rebuild

Author: abretaud

chakin/commands/expression/add_expression.py

@@ -19,14 +19,36 @@
     help="The units associated with the loaded values (ie, FPKM, RPKM, raw counts)",
     type=str
 )
+@click.option(
+    "--query_type",
+    help="The feature type (e.g. 'gene', 'mRNA', 'polypeptide', 'contig') of the query. It must be a valid Sequence Ontology term.",
+    default="mRNA",
+    show_default=True,
+    type=str
+)
+@click.option(
+    "--match_on_name",
+    help="Match features using their name instead of their uniquename",
+    is_flag=True
+)
+@click.option(
+    "--re_name",
+    help="Regular expression to extract the feature name from the input file (first capturing group will be used).",
+    type=str
+)
+@click.option(
+    "--skip_missing",
+    help="Skip lines with unknown features or GO id instead of aborting everything.",
+    is_flag=True
+)
 @pass_context
 @custom_exception
 @str_output
-def cli(ctx, organism_id, analysis_id, file_path, separator="	", unit=""):
+def cli(ctx, organism_id, analysis_id, file_path, separator="	", unit="", query_type="mRNA", match_on_name=False, re_name="", skip_missing=False):
     """Add an expression matrix file to the database
 
 Output:
 
     Number of expression data loaded
     """
-    return ctx.gi.expression.add_expression(organism_id, analysis_id, file_path, separator=separator, unit=unit)
+    return ctx.gi.expression.add_expression(organism_id, analysis_id, file_path, separator=separator, unit=unit, query_type=query_type, match_on_name=match_on_name, re_name=re_name, skip_missing=skip_missing)

docs/commands/expression.rst

@@ -54,11 +54,19 @@ Add an expression matrix file to the database
 **Options**::
 
 
-      --separator TEXT  Separating character in the matrix file (ex : ','). Default
-                        character is tab.  [default:        ]
-      --unit TEXT       The units associated with the loaded values (ie, FPKM, RPKM,
-                        raw counts)
-      -h, --help        Show this message and exit.
+      --separator TEXT   Separating character in the matrix file (ex : ','). Default
+                         character is tab.  [default:        ]
+      --unit TEXT        The units associated with the loaded values (ie, FPKM,
+                         RPKM, raw counts)
+      --query_type TEXT  The feature type (e.g. 'gene', 'mRNA', 'polypeptide',
+                         'contig') of the query. It must be a valid Sequence
+                         Ontology term.  [default: mRNA]
+      --match_on_name    Match features using their name instead of their uniquename
+      --re_name TEXT     Regular expression to extract the feature name from the
+                         input file (first capturing group will be used).
+      --skip_missing     Skip lines with unknown features or GO id instead of
+                         aborting everything.
+      -h, --help         Show this message and exit.
     
 
 ``delete_all_biomaterials`` command

galaxy/expression_add_expression.xml

@@ -17,6 +17,18 @@ chakin expression add_expression
 #if $unit:
   --unit '$unit'
 #end if
+#if $query_type:
+  --query_type '$query_type'
+#end if
+#if $match_on_name:
+  $match_on_name
+#end if
+#if $re_name:
+  --re_name '$re_name'
+#end if
+#if $skip_missing:
+  $skip_missing
+#end if
 
 | jq -S . > $results
 </command>
@@ -29,6 +41,10 @@ chakin expression add_expression
     <!-- options -->
 	<param name="separator" label="Separator" argument="separator" type="text" help="Separating character in the matrix file (ex : ','). Default character is tab." />
 	<param name="unit" label="Unit" argument="unit" type="text" help="The units associated with the loaded values (ie, FPKM, RPKM, raw counts)" />
+	<param name="query_type" label="Query Type" argument="query_type" type="text" help="The feature type (e.g. 'gene', 'mRNA', 'polypeptide', 'contig') of the query. It must be a valid Sequence Ontology term." />
+	<param name="match_on_name" label="Match On Name" argument="match_on_name" type="boolean" truevalue="--match_on_name" falsevalue="" help="Match features using their name instead of their uniquename" />
+	<param name="re_name" label="Re Name" argument="re_name" type="text" help="Regular expression to extract the feature name from the input file (first capturing group will be used)." />
+	<param name="skip_missing" label="Skip Missing" argument="skip_missing" type="boolean" truevalue="--skip_missing" falsevalue="" help="Skip lines with unknown features or GO id instead of aborting everything." />
 
 	</inputs>
 	<outputs>