Mercurial > repos > bernhardlutz > rest_tool
diff rest_tool.xml @ 8:3c1e862e8cd6 draft
Uploaded
| author | bernhardlutz |
|---|---|
| date | Fri, 02 May 2014 05:40:28 -0400 |
| parents | 9ee84d9fd3a7 |
| children | 80bf0039c0dc |
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--- a/rest_tool.xml Thu Apr 03 06:51:54 2014 -0400 +++ b/rest_tool.xml Fri May 02 05:40:28 2014 -0400 @@ -6,17 +6,15 @@ </requirements> <macros> <import>rest_tool_macros.xml</import> + <import>rest_tool_macro_advanced.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': + #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 + #if $choose_action.field_or_file.field_or_file_select == 'field': + --id $choose_action.field_or_file.id_value #else: - --id-file $choose_action.field_or_file1.file_ids_1 + --id-file $choose_action.field_or_file.id_value #end if --type $choose_action.choose_acs.input_type @@ -24,43 +22,31 @@ --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 + #elif $choose_action.choose_acs.operation_assay.operation_assay == 'aids' or $choose_action.choose_acs.operation_assay.operation_assay == 'cids' or $choose_action.choose_acs.operation_assay.operation_assay == 'sids': + --id-type $choose_action.choose_acs.operation_assay.ids_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 + #elif $choose_action.choose_acs.operation_compound.operation_compound == 'aids' or $choose_action.choose_acs.operation_compound.operation_compound == 'cids' or $choose_action.choose_acs.operation_compound.operation_compound == 'sids': + --id-type $choose_action.choose_acs.operation_compound.ids_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 + #elif $choose_action.choose_acs.operation_substance.operation_substance == 'aids' or $choose_action.choose_acs.operation_substance.operation_substance == 'cids' or $choose_action.choose_acs.operation_substance.operation_substance == 'sids': + --id-type $choose_action.choose_acs.operation_substance.ids_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 + #if $choose_action.field_or_file.field_or_file_select == 'field': + --aid $choose_action.field_or_file.id_value #else: - --aid-file $choose_action.field_or_file2.file_ids_2 + --aid-file $choose_action.field_or_file.id_value #end if --outfile $output #elif $choose_action.action == 'assays_by_activity_or_target': @@ -72,23 +58,81 @@ --target-type $choose_action.activity_or_target.target_identifier_type #end if --outfile $output - + #elif $choose_action.action == 'advanced': + rest_tool_advanced.py + --outfile $output + --type $choose_action.input_type.input_type_select + --id-type $choose_action.input_type.namespace_id.namespace_id_select + #if $choose_action.input_type.input_type_select == 'assay': + #if $choose_action.input_type.namespace_id.namespace_id_select == 'aid': + --id-type-ff $choose_action.input_type.namespace_id.field_or_file.field_or_file_select + --id-value $choose_action.input_type.namespace_id.field_or_file.id_value + #elif $choose_action.input_type.namespace_id.namespace_id_select == 'target': + --id-value $choose_action.input_type.namespace_id.target_select + #elif $choose_action.input_type.namespace_id.namespace_id_select == 'type': + --id-value $choose_action.input_type.namespace_id.type_select + #elif $choose_action.input_type.namespace_id.namespace_id_select == 'activity': + --id-value $choose_action.input_type.namespace_id.activity_select + #end if + + --operation $choose_action.input_type.operation_assay.operation_assay_select + + #if $choose_action.input_type.operation_assay.operation_assay_select == 'property': + --operation-value $choose_action.input_type.operation_assay.operation_assay_select.property_assay + #elif $choose_action.input_type.operation_assay.operation_assay_select == 'target': + --operation-value $choose_action.input_type.operation_assay.operation_assay_select.target_assay + #elif $choose_action.input_type.operation_assay.operation_assay_select == 'aids' or $choose_action.input_type.operation_assay.operation_assay_select == 'cids' or $choose_action.input_type.operation_assay.operation_assay_select == 'sids': + --ids-operation-type $choose_action.input_type.operation_assay.ids_type_assay + #end if + #elif $choose_action.input_type.input_type_select == 'compound': + #if $choose_action.input_type.namespace_id.namespace_id_select == 