Mercurial > repos > bgruening > eden_toolbox
comparison EDeN_feature.xml @ 1:64a1fb09b10d draft
Uploaded
| author | bgruening |
|---|---|
| date | Wed, 04 Sep 2013 07:59:08 -0400 |
| parents | 99091a5d5c84 |
| children | a3edc97e056c |
comparison
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| 0:99091a5d5c84 | 1:64a1fb09b10d |
|---|---|
| 12 #set $temp_gspan = tempfile.NamedTemporaryFile( delete=False ) | 12 #set $temp_gspan = tempfile.NamedTemporaryFile( delete=False ) |
| 13 #silent $temp_gspan.close() | 13 #silent $temp_gspan.close() |
| 14 #set $temp_gspan = $temp_gspan.name | 14 #set $temp_gspan = $temp_gspan.name |
| 15 | 15 |
| 16 #if $file_type_opts.file_type_opts_selector == 'sdf': | 16 #if $file_type_opts.file_type_opts_selector == 'sdf': |
| 17 obabel -i sdf -o sdf $infile | \$EDEN_SCRIPT_PATH/mol2gspan.py --infile - --outfile $temp_gspan | 17 obabel -i sdf -o sdf $infile | python \$EDEN_SCRIPT_PATH/mol2gspan.py --infile - --outfile $temp_gspan |
| 18 #set $file_type = 'GRAPH' | 18 #set $file_type = 'GRAPH' |
| 19 #elif $file_type_opts.file_type_opts_selector == 'smi': | 19 #elif $file_type_opts.file_type_opts_selector == 'smi': |
| 20 obabel -i smi -o sdf $infile | \$EDEN_SCRIPT_PATH/mol2gspan.py --infile - --outfile $temp_gspan | 20 obabel -i smi -o sdf $infile | python \$EDEN_SCRIPT_PATH/mol2gspan.py --infile - --outfile $temp_gspan |
| 21 #set $file_type = 'GRAPH' | 21 #set $file_type = 'GRAPH' |
| 22 #else: | 22 #else: |
| 23 #set $temp_gspan = $infile | 23 #set $temp_gspan = $infile |
| 24 #set $file_type = $file_type_opts.file_type_opts_selector | 24 #set $file_type = $file_type_opts.file_type_opts_selector |
| 25 #end if | 25 #end if |
| 90 <inputs> | 90 <inputs> |
| 91 <param format="smi,gspan,inchi,sdf,mol,mol2,txt" name="infile" type="data" label="Input file" | 91 <param format="smi,gspan,inchi,sdf,mol,mol2,txt" name="infile" type="data" label="Input file" |
| 92 help="File can contain molecule data types (SMILES, InChI, SDF) or Graph datatypes (gSpan, sparse vector, sequence)."/> | 92 help="File can contain molecule data types (SMILES, InChI, SDF) or Graph datatypes (gSpan, sparse vector, sequence)."/> |
| 93 | 93 |
| 94 <conditional name="file_type_opts"> | 94 <conditional name="file_type_opts"> |
| 95 <param name="file_type_opts_selector" type="select" display="radio" label="Type of Input file"> | 95 <param name="file_type_opts_selector" type="select" label="Type of Input file"> |
| 96 <option value="GRAPH">Graph</option> | 96 <option value="GRAPH">Graph</option> |
| 97 <option value="SPARSE_VECTOR">sparse vector</option> | 97 <option value="SPARSE_VECTOR">sparse vector</option> |
| 98 <option value="SEQUENCE">Sequence</option> | 98 <option value="SEQUENCE">Sequence</option> |
| 99 <option value="sdf">SDF</option> | 99 <option value="sdf">SDF</option> |
| 100 <option value="smi">SMILES</option> | 100 <option value="smi">SMILES</option> |