Mercurial > repos > bernhardlutz > rest_tool
diff rest_tool.xml @ 6:9ee84d9fd3a7 draft
Uploaded
| author | bernhardlutz |
|---|---|
| date | Thu, 03 Apr 2014 06:50:57 -0400 |
| parents | |
| children | 3c1e862e8cd6 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rest_tool.xml Thu Apr 03 06:50:57 2014 -0400 @@ -0,0 +1,256 @@ +<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> + <macros> + <import>rest_tool_macros.xml</import> + </macros> + <command interpreter="python"> + #if $choose_action.action == 'search': + rest_tool_search.py --type $choose_action.input_type_search --name $choose_action.search_name --outfile $output + + #elif $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: + --id-file $choose_action.field_or_file1.file_ids_1 + #end if + --type $choose_action.choose_acs.input_type + + #if $choose_action.choose_acs.input_type == 'assay': + --operation $choose_action.choose_acs.operation_assay.operation_assay + #if $choose_action.choose_acs.operation_assay.operation_assay == 'property': + --property-value $choose_action.choose_acs.operation_assay.property_assay + #elif $choose_action.choose_acs.operation_assay.operation_assay == 'aids': + --id-type $choose_action.choose_acs.operation_assay.aids_type_assay + #elif $choose_action.choose_acs.operation_assay.operation_assay == 'cids': + --id-type $choose_action.choose_acs.operation_assay.cids_type_assay + #elif $choose_action.choose_acs.operation_assay.operation_assay == 'sids': + --id-type $choose_action.choose_acs.operation_assay.sids_type_assay + #end if + #elif $choose_action.choose_acs.input_type == 'compound': + --operation $choose_action.choose_acs.operation_compound.operation_compound + #if $choose_action.choose_acs.operation_compound.operation_compound == 'property': + --property-value $choose_action.choose_acs.operation_compound.property_compound + #elif $choose_action.choose_acs.operation_compound.operation_compound == 'aids': + --id-type $choose_action.choose_acs.operation_compound.aids_type_compound + #elif $choose_action.choose_acs.operation_compound.operation_compound == 'cids': + --id-type $choose_action.choose_acs.operation_compound.cids_type_compound + #elif $choose_action.choose_acs.operation_compound.operation_compound == 'sids': + --id-type $choose_action.choose_acs.operation_compound.sids_type_compound + #end if + #else: + --operation $choose_action.choose_acs.operation_substance.operation_substance + #if $choose_action.choose_acs.operation_substance.operation_substance == 'property': + --property-value $choose_action.choose_acs.operation_substance.property_substance + #elif $choose_action.choose_acs.operation_substance.operation_substance == 'aids': + --id-type $choose_action.choose_acs.operation_substance.aids_type_substance + #elif $choose_action.choose_acs.operation_substance.operation_substance == 'cids': + --id-type $choose_action.choose_acs.operation_substance.cids_type_substance + #elif $choose_action.choose_acs.operation_substance.operation_substance == 'sids': + --id-type $choose_action.choose_acs.operation_substance.sids_type_substance + #end if + #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: + --aid-file $choose_action.field_or_file2.file_ids_2 + #end if + --outfile $output + #elif $choose_action.action == 'assays_by_activity_or_target': + rest_tool_assay_by_activity_or_target.py + #if $choose_action.activity_or_target.activity_or_target == 'activity': + --activity $choose_action.activity_or_target.activity + #else: + --target $choose_action.activity_or_target.target_id + --target-type $choose_action.activity_or_target.target_identifier_type + #end if + --outfile $output + + #end if + </command> + + <inputs> + <conditional name="choose_action"> + <param name="action" multiple="false" type="select" label="Choose action"> + <option value="search">Search for Assay/Compound/Substance</option> + <option value="specific_data">Get Data for specific Assay/Compound/Substance</option> + <option value="compounds_for_assay">Get all compound IDs given BioAssay IDs</option> + <option value="assays_by_activity_or_target">Get BioAssay IDs given activity/target</option> + </param> + <when value="search"> + <param name="input_type_search" multiple="false" type="select" label="Search for"> + <option value="assay">BioAssay</option> + <option value="compound">Compound</option> + <option value="substance">Substance</option> + </param> + <param name="input_type" multiple="false" type="select" label="Search By"> + <option value="name">Name</option> + </param> + <param format="txt" name="search_name" type="text" label="Enter the Name" /> + </when> + <when value="specific_data"> + <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="file"> + <param format="txt,csv" name="file_ids_1" type="data" label="Give the file" /> + </when> + </conditional> + <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="operation_assay"> + <param name="operation_assay" type="select" multiple="false" label="Operation"> + <expand macro="aid_cid_sid" /> + <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_assay" label="Specify Property" type="text" /> + </when> + <when value="aids"> + <param name="aids_type_assay" multiple="false" type="select" label="AID Type"> + <expand macro="aids_when_options" /> + </param> + </when> + <when value="cids"> + <param name="cids_type_assay" multiple="false" type="select" label="CID Type"> + <expand macro="aids_when_options" /> + + </param> + </when> + <when value="sids"> + <param name="sids_type_assay" multiple="false" type="select" label="SID Type"> + <expand macro="aids_when_options" /> + <option value="doseresponse">doseresponse</option> + </param> + </when> + </conditional> + </when> + <when value="compound"> + <conditional name="operation_compound"> + <param name="operation_compound" type="select" multiple="false" label="Operation"> + <expand macro="aid_cid_sid" /> + <expand macro="option_compound_substance" /> + <option value="property">Property</option> + </param> + <when value="property"> + <param name="property_compound" label="Specify Property" type="text" /> + </when> + <when value="aids"> + <param name="aids_type_compound" multiple="false" type="select" label="AID Type"> + <expand macro="aids_when_options" /> + </param> + </when> + <when value="sids"> + <param name="sids_type_compound" multiple="false" type="select" label="SID Type"> + + <expand macro="cid_sid_type_options" /> + </param> + </when> + <when value="cids"> + <param name="cids_type_compound" multiple="false" type="select" label="CID Type"> + <expand macro="cid_cid_type_options" /> + </param> + </when> + </conditional> + </when> + <when value="substance"> + <conditional name="operation_substance"> + <param name="operation_substance" type="select" multiple="false" label="Operation"> + <expand macro="aid_cid_sid" /> + <expand macro="option_compound_substance" /> + </param> + <when value="property"> + <param name="property_substance" label="Specify Property" type="text" /> + </when> + <when value="aids"> + <param name="aids_type_substance" multiple="false" type="select" label="AID Type"> + <expand macro="aids_when_options" /> + </param> + </when> + <when value="cids"> + <param name="cids_type_substance" multiple="false" type="select" label="CID Type"> + <expand macro="sid_cid_type_options" /> + </param> + </when> + <when value="sids"> + <param name="sids_type_substance" multiple="false" type="select" label="SID Type"> + <expand macro="sid_sid_type_options" /> + </param> + </when> + + </conditional> + </when> + </conditional> + </when> + <!-- second option --> + <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> + <!-- third option --> + <when value="assays_by_activity_or_target"> + <conditional name="activity_or_target"> + <param name="activity_or_target" multiple="false" type="select" label="Look for"> + <option value="target">Target</option> + <option value="activity">Activity</option> + </param> + <when value="activity"> + <param format="txt" name="activity" type="text" label="Enter the activity" /> + </when> + + <when value="target"> + <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> + </when> + + </conditional> + </inputs> + <outputs> + <data format="csv" name="output" /> + </outputs> + <tests> + </tests> + <help> +**What it does** + +This tool fetches data from pubchem + </help> +</tool>