'cid' or $choose_action.input_type.namespace_id.namespace_id_select == 'name' or $choose_action.input_type.namespace_id.namespace_id_select == 'smiles' or $choose_action.input_type.namespace_id.namespace_id_select == 'inchi' or $choose_action.input_type.namespace_id.namespace_id_select == 'inchikey' or $choose_action.input_type.namespace_id.namespace_id_select == 'sdf': + --id-type-ff $choose_action.input_type.namespace_id.field_or_file.field_or_file_select + --id-value $choose_action.input_type.namespace_id.field_or_file.id_value + #elif $choose_action.input_type.namespace_id.namespace_id_select == 'xref': + --xref $choose_action.input_type.namespace_id.xref_select + --xref-value $choose_action.input_type.namespace_id.xref_value + #end if + + --operation $choose_action.input_type.operation_compound.operation_compound_select + #if $choose_action.input_type.operation_compound.operation_compound_select == 'property': + --operation-value $choose_action.input_type.operation_compound.property_compound + #elif $choose_action.input_type.operation_compound.operation_compound_select == 'xrefs': + --operation-value $choose_action.input_type.operation_compound.xref_compound + #elif $choose_action.input_type.operation_compound.operation_compound_select == 'aids' or $choose_action.input_type.operation_compound.operation_compound_select == 'cids' or $choose_action.input_type.operation_compound.operation_compound_select == 'sids': + --ids-operation-type $choose_action.input_type.operation_compound.ids_type_compound + #end if + + #elif $choose_action.input_type.input_type_select == 'substance': + #if $choose_action.input_type.namespace_id.namespace_id_select == 'sid' or $choose_action.input_type.namespace_id.namespace_id_select == 'name': + --id-type-ff $choose_action.input_type.namespace_id.field_or_file.field_or_file_select + --id-value $choose_action.input_type.namespace_id.field_or_file.id_value + #elif $choose_action.input_type.namespace_id.namespace_id_select == 'xrefs': + --xref $choose_action.input_type.namespace_id.xref_select + --xref-value $choose_action.input_type.namespace_id.xref_value + #end if + --operation $choose_action.input_type.operation_substance.operation_substance_select + #if $choose_action.input_type.operation_substance.operation_substance_select == 'property': + --operation-value $choose_action.input_type.operation_substance.operation_substance_select.property_substance + #elif $choose_action.input_type.operation_substance.operation_substance_select == 'xref': + --operation-value $choose_action.input_type.operation_substance.xref_substance + #elif $choose_action.input_type.operation_substance.operation_substance_select == 'aids' or $choose_action.input_type.operation_substance.operation_substance_select == 'cids' or $choose_action.input_type.operation_substance.operation_substance_select == 'sids': + --ids-operation-type $choose_action.input_type.operation_substance.ids_type_substance + #end if + #end if #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> + <option value="advanced" selected="True">Advanced</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> + <expand macro="acs_options" /> </param> <param name="input_type" multiple="false" type="select" label="Search By"> <option value="name">Name</option> @@ -96,128 +140,26 @@ <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> + <expand macro="field_or_file" /> <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> + <expand macro="acs_options" /> </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> + <expand macro="conditional_operation_assay" /> </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> + <expand macro="conditional_operation_compound" /> </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> + <expand macro="conditional_operation_substance" /> </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> + <expand macro="field_or_file" /> </when> <!-- third option --> <when value="assays_by_activity_or_target"> @@ -240,7 +182,9 @@ </when> </conditional> </when> - + <when value="advanced"> + <expand macro="advanced2" /> + </when> </conditional> </inputs> <outputs> @@ -251,6 +195,6 @@ <help> **What it does** -This tool fetches data from pubchem +This tool fetches data from pubchem. The outputformat will be if possible csv > txt > xml </help> </tool>