[hg] galaxy 1559: Added Validator to a bunch of tools..

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[hg] galaxy 1559: Added Validator to a bunch of tools..

Nate Coraor (nate@bx.psu.edu)
details:   http://www.bx.psu.edu/hg/galaxy/rev/f802eb92a49a
changeset: 1559:f802eb92a49a
user:      guru
date:      Fri Oct 17 13:02:26 2008 -0400
description:
Added Validator to a bunch of tools..

3 file(s) affected in this change:

tools/extract/liftOver_wrapper.xml
tools/extract/phastOdds/phastOdds_tool.xml
tools/stats/aggregate_binned_scores_in_intervals.xml

diffs (58 lines):

diff -r f5b051c51295 -r f802eb92a49a tools/extract/liftOver_wrapper.xml
--- a/tools/extract/liftOver_wrapper.xml Fri Oct 17 10:46:29 2008 -0400
+++ b/tools/extract/liftOver_wrapper.xml Fri Oct 17 13:02:26 2008 -0400
@@ -3,7 +3,8 @@
   <command interpreter="python">liftOver_wrapper.py $input "$out_file1" "$out_file2" $dbkey $to_dbkey</command>
   <inputs>
     <param format="interval" name="input" type="data" label="Convert coordinates of">
-      <validator type="unspecified_build" />
+      <validator type="unspecified_build" />
+      <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="Liftover mappings are currently not available for the specified build." />
     </param>
     <param name="to_dbkey" type="select" label="To">
       <options from_file="liftOver.loc">
@@ -11,7 +12,7 @@
         <column name="value" index="2"/>
         <column name="dbkey" index="0"/>
         <filter type="data_meta" ref="input" key="dbkey" column="0" />
-      </options>
+      </options>
     </param>
   </inputs>
   <outputs>
@@ -39,11 +40,7 @@
 
 .. class:: warningmark
 
-The **To** list will be empty if we don't carry any liftover mappings corresponding to the genome build of the input dataset.
-
-.. class:: warningmark
-
-This tool will only work on interval datasets with chromosome in column 1, start co-ordinate in column 2 and end co-ordinate in column 3. If this is not the case, it will return empty output datasets.
+This tool will only work on interval datasets with chromosome in column 1, start co-ordinate in column 2 and end co-ordinate in column 3. If this is not the case with any line of the input dataset, the tool will return empty output datasets.
 
 -----
 
diff -r f5b051c51295 -r f802eb92a49a tools/extract/phastOdds/phastOdds_tool.xml
--- a/tools/extract/phastOdds/phastOdds_tool.xml Fri Oct 17 10:46:29 2008 -0400
+++ b/tools/extract/phastOdds/phastOdds_tool.xml Fri Oct 17 13:02:26 2008 -0400
@@ -4,6 +4,7 @@
   <inputs>
     <param format="interval" name="input" type="data" label="Interval file">
       <validator type="unspecified_build" message="Unspecified build, this tool works with data from genome builds hg17. Click the pencil icon in your history item to set the genome build."/>
+      <validator type="dataset_metadata_in_file" filename="phastOdds.loc" metadata_name="dbkey" metadata_column="0" message="Sequences are currently unavailable for the specified build." />
     </param>
     <param name="score_file" type="select" label="Available datasets">
       <options from_file="phastOdds.loc">
diff -r f5b051c51295 -r f802eb92a49a tools/stats/aggregate_binned_scores_in_intervals.xml
--- a/tools/stats/aggregate_binned_scores_in_intervals.xml Fri Oct 17 10:46:29 2008 -0400
+++ b/tools/stats/aggregate_binned_scores_in_intervals.xml Fri Oct 17 13:02:26 2008 -0400
@@ -8,6 +8,8 @@
   <inputs>
     <param format="interval" name="input1" type="data" label="Interval file">
       <validator type="unspecified_build" message="Unspecified build, this tool works with data from genome builds hg16, hg17 or hg18. Click the pencil icon in your history item to set the genome build."/>
+      <validator type="dataset_metadata_in_file" filename="binned_scores.loc" metadata_name="dbkey" metadata_column="0" message="Data is currently not available for the specified build." />
+      
     </param>
     <conditional name="score_source_type">
       <param name="score_source" type="select" label="Score Source">