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comparison visualisation/ob_depiction_svg.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
2 <description>of compounds</description> 2 <description>of compounds</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.3.2">openbabel</requirement> 4 <requirement type="package" version="2.3.2">openbabel</requirement>
5 </requirements> 5 </requirements>
6 <command> 6 <command>
7 <![CDATA[
7 obabel -i${infile.ext} $infile 8 obabel -i${infile.ext} $infile
8 $embed_molecule_as_cml 9 $embed_molecule_as_cml
9 $draw_all_carbon_atoms 10 $draw_all_carbon_atoms
10 -xC 11 -xC
11 -O 12 -O
12 $outfile -o$oformat 13 $outfile -o$oformat
13 #if str($sort) != "none": 14 #if str($sort) != "none":
14 --sort $sort 15 --sort $sort
15 #end if 16 #end if
16 #if str($display_name) != "None" and len(str($display_name)) > 0 and str($display_name) != 'title': 17 #if str($display_name) != "None" and len(str($display_name)) > 0 and str($display_name) != 'title':
17 --append "$display_name" 18 --append "$display_name"
18 --title "" 19 --title ""
19 #end if 20 #end if
20 $thick_lines 21 $thick_lines
21 2>&#38;1 22 2>&1
23 ]]>
22 </command> 24 </command>
23 <inputs> 25 <inputs>
24 <param name="infile" type="data" format="mol,sdf,smi,inchi" label="Input format"/> 26 <param name="infile" type="data" format="mol,sdf,smi,inchi" label="Input format"/>
25 <param name="embed_molecule_as_cml" type="boolean" truevalue="-e" falsevalue="" label="Embed molecule as CML"/> 27 <param name="embed_molecule_as_cml" type="boolean" truevalue="-e" falsevalue="" label="Embed molecule as CML"/>
26 <param name="draw_all_carbon_atoms" type="boolean" truevalue="-a" falsevalue="" label="draw all carbon atoms"/> 28 <param name="draw_all_carbon_atoms" type="boolean" truevalue="-a" falsevalue="" label="draw all carbon atoms"/>
93 <param name='sort' value='none' /> 95 <param name='sort' value='none' />
94 <output name="outfile" ftype="svg" file="ob_depiction_svg_on_8_mol.svg" /> 96 <output name="outfile" ftype="svg" file="ob_depiction_svg_on_8_mol.svg" />
95 </test> 97 </test>
96 </tests> 98 </tests>
97 <help> 99 <help>
100 <![CDATA[
98 101
99 .. class:: infomark 102 .. class:: infomark
100 103
101 **What this tool does** 104 **What this tool does**
102 105
121 124
122 `Open Babel`_ 125 `Open Babel`_
123 126
124 .. _Open Babel: http://openbabel.org/wiki/Main_Page 127 .. _Open Babel: http://openbabel.org/wiki/Main_Page
125 128
129 ]]>
126 </help> 130 </help>
127 </tool> 131 </tool>