Mercurial > repos > bgruening > chemfp

annotate sdf2fps.xml @ 11:92c7cdc243e8 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 70d32dc05d264ffbe03b0c62e54acd5e904c9b7e-dirty"
author bgruening
date Wed, 24 Jun 2020 13:12:05 -0400
parents 0d88631bb7de
children 3b14765c22ee
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92c7cdc243e8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 70d32dc05d264ffbe03b0c62e54acd5e904c9b7e-dirty"
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1 <tool id="ctb_sdf2fps" name="SDF to Fingerprint" version="1.6">
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0d88631bb7de planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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2 <description>- extract fingerprints from sdf file metadata</description>
2
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3 <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism-->
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4 <requirements>
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92c7cdc243e8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 70d32dc05d264ffbe03b0c62e54acd5e904c9b7e-dirty"
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5 <requirement type="package" version="1.6">chemfp</requirement>
2
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6 </requirements>
70b071de9bee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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7 <command>
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8 <![CDATA[
70b071de9bee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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9 sdf2fps --pubchem '${infile}' > '${outfile}'
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10 ]]>
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11 </command>
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12 <inputs>
7
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13 <param name="infile" type='data' format="sdf" label="SD-file with fingerprints as metadata"/>
2
70b071de9bee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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14 </inputs>
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15 <outputs>
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16 <data name="outfile" format="fps"/>
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17 </outputs>
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18 <tests>
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19 <test>
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20 <param name="infile" ftype="sdf" value="CID_2244.sdf" />
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21 <output name="outfile" file='sdf2fps_result1.fps' ftype="fps" lines_diff="4" />
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22 </test>
70b071de9bee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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23 </tests>
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24 <help>
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25 <![CDATA[
70b071de9bee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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26
70b071de9bee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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27 .. class:: infomark
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28
70b071de9bee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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29 **What this tool does**
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30
70b071de9bee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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31 Read an input SD file, extract the fingerprints and store them in a FPS-file.
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32
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33 -----
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34
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35 .. class:: infomark
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36
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37 **Input**
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38
7
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39 `SD-Format`_, storing the atom types, together with the Cartesian coordinates.
2
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40
70b071de9bee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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41 .. _`SD-Format`: http://en.wikipedia.org/wiki/Chemical_table_file
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42
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43 * Example::
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44
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45 28434379
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46 -OEChem-02031205132D
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47
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48 37 39 0 0 0 0 0 0 0999 V2000
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49 8.1648 -1.8842 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
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50 6.0812 -0.2134 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
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51 6.0812 -1.8229 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
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52 2.5369 -2.0182 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
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53 6.3919 0.7371 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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54 7.3704 0.9433 0.0000 C 0 0 0 0
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55 ......
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56 1 15 1 0 0 0 0
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57 1 35 1 0 0 0 0
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58 2 5 1 0 0 0 0
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59 2 11 1 0 0 0 0
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60 2 12 1 0 0 0 0
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61 3 12 2 0 0 0 0
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62 3 13 1 0 0 0 0
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63 4 18 1 0 0 0 0
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64 ......
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65
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66 >PUBCHEM_COMPOUND_CID<
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67 28434379
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68
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69 > <PUBCHEM_COMPOUND_CANONICALIZED>
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70 1
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71
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72 > <PUBCHEM_CACTVS_COMPLEXITY>
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73 280
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75 > <PUBCHEM_CACTVS_HBOND_ACCEPTOR>
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76 2
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78 > <PUBCHEM_CACTVS_HBOND_DONOR>
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79 2
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80
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81 > <PUBCHEM_CACTVS_ROTATABLE_BOND>
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82 2
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84 > <PUBCHEM_CACTVS_SUBSKEYS>
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85 AAADceBzIAAAAAAAAAAAAAAAAAAAAWAAAAAwYAAAAAAAAFgB8AAAHgAQCAAACCjhlwYx0LdMEgCgASZiZASCgC0hEqAJ2CA4dJiKeKLA2dGUJAhokALYyCcQAAAAAACAAAQAACAAAQAACAAAQAAAAAAAAA==
70b071de9bee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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86
70b071de9bee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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87 >
70b071de9bee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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88
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89 -----
70b071de9bee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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90
70b071de9bee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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91 .. class:: infomark
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92
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93 **Output**
70b071de9bee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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94
7
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95 After the first few lines, starting with a hash symbol, which contain generic information, the fingerprints are listed as hexadecimal strings.
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96
2
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97 * Example::
70b071de9bee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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98
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99 #FPS1
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100 #num_bits=881
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101 #type=CACTVS-E_SCREEN/1.0 extended=2
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102 #software=CACTVS/unknown
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103 #source=/home/mohammed/galaxy-central/database/files/000/dataset_409.dat
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104 #date=2012-02-03T10:44:12
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105 07ce04000000000000000000000000000080060000000c0600
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106 00000000001a800f0000780008100000101487e9608c0bed32
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107 48000580644626204101b4844805901b041c2e19511e45039b
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108 8b2924101609401b13e4080000000000010020000004008000
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109 0010000002000000000000 28434379
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110
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111
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112 ]]>
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113 </help>
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114 <citations>
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115 <citation type="doi">10.1186/1758-2946-5-S1-P36</citation>
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116 </citations>
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117 </tool>