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comparison filter/ob_grep.xml @ 2:125da3a296ca draft default tip

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author bgruening
date Wed, 15 Jul 2015 12:13:08 -0400
parents 527ecd2fc500
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1:b52872a1755a 2:125da3a296ca
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>&#38;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>