Mercurial > repos > bgruening > openbabel
comparison filter/ob_grep.xml @ 2:125da3a296ca draft default tip
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author | bgruening |
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date | Wed, 15 Jul 2015 12:13:08 -0400 |
parents | 527ecd2fc500 |
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1:b52872a1755a | 2:125da3a296ca |
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3 <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism> | 3 <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism> |
4 <requirements> | 4 <requirements> |
5 <requirement type="package" version="2.3.2">openbabel</requirement> | 5 <requirement type="package" version="2.3.2">openbabel</requirement> |
6 </requirements> | 6 </requirements> |
7 <command> | 7 <command> |
8 <![CDATA[ | |
8 ## The command is a Cheetah template which allows some Python based syntax. | 9 ## The command is a Cheetah template which allows some Python based syntax. |
9 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces | 10 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces |
10 obgrep | 11 obgrep |
11 | 12 |
12 $invert_matches | 13 $invert_matches |
18 $full_match | 19 $full_match |
19 $number_of_matches | 20 $number_of_matches |
20 -i ${infile.ext} | 21 -i ${infile.ext} |
21 "${smarts_pattern}" | 22 "${smarts_pattern}" |
22 "${infile}" | 23 "${infile}" |
23 > "${outfile}" 2>&1 | 24 > "${outfile}" 2>&1 |
25 ]]> | |
24 </command> | 26 </command> |
25 <inputs> | 27 <inputs> |
26 <param name="infile" type="data" format="sdf,mol,mol2,cml,inchi,smi" label="Compound File" help="Specify a compound file in SDF Format."/> | 28 <param name="infile" type="data" format="sdf,mol,mol2,cml,inchi,smi" label="Compound File" help="Specify a compound file in SDF Format."/> |
27 <param name="smarts_pattern" type="text" format="text" label="SMARTS Pattern" help="Specify a SMARTS Pattern for your search."/> | 29 <param name="smarts_pattern" type="text" format="text" label="SMARTS Pattern" help="Specify a SMARTS Pattern for your search."/> |
28 <param name="invert_matches" type="boolean" label="Invert the matching, print non-matching molecules" truevalue="-v" falsevalue="" checked="false" /> | 30 <param name="invert_matches" type="boolean" label="Invert the matching, print non-matching molecules" truevalue="-v" falsevalue="" checked="false" /> |
46 <param name="number_of_matches" value="" /> | 48 <param name="number_of_matches" value="" /> |
47 <output name="outfile" ftype="smi" file="obgrep_on_8_mol.smi"/> | 49 <output name="outfile" ftype="smi" file="obgrep_on_8_mol.smi"/> |
48 </test> | 50 </test> |
49 </tests> | 51 </tests> |
50 <help> | 52 <help> |
53 <![CDATA[ | |
51 | 54 |
52 .. class:: infomark | 55 .. class:: infomark |
53 | 56 |
54 **What this tool does** | 57 **What this tool does** |
55 | 58 |
92 | 95 |
93 `Open Babel`_ | 96 `Open Babel`_ |
94 | 97 |
95 .. _`Open Babel`: http://openbabel.org/wiki/Main_Page | 98 .. _`Open Babel`: http://openbabel.org/wiki/Main_Page |
96 | 99 |
100 ]]> | |
97 </help> | 101 </help> |
98 </tool> | 102 </tool> |