Mercurial > repos > bernhardlutz > rest_tool
view rest_tool_alt.xml @ 6:9ee84d9fd3a7 draft
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author | bernhardlutz |
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date | Thu, 03 Apr 2014 06:50:57 -0400 |
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<tool id="rest_tool" name="Fetch Data from pubchem" version="0.1.0"> <description>Fetch pubchem data</description> <version_command>echo "0.1.0"</version_command> <requirements> <requirement type="set_environment">REST_TOOL_SCRIPT_PATH</requirement> </requirements> <command interpreter="python"> #if $choose_action.action == 'specific_data': rest_tool.py #if $choose_action.field_or_file1.field_or_file1 == 'field': --id $choose_action.field_or_file1.id1 #else: --idfile $choose_action.field_or_file1.file_ids_1 #end if --type $choose_action.input_type --operation $choose_action.operation_property.operation #if $choose_action.operation_property.operation == 'property': --property-value $choose_action.operation_property.property #end if --outfile $output #elif $choose_action.action == 'compounds_for_assay': rest_tool_comp_for_assay.py #if $choose_action.field_or_file2.field_or_file2 == 'field': --aid $choose_action.field_or_file2.id2 #else: --aidfile $choose_action.field_or_file2.file_ids_2 #end if --outfile $output #elif $choose_action.action == 'assays_by_activity': rest_tool_assay_by_activity_or_target.py --activity $choose_action.activity --outfile $output #elif $choose_action.action == 'assays_by_targets': rest_tool_assay_by_activity_or_target.py --targettype $choose_action.target_identifier_type --targetid $choose_action.target_id --outfile $output #end if </command> <inputs> <conditional name="choose_action"> <param name="action" multiple="false" type="select" label="Choose action"> <option value="specific_data">Get Data for specific a/some Assay/Compound/Substance</option> <option value="compounds_for_assay">Get all compound IDs to given BioAssay IDs</option> <option value="assays_by_activity">Get BioAssay IDs with compound IDs given activity/target</option> </param> <when value="specific_data"> <conditional name="choose_acs"> <param name="input_type" multiple="false" type="select" label="Input Type"> <option value="assay">BioAssay</option> <option value="compound">Compound</option> <option value="substance">Substance</option> </param> <when value="assay"> <conditional name="field_or_file1"> <param name="field_or_file1" multiple="false" type="select" label="Specify the ID by"> <option value="field" selected="True">Textfield</option> <option value="file">File</option> </param> <when value="field"> <param format="txt" name="id1" type="text" label="Enter the ID(s)" /> </when> <when value="assay"> <param format="txt,csv" name="file_ids_1" type="data" label="Give the file" /> </when> </conditional> </when> <when value="assay"> <conditional name="operation_property"> <param name="operation" type="select" multiple="false" label="Operation"> <option value="cids">CIDs</option> <option value="sids">SIDs</option> <option value="record">Record</option> <option value="classification">Classification</option> <option value="property">Property</option> <option value="description">Discription</option> <option value="summary">Summary</option> </param> <when value="property"> <param name="property" label="Specify Property" type="text" /> </when> </conditional> </when> <when value="compound"> <conditional name="operation_property"> <param name="operation" type="select" multiple="false" label="Operation"> <option value="aids">AIDs</option> <option value="sids">SIDs</option> <option value="assaysummary">Assaysummary</option> <option value="synonyms">Synonyms</option> <option value="record">Record</option> <option value="classification">Classification</option> <option value="property">Property</option> <option value="description">Discription</option> </param> <when value="property"> <param name="property" label="Specify Property" type="text" /> </when> </conditional> </when> <when value="substance"> <conditional name="operation_property"> <param name="operation" type="select" multiple="false" label="Operation"> <option value="cids">CIDs</option> <option value="sids">SIDs</option> <option value="assaysummary">Assaysummary</option> <option value="synonyms">Synonyms</option> <option value="record">Record</option> <option value="classification">Classification</option> <option value="property">Property</option> <option value="description">Discription</option> </param> <when value="property"> <param name="property" label="Specify Property" type="text" /> </when> </conditional> </when> </conditional> </when> <when value="compounds_for_assay"> <conditional name="field_or_file2"> <param name="field_or_file2" multiple="false" type="select" label="Specify the ID by"> <option value="field">Textfield</option> <option value="file">File</option> </param> <when value="field"> <param format="txt" name="id2" type="text" label="Enter the ID(s)" /> </when> <when value="file"> <param format="txt,csv" name="file_ids_2" type="data" label="Give the file" /> </when> </conditional> </when> <when value="assays_by_activity"> <param format="txt" name="activity" type="text" label="Enter the activity " /> </when> <when value="assays_by_targets"> <param name="target_identifier_type" multiple="false" type="select" label="Choose target identifier"> <option value="gi">GI</option> <option value="geneid">Gene ID</option> <option value="genesymbol">Gene Symbol</option> </param> <param format="txt" name="target_id" type="text" label="Enter the target" /> </when> </conditional> </inputs> <outputs> <data format="csv" name="output" /> </outputs> <tests> </tests> <help> **What it does** This tool fetches data from pubchem </help> </tool>