Mercurial > repos > bgruening > eden_toolbox
changeset 7:59b3b6ce10bb draft
Uploaded
| author | bgruening |
|---|---|
| date | Tue, 29 Oct 2013 11:07:49 -0400 |
| parents | 7d49e315cb95 |
| children | 9262f801d739 |
| files | EDeN_feature.xml EDeN_nearest_neighbor.xml EDeN_test.xml EDeN_train.xml datatypes_conf.xml eden.py eden_macros.xml mol2gspan.py mol2gspan.xml tool_dependencies.xml |
| diffstat | 10 files changed, 241 insertions(+), 248 deletions(-) [+] |
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--- a/EDeN_feature.xml Thu Sep 05 12:52:45 2013 -0400 +++ b/EDeN_feature.xml Tue Oct 29 11:07:49 2013 -0400 @@ -1,93 +1,42 @@ -<tool id="bg_eden_feature" name="EDeN Converter" version="0.1"> - <description></description> - <requirements> - <requirement type="package" version="2.3.2">openbabel</requirement> - <requirement type="set_environment">EDEN_SCRIPT_PATH</requirement> - </requirements> +<tool id="bg_eden_feature" name="EDeN Converters" version="0.1"> + <description>to produce sparce vectors</description> <macros> <import>eden_macros.xml</import> </macros> + <expand macro="requirements" /> <command> - - ## pre-processing step if we have a molecule type we need to convert it to the gSpan format at first - - #import tempfile, os - #set $temp_gspan = tempfile.NamedTemporaryFile( delete=False ) - #silent $temp_gspan.close() - #set $temp_gspan = $temp_gspan.name - - #if $file_type_opts.file_type_opts_selector == 'sdf': - obabel -i sdf -o sdf $infile ---errorlevel 1 | python \$EDEN_SCRIPT_PATH/mol2gspan.py --infile - --outfile $temp_gspan - #set $file_type = 'GRAPH' - #elif $file_type_opts.file_type_opts_selector == 'smi': - obabel -i smi -o sdf $infile ---errorlevel 1 | python \$EDEN_SCRIPT_PATH/mol2gspan.py --infile - --outfile $temp_gspan - #set $file_type = 'GRAPH' - #else: - #set $temp_gspan = $infile - #set $file_type = $file_type_opts.file_type_opts_selector - #end if - ; + tmp_dir=`mktemp -d -u`; EDeN --action FEATURE - --input_data_file_name $temp_gspan + --output_directory_path \$tmp_dir + + --input_data_file_name $infile --model_file_name $outfile - ## if we have an molecule datatype the file_type is set to GRAPH, after convertion to the gSpan Graph format - --file_type $file_type + --file_type $file_type_opts.file_type_opts_selector --binary_file_type ## create a binary sparse vector as output - - $no_normalization - $min_kernel - - --hash_bit_size $hash_bit_size - --radius $radius - --distance $distance - --vertex_degree_threshold $vertex_degree_threshold - - $no_normalization - $min_kernel + @normalization_kernel_hash_radius_dist_vertex@ --kernel_type $kernel_type_opts.kernel_type_opts_selector --graph_type $graph_type #if $file_type_opts.file_type_opts_selector == 'SEQUENCE': - --sequence_degree $sequence_degree $sequence_token $sequence_multi_line $sequence_pairwise_interaction - - #end if - - #if $kernel_type_opts.kernel_type_opts_selector in ['DDK','NSDDK','SK']: - --tree_lambda $kernel_type_opts.tree_lambda - --radius_two $kernel_type_opts.radius_two #end if - ### Adds rescaled features from nearest neighbors ### - - #if $smooth_opts.smooth_opts_selector == 'smooth': - --smooth - --smooth_param $smooth_opts.smoother_param + @kernel_type_options@ - --row_index_file_name $row_index_file_name - --col_index_file_name $col_index_file_name - --num_hash_functions $smooth_opts.num_hash_functions - --num_repeat_hash_functions $smooth_opts.num_repeat_hash_functions - --max_size_bin $smooth_opts.max_size_bin - --eccess_neighbour_size_factor $smooth_opts.eccess_neighbour_size_factor - --num_nearest_neighbours $smooth_opts.num_nearest_neighbours - $smooth_opts.shared_neighborhood - $smooth_opts.no_neighborhood_cache - $smooth_opts.no_minhash_cache - #end if + @input_smooth_conditional@ ; - rm $temp_gspan - + cp \$tmp_dir/feature $outfile; + rm \$tmp_dir -rf; </command> <stdio> @@ -97,16 +46,14 @@ description="An error occured with your Job." /> </stdio> <inputs> - <param format="smi,gspan,inchi,sdf,mol,mol2,txt" name="infile" type="data" label="Input file" - help="File can contain molecule data types (SMILES, InChI, SDF) or Graph datatypes (gSpan, sparse vector, sequence)."/> + <param format="gspan,txt" name="infile" type="data" label="Input file" + help="File can contain Graph datatypes (gSpan, sparse vector, sequence)."/> <conditional name="file_type_opts"> <param name="file_type_opts_selector" type="select" label="Type of Input file"> <option value="GRAPH">Graph</option> <option value="SPARSE_VECTOR">sparse vector</option> <option value="SEQUENCE">Sequence</option> - <option value="sdf">SDF</option> - <option value="smi">SMILES</option> </param> <when value="GRAPH" /> <when value="SPARSE_VECTOR" /> @@ -122,70 +69,13 @@ <when value="smi" /> </conditional> - <conditional name="kernel_type_opts"> - <param name="kernel_type_opts_selector" type="select" label="Type of the Kernel"> - <option value="NSPDK">NSPDK</option> - <option value="WDK">WDK</option> - <option value="PBK">PBK</option> - <option value="USPK">USPK</option> - <option value="DDK">DDK</option> - <option value="NSDDK">ANSDDK</option> - <option value="SK">SK [NSPDK]</option> - </param> - <when value="NSPDK" /> - <when value="WDK" /> - <when value="PBK" /> - <when value="USPK" /> - <when value="SK"> - <param name="radius_two" type="integer" value="2" label="Radius Two" help=""> - <validator type="in_range" min="1" /> - </param> - <param name="tree_lambda" type="float" value="1.2" label="Tree lambda" help=""> - <validator type="in_range" min="0.0" /> - </param> - </when> - <when value="DDK"> - <param name="radius_two" type="integer" value="2" label="Radius Two" help=""> - <validator type="in_range" min="1" /> - </param> - <param name="tree_lambda" type="float" value="1.2" label="Tree lambda" help=""> - <validator type="in_range" min="0.0" /> - </param> - </when> - <when value="NSDDK"> - <param name="radius_two" type="integer" value="2" label="Radius Two" help=""> - <validator type="in_range" min="1" /> - </param> - <param name="tree_lambda" type="float" value="1.2" label="Tree lambda" help=""> - <validator type="in_range" min="0.0" /> - </param> - </when> - </conditional> + <expand macro="kernel_type_options" /> - - <param name="graph_type" type="select" display="radio" label="Type of Graph"> - <option value="DIRECTED">directed</option> - <option value="UNDIRECTED">undirected</option> - </param> + <expand macro="graph_types" /> <expand macro="input_smooth_conditional" /> - <param name="no_normalization" type="boolean" label="Skip normalization" truevalue="--no_normalization" falsevalue="" checked="false" /> - <param name="min_kernel" type="boolean" label="Use min kernel" truevalue="--min_kernel" falsevalue="" checked="false" /> - - <param name="hash_bit_size" type="integer" value="15" label="Bit size of the used hashing function" help=""> - <validator type="in_range" min="1" /> - </param> - <param name="radius" type="integer" value="2" label="Radius that defines a neighborhood" help=""> - <validator type="in_range" min="1" /> - </param> - <param name="distance" type="integer" value="5" label="Distance that defines a neighborhood" help=""> - <validator type="in_range" min="1" /> - </param> - <param