Merge pull request #2379 from mvdbeek/edam_operations

Add EDAM operations to tools and expose in API

lib/galaxy/tools/__init__.py

@@ -443,6 +443,8 @@ class Tool( object, Dictifiable ):
             else:
                 raise Exception( "Missing tool 'version' for tool with id '%s' at '%s'" % (self.id, tool_source) )
 
+        self.edam_operations = tool_source.parse_edam_operations()
+
         # Support multi-byte tools
         self.is_multi_byte = tool_source.parse_is_multi_byte()
         # Legacy feature, ignored by UI.
@@ -1539,6 +1541,8 @@ class Tool( object, Dictifiable ):
         # Basic information
         tool_dict = super( Tool, self ).to_dict()
 
+        tool_dict["edam_operations"] = self.edam_operations
+
         # Fill in ToolShedRepository info
         if hasattr(self, 'tool_shed') and self.tool_shed:
             tool_dict['tool_shed_repository'] = {

lib/galaxy/tools/parser/xml.py

@@ -78,6 +78,12 @@ class XmlToolSource(ToolSource):
     def parse_name(self):
         return self.root.get( "name" )
 
+    def parse_edam_operations(self):
+        edam_ops = self.root.find("edam_operations")
+        if edam_ops is None:
+            return []
+        return [ edam_op.text for edam_op in edam_ops.findall("edam_operation") ]
+
     def parse_description(self):
         return xml_text(self.root, "description")
 

lib/galaxy/tools/parser/yaml.py

@@ -33,6 +33,9 @@ class YamlToolSource(ToolSource):
     def parse_description(self):
         return self.root_dict.get("description", "")
 
+    def parse_edam_operations(self):
+        return self.root_dict.get("edam_operations", [])
+
     def parse_is_multi_byte(self):
         return self.root_dict.get("is_multi_byte", self.default_is_multi_byte)
 

test/functional/tools/simple_constructs.yml

@@ -2,6 +2,10 @@ id: simple_constructs_y
 name: simple_constructs_y
 class: GalaxyTool
 version: 1.0
+description: Simple constructs
+edam_operations:
+  - operation_0004
+  - operation_0336
 command:
   >
     echo "$booltest"  >> $out_file1;

tools/filters/axt_to_concat_fasta.xml

@@ -1,5 +1,8 @@
 <tool id="axt_to_concat_fasta" name="AXT to concatenated FASTA" version="1.0.0">
   <description>Converts an AXT formatted file to a concatenated FASTA alignment</description>
+  <edam_operations>
+    <edam_operation>operation_3434</edam_operation>
+  </edam_operations>
   <command interpreter="python">axt_to_concat_fasta.py $dbkey_1 $dbkey_2 &lt; $axt_input &gt; $out_file1</command>
   <inputs>
     <param format="axt" name="axt_input" type="data" label="AXT file"/>

tools/filters/axt_to_fasta.xml

@@ -1,5 +1,8 @@
 <tool id="axt_to_fasta" name="AXT to FASTA" version="1.0.0">
   <description>Converts an AXT formatted file to FASTA format</description>
+  <edam_operations>
+    <edam_operation>operation_3434</edam_operation>
+  </edam_operations>
   <command interpreter="python">axt_to_fasta.py $dbkey_1 $dbkey_2 &lt; $axt_input &gt; $out_file1</command>
   <inputs>
     <param format="axt" name="axt_input" type="data" label="AXT file"/>

tools/filters/axt_to_lav.xml

@@ -1,5 +1,8 @@
 <tool id="axt_to_lav_1" name="AXT to LAV" version="1.0.0">
   <description>Converts an AXT formatted file to LAV format</description>
+  <edam_operations>
+    <edam_operation>operation_3434</edam_operation>
+  </edam_operations>
   <command interpreter="python">axt_to_lav.py /galaxy/data/$dbkey_1/seq/%s.nib:$dbkey_1:${GALAXY_DATA_INDEX_DIR}/shared/ucsc/chrom/${dbkey_1}.len /galaxy/data/$dbkey_2/seq/%s.nib:$dbkey_2:${GALAXY_DATA_INDEX_DIR}/shared/ucsc/chrom/${dbkey_2}.len $align_input $lav_file $seq_file1 $seq_file2</command>
   <inputs>
     <param name="align_input" type="data" format="axt" label="Alignment File" optional="False"/>

tools/filters/bed2gff.xml

@@ -1,5 +1,8 @@
 <tool id="bed2gff1" name="BED-to-GFF" version="2.0.0">
   <description>converter</description>
+  <edam_operations>
+    <edam_operation>operation_3434</edam_operation>
+  </edam_operations>
   <command interpreter="python">bed_to_gff_converter.py $input $out_file1</command>
   <inputs>
     <param format="bed" name="input" type="data" label="Convert this dataset"/>

tools/filters/bed_to_bigbed.xml

@@ -1,6 +1,9 @@
 <tool id="bed_to_bigBed" name="BED-to-bigBed" version="1.0.0">
   <description>converter</description>
-  <command>bedToBigBed $input1 $chromInfo $out_file1 
+  <edam_operations>
+    <edam_operation>operation_3434</edam_operation>
+  </edam_operations>
+  <command>bedToBigBed $input1 $chromInfo $out_file1
     #if $settings.settingsType == "full":
       -blockSize=${settings.blockSize} -itemsPerSlot=${settings.itemsPerSlot} ${settings.unc}
     #end if

tools/filters/gff2bed.xml

@@ -1,5 +1,8 @@
 <tool id="gff2bed1" name="GFF-to-BED" version="1.0.1">
   <description>converter</description>
+  <edam_operations>
+    <edam_operation>operation_3434</edam_operation>
+  </edam_operations>
   <command interpreter="python">gff_to_bed_converter.py $input $out_file1</command>
   <inputs>
     <param format="gff" name="input" type="data" label="Convert this dataset"/>

tools/filters/gtf2bedgraph.xml

@@ -1,5 +1,8 @@
 <tool id="gtf2bedgraph" name="GTF-to-BEDGraph" version="1.0.0">
   <description>converter</description>
+  <edam_operations>
+    <edam_operation>operation_3434</edam_operation>
+  </edam_operations>
   <command interpreter="python">gtf_to_bedgraph_converter.py $input $out_file1 $attribute_name</command>
   <inputs>
     <param format="gtf" name="input" type="data" label="Convert this query"/>

tools/stats/filtering.xml

@@ -1,5 +1,8 @@
 <tool id="Filter1" name="Filter" version="1.1.0">
   <description>data on any column using simple expressions</description>
+  <edam_operations>
+    <edam_operation>operation_0335</edam_operation>
+  </edam_operations>
   <command interpreter="python">
     filtering.py $input $out_file1 "$cond" ${input.metadata.columns} "${input.metadata.column_types}" $header_lines
   </command>