626204101b4844805901b041c2e19511e45039b
	8b2924101609401b13e4080000000000010020000004008000
	0010000002000000000000	28434379


]]>
    </help>
    <citations>
        <citation type="doi">10.1186/1758-2946-5-S1-P36</citation>
    </citations>
</tool>