name="vertex_degree_threshold" type="integer" value="7" label="Vertex degree threshold" help=""> - <validator type="in_range" min="1" /> - </param> - + <expand macro="normalization_kernel_hash_radius_dist_vertex" /> </inputs> <configfiles> @@ -224,7 +114,7 @@ </configfile> </configfiles> <outputs> - <data format="eden_sparse_vector" name="outfile" label="Sparse vector from ${on_string}"/> + <data format="sparsevector" name="outfile" label="Sparse Vector from ${on_string}"/> </outputs> <tests> <test> @@ -242,7 +132,7 @@ When the target information is 0, a self-training algorithm is used to impute a positive or negative class to the unsupervised instances. If the target information is imbalanced a minority class resampling technique is used to rebalance the training set. -This tool is part of the EDeN (Explicit Decomposition with Neighborhoods) suite, developed by Fabrizio Costa. +@references@ </help> </tool>
--- a/EDeN_nearest_neighbor.xml Thu Sep 05 12:52:45 2013 -0400 +++ b/EDeN_nearest_neighbor.xml Tue Oct 29 11:07:49 2013 -0400 @@ -1,11 +1,11 @@ <tool id="bg_eden_nearest_neighbor" name="EDeN Nearest Neighbors" version="0.1"> <description></description> - <requirements> - </requirements> + <expand macro="requirements" /> <macros> <import>eden_macros.xml</import> </macros> <command> + tmp_dir=`mktemp -d -u`; EDeN --action NEAREST_NEIGHBOR --input_data_file_name $infile @@ -14,22 +14,38 @@ --file_type "SPARSE_VECTOR" --binary_file_type - ### Adds rescaled features from nearest neighbors ### + @kernel_type_options@ + --graph_type $graph_type + @input_smooth_conditional@ + + @normalization_kernel_hash_radius_dist_vertex@ - #if $smooth_opts.smooth_opts_selector == 'smooth': - --smooth - --smooth_param $smooth_opts.smoother_param + --output_directory_path \$tmp_dir + + + ## + ## shuffling files to create the correct outputs for Galaxy + ## - --row_index_file_name $row_index_file_name - --col_index_file_name $col_index_file_name - --num_hash_functions $smooth_opts.num_hash_functions - --num_repeat_hash_functions $smooth_opts.num_repeat_hash_functions - --max_size_bin $smooth_opts.max_size_bin - --eccess_neighbour_size_factor $smooth_opts.eccess_neighbour_size_factor - --num_nearest_neighbours $smooth_opts.num_nearest_neighbours - $smooth_opts.shared_neighborhood - $smooth_opts.no_neighborhood_cache - $smooth_opts.no_minhash_cache + ; + cp \$tmp_dir/knn $ofile_nnlist 2> /dev/null + + ## Nearest neighbor feature representation + #if 'nnf' in str($additional_outputs).split(','): + ; + cp \$tmp_dir/knn_feature $ofile_nnf 2> /dev/null + #end if + + ## Nearest neighbor target value list + #if 'nnt' in str($additional_outputs).split(','): + ; + cp \$tmp_dir/knn_target_value $ofile_nnt 2> /dev/null + #end if + + ## Nearest neighbor kernel value list + #if 'nnk' in str($additional_outputs).split(','): + ; + cp \$tmp_dir/knn_kernel_value $ofile_nnk 2> /dev/null #end if </command> @@ -40,9 +56,31 @@ <expand macro="input_smooth_conditional" /> + <expand macro="kernel_type_options" /> + + <expand macro="graph_types" /> + + <expand macro="normalization_kernel_hash_radius_dist_vertex" /> + + <param name="additional_outputs" type="select" multiple="true" optional="True" label="Additional outputs"> + <option value="none" selected="True">No additional output</option> + <option value="nnk">Nearest neighbor kernel value list</option> + <option value="nnt">Nearest neighbor target value list</option> + <option value="nnf">Nearest neighbor feature representation</option> + </param> + </inputs> <outputs> - <data format="gspan" name="outfile" label="gSpan from ${on_string}"/> + <data format="tabular" name="ofile_nnlist" label="${tool.name} on ${on_string}"/> + <data format="tabular" name="ofile_nnf" label="${tool.name} on ${on_string} (Nearest neighbor feature representation)"> + <filter>'nnf' in additional_outputs</filter> + </data> + <data format="tabular" name="ofile_nnt" label="${tool.name} on ${on_string} (Nearest neighbor target value list)"> + <filter>'nnt' in additional_outputs</filter> + </data> + <data format="tabular" name="ofile_nnk" label="${tool.name} on ${on_string} (Nearest neighbor kernel value list)"> + <filter>'nnk' in additional_outputs</filter> + </data> </outputs> <tests> <test> @@ -58,7 +96,7 @@ Nearest neighbors are efficiently identified with a locality sensitive hashing technique. -This tool is part of the EDeN (Explicit Decomposition with Neighborhoods) suite, developed by Fabrizio Costa. +@references@ </help> </tool>
--- a/EDeN_test.xml Thu Sep 05 12:52:45 2013 -0400 +++ b/EDeN_test.xml Tue Oct 29 11:07:49 2013 -0400 @@ -1,15 +1,31 @@ <tool id="bg_eden_test" name="EDeN Test" version="0.1"> <description></description> - <requirements> - </requirements> + <macros> + <import>eden_macros.xml</import> + </macros> + <expand macro="requirements" /> <command> + tmp_dir=`mktemp -d -u`; EDeN --action TEST - --input_data_file_name $sparse_vector_infile + --input_data_file_name $sparse_vector_infile + --file_type "SPARSE_VECTOR" + --binary_file_type + --model_file_name $model_infile - --file_type "SPARSE_VECTOR" - --binary_file_type + @kernel_type_options@ + + --graph_type $graph_type + + @normalization_kernel_hash_radius_dist_vertex@ + + --output_directory_path \$tmp_dir + --minimal_output + + ; + cp \$tmp_dir/prediction $output; + rm \$tmp_dir -rf </command> <inputs> @@ -17,6 +33,12 @@ <param format="txt" name="model_infile" type="data" label="Input Model" help="created with the EDeN Train program"/> + <expand macro="kernel_type_options" /> + + <expand macro="graph_types" /> + + <expand macro="normalization_kernel_hash_radius_dist_vertex" /> + </inputs> <outputs> <data format="tabular" name="output" label="Generated from ${on_string}"/> @@ -35,7 +57,7 @@ When the target information is 0, a self-training algorithm is used to impute a positive or negative class to the unsupervised instances. If the target information is imbalanced a minority class resampling technique is used to rebalance the training set. -This tool is part of the EDeN (Explicit Decomposition with Neighborhoods) suite, developed by Fabrizio Costa. +@references@ </help> </tool>
--- a/EDeN_train.xml Thu Sep 05 12:52:45 2013 -0400 +++ b/EDeN_train.xml Tue Oct 29 11:07:49 2013 -0400 @@ -1,14 +1,20 @@ <tool id="bg_eden_train" name="EDeN Train" version="0.1"> <description></description> - <requirements> - </requirements> + <macros> + <import>eden_macros.xml</import> + </macros> + <expand macro="requirements" /> <command> + tmp_dir=`mktemp -d -u`; + EDeN --action TRAIN --input_data_file_name $infile --file_type "SPARSE_VECTOR" --binary_file_type + ##--output_directory_path \$tmp_dir + ## TODO: we need a tool that creates such a file, maybe from the metadata of an SDF file ## target_file_name is a file with 1 or -1 one in each row, indicating the class --target_file_name $target_infile @@ -40,15 +46,15 @@ <!-- Semi-supervised-settings --> <param name="threshold" type="float" value="1.0" label="Top and low quantile" - help="Only the top and low quantile will be used as positives and negative instances. A threshold of 1 means that all unsupervised instaces are used in the next phase. "> + help="Only the top and low quantile will be used as positives and negative instances. A threshold of 1 means that all unsupervised instaces are used in the next phase."> <validator type="in_range" min="0.0" /> </param> - <param name="num_iterations" type="integer" value="3" label="Number of iterations"> + <param name="num_iterations" type="integer" value="3" label="Number of iterations" /> <param name="only_negative" type="boolean" label="Induce only negative class instances." truevalue="--only_negative" falsevalue="" checked="false" /> <param name="only_positive" type="boolean" label="Induce only positive class instances." truevalue="--only_positive" falsevalue="" checked="false" /> - <param name="topological_regularization_decay_rate" type="float" value="0.01" label="Topological regularization decay rate" /> + <param name="topological_regularization_decay_rate" type="float" value="0.01" label="Topological regularization decay rate"> <validator type="in_range" min="0.0" /> </param> <param name="topological_regularization_num_neighbors" type="integer" value="0" label="Topological regularization number of neighbors"> @@ -58,7 +64,7 @@ <validator type="in_range" min="0" /> </param> - <param name="random_seed" type="integer" value="1" label="Randam Seed" help="" /> + <param name="random_seed" type="integer" value="1" label="Random Seed" help="" /> </inputs> <outputs> @@ -80,13 +86,10 @@ When the target information is 0, a self-training algorithm is used to impute a positive or negative class to the unsupervised instances. If the target information is imbalanced a minority class resampling technique is used to rebalance the training set. -This tool is part of the EDeN (Explicit Decomposition with Neighborhoods) suite, developed by Fabrizio Costa. - +@references@ -REFERENCES -========== - -The code for Stochastic Gradient Descent SVM is adapted from http://leon.bottou.org/projects/sgd. Léon Bottou and Yann LeCun, ''Large Scale Online Learning'', Advances in Neural Information Processing Systems 16, Edited by Sebastian Thrun, Lawrence Saul and Bernhard Schölkopf, MIT Press, Cambridge, MA, 2004. +The code for Stochastic Gradient Descent SVM is adapted from http://leon.bottou.org/projects/sgd. Léon Bottou and Yann LeCun, ''Large Scale Online Learning'', +Advances in Neural Information Processing Systems 16, Edited by Sebastian Thrun, Lawrence Saul and Bernhard Schölkopf, MIT Press, Cambridge, MA, 2004.
--- a/datatypes_conf.xml Thu Sep 05 12:52:45 2013 -0400 +++ b/datatypes_conf.xml Tue Oct 29 11:07:49 2013 -0400 @@ -5,6 +5,6 @@ </datatype_files> <registration> <datatype extension="gspan" type="galaxy.datatypes.eden:Gspan" mimetype="application/octet-stream" subclass="True" display_in_upload="false"/> - <datatype extension="gspan" type="galaxy.datatypes.eden:SparseVector" mimetype="application/octet-stream" subclass="True" display_in_upload="false"/> + <datatype extension="sparsevector" type="galaxy.datatypes.eden:SparseVector" mimetype="application/octet-stream" subclass="True" display_in_upload="false"/> </registration> </datatypes>
--- a/eden.py Thu Sep 05 12:52:45 2013 -0400 +++ b/eden.py Tue Oct 29 11:07:49 2013 -0400 @@ -24,7 +24,7 @@ class SparseVector( Binary ): """Class describing an SparseVector file""" - file_ext = "sparse" + file_ext = "sparsevector" def set_peek( self, dataset, is_multi_byte=False ): if not dataset.dataset.purged:
--- a/eden_macros.xml Thu Sep 05 12:52:45 2013 -0400 +++ b/eden_macros.xml Tue Oct 29 11:07:49 2013 -0400 @@ -60,4 +60,122 @@ </when> </conditional> </macro> + + <macro name="normalization_kernel_hash_radius_dist_vertex"> + <param name="no_normalization" type="boolean" label="Skip normalization" truevalue="--no_normalization" falsevalue="" checked="false" /> + <param name="min_kernel" type="boolean" label="Use min kernel" truevalue="--min_kernel" falsevalue="" checked="false" /> + + <param name="hash_bit_size" type="integer" value="15" label="Bit size of the used hashing function" help=""> + <validator type="in_range" min="1" /> + </param> + <param name="radius" type="integer" value="2" label="Radius that defines a neighborhood" help=""> + <validator type="in_range" min="1" /> + </param> + <param name="distance" type="integer" value="5" label="Distance that defines a neighborhood" help=""> + <validator type="in_range" min="1" /> + </param> + <param name="vertex_degree_threshold" type="integer" value="7" label="Vertex degree threshold" help=""> + <validator type="in_range" min="1" /> + </param> + </macro> + + <macro name="graph_types"> + <param name="graph_type" type="select" display="radio" label="Type of Graph"> + <option value="DIRECTED">directed</option> + <option value="UNDIRECTED">undirected</option> + </param> + </macro> + + <xml name="requirements"> + <requirements> + <requirement type="package" version="1.1">eden</requirement> + <yield /> + </requirements> + <!--<version_command>EDeN -version</version_command>--> + </xml> + + <macro name="kernel_type_options"> + <conditional name="kernel_type_opts"> + <param name="kernel_type_opts_selector" type="select" label="Type of the Kernel"> + <option value="NSPDK">NSPDK</option> + <option value="WDK">WDK</option> + <option value="PBK">PBK</option> + <option value="USPK">USPK</option> + <option value="DDK">DDK</option> + <option value="NSDDK">ANSDDK</option> + <option value="SK">SK [NSPDK]</option> + </param> + <when value="NSPDK" /> + <when value="WDK" /> + <when value="PBK" /> + <when value="USPK" /> + <when value="SK"> + <param name="radius_two" type="integer" value="2" label="Radius Two" help=""> + <validator type="in_range" min="1" /> + </param> + <param name="tree_lambda" type="float" value="1.2" label="Tree lambda" help=""> + <validator type="in_range" min="0.0" /> + </param> + </when> + <when value="DDK"> + <param name="radius_two" type="integer" value="2" label="Radius Two" help=""> + <validator type="in_range" min="1" /> + </param> + <param name="tree_lambda" type="float" value="1.2" label="Tree lambda" help=""> + <validator type="in_range" min="0.0" /> + </param> + </when> + <when value="NSDDK"> + <param name="radius_two" type="integer" value="2" label="Radius Two" help=""> + <validator type="in_range" min="1" /> + </param> + <param name="tree_lambda" type="float" value="1.2" label="Tree lambda" help=""> + <validator type="in_range" min="0.0" /> + </param> + </when> + </conditional> + </macro> + + <token name="@normalization_kernel_hash_radius_dist_vertex@"> + $no_normalization + $min_kernel + + --hash_bit_size $hash_bit_size + --radius $radius + --distance $distance + --vertex_degree_threshold $vertex_degree_threshold + </token> + + <token name="@input_smooth_conditional@"> + #if $smooth_opts.smooth_opts_selector == 'smooth': + --smooth + --smooth_param $smooth_opts.smoother_param + + --row_index_file_name $row_index_file_name + --col_index_file_name $col_index_file_name + --num_hash_functions $smooth_opts.num_hash_functions + --num_repeat_hash_functions $smooth_opts.num_repeat_hash_functions + --max_size_bin $smooth_opts.max_size_bin + --eccess_neighbour_size_factor $smooth_opts.eccess_neighbour_size_factor + --num_nearest_neighbours $smooth_opts.num_nearest_neighbours + $smooth_opts.shared_neighborhood + $smooth_opts.no_neighborhood_cache + $smooth_opts.no_minhash_cache + #end if + </token> + + <token name="@kernel_type_options@"> + #if $kernel_type_opts.kernel_type_opts_selector in ['DDK','NSDDK','SK']: + --tree_lambda $kernel_type_opts.tree_lambda + --radius_two $kernel_type_opts.radius_two + #end if + </token> + + <token name="@references@"> +This tool is part of the EDeN (Explicit Decomposition with Neighborhoods) suite, developed by Fabrizio Costa. + </token> + + + + </macros>
--- a/mol2gspan.py Thu Sep 05 12:52:45 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,43 +0,0 @@ -#!/usr/bin/env python - -import os, sys -import argparse - -def main(args ): - - begin = True - iid = 0 - graph_counter = 1 - - for line in args.infile: - if line.rstrip(): - if line.strip().endswith('END'): - begin = False - elif line.strip() == '$$$$': - graph_counter += 1 - iid = 0 - else: - # found header line, like: 21 21 0 0 0 0 0 0 0 0999 V2000 - if len(line.split()) >= 5 and line.split()[-1] == 'V2000': - args.outfile.write('t # id %s\n' % graph_counter) - begin=True - continue - # connection or coordinate/atom table - if len(line.split()) >= 4 and begin: - # coordinate/atom table - if line.split()[3].isalpha(): - args.outfile.write( 'v %s %s \n' % (iid, line.split()[3]) ) - iid += 1 - else: - #connection table - id, node, edge, trash = line.split(None, 3) - args.outfile.write( 'e %s %s %s\n' % ( int(id) - 1 , int(node) -1, edge ) ) - -if __name__ == "__main__": - parser = argparse.ArgumentParser() - parser.add_argument('--infile', nargs='?', type=argparse.FileType('r'), - default=sys.stdin, help="Specify one or more input files") - parser.add_argument('--outfile', type=argparse.FileType('w'), - default=sys.stdout, help="Specify one output file") - args = parser.parse_args() - main( args )
--- a/mol2gspan.xml Thu Sep 05 12:52:45 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,32 +0,0 @@ -<tool id="bg_mol2gspan" name="Molecule to gSpan" version="0.1"> - <description>converter</description> - <requirements> - <requirement type="package" version="2.3.2">openbabel</requirement> - <requirement type="set_environment">EDEN_SCRIPT_PATH</requirement> - </requirements> - <command> - obabel -i smi -o sdf $infile | \$EDEN_SCRIPT_PATH/mol2gspan.py --infile - --outfile $outfile - </command> - <inputs> - <param format="smi,sdf,mol,inchi,mol2" name="infile" type="data" - label="Input molecules" help=""/> - </inputs> - <outputs> - <data format="gspan" name="outfile" label="gSpan from ${on_string}"/> - </outputs> - <tests> - <test> - <param name="infile" value="3_molceuls.sdf" /> - <output name="outfile" file="3_molecules.gspan" /> - </test> - </tests> - <help> - -.. class:: infomark - -**What it does** - -That converter will convert arbitratry molecule files to the gSpan format. - - </help> -</tool>
--- a/tool_dependencies.xml Thu Sep 05 12:52:45 2013 -0400 +++ b/tool_dependencies.xml Tue Oct 29 11:07:49 2013 -0400 @@ -1,9 +1,6 @@ <?xml version="1.0"?> <tool_dependency> - <package name="openbabel" version="2.3.2"> - <repository changeset_revision="7601c962048a" name="package_openbabel_2_3" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + <package name="eden" version="1.1"> + <repository changeset_revision="25d3b2b5b677" name="package_eden_1_1" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu" /> </package> - <set_environment version="1.0"> - <environment_variable action="set_to" name="EDEN_SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable> - </set_environment> </tool_dependency>