From 6859f36c8c3c4ba9ae378e9ff5e12ce6e5496d33 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Fri, 23 May 2008 20:38:01 +0000
Subject: [PATCH] Update nowarn Options for GMAJ tool.

---
 tools/visualization/GMAJ.xml | 96 ++++++++++++++++++------------------
 1 file changed, 47 insertions(+), 49 deletions(-)

diff --git a/tools/visualization/GMAJ.xml b/tools/visualization/GMAJ.xml
index 6c94cac605b..0afb7e2f175 100644
--- a/tools/visualization/GMAJ.xml
+++ b/tools/visualization/GMAJ.xml
@@ -3,55 +3,6 @@
   <command interpreter="python">GMAJ.py $out_file1 $maf_input $gmaj_file $filenames_file</command>
   <inputs>
       <param name="maf_input" type="data" format="maf" label="Alignment File" optional="False"/>
-      <param name="nowarn" type="drill_down" display="checkbox" hierarchy="recurse" multiple="true" label="Choose Warnings to Suppress" separator=" " help="These do not affect behavior, only suppress warning messages.">
-        <options>    
-          <option name="All" value="all">
-            <option name="MAF File" value="maf">
-              <option name="Invalid Version (maf_version)" value="maf_version"/>
-              <option name="Invalid Paragraph (maf_paragraph)" value="maf_paragraph"/>
-              <option name="Reconstruction Annotations Missing Sequence (recon_noseq)" value="recon_noseq"/>
-              <option name="Reconstruction Annotations Missing Row (recon_missing)" value="recon_missing"/>
-              <option name="Missing MAF File (unused_maf)" value="unused_maf"/>
-            </option>
-            <option name="Annotation Files" value="annotations">
-              <option name="Semantic Assumptions" value="semantics">
-                <option name="BED Format" value = "bed">
-                  <option name="BED12 Blocks are exons (bed_blocks)" value="bed_blocks"/>
-                  <option name="BED ThickStart/End are CDS (bed_thick)" value="bed_thick"/>
-                  <option name="BED name is Gene Name when loading exons for gene BED (bed_name)" value="bed_name"/>
-                  <option name="BED name used as prefix when loading exons for exon BED (bed_name_prefix)" value="bed_name_prefix"/>
-                  <option name="Using full BED name as gene when loading exons using entire region (bed_name_full)" value="bed_name_full"/>
-                </option>
-                <option name="Using GFF group as gene name (gff_group)" value="gff_group"/>
-              </option>
-              <option name="Skipped Annotations" value="skipped">
-                <option name="Unrecognized Format (annot_format)" value="annot_format"/>
-                <option name="Skip lines with no gene name (gene_missing)" value="gene_missing"/>
-                <option name="Skip lone start/stop codons when strand is unknown (ambiguous_codon)" value="ambiguous_codon"/>
-                <option name="Ignore unrecognized repeats (unrec_repeat)" value="unrec_repeat"/>
-                <option name="Use 'other' for repeat type when unavailable (repeat_type_missing)" value="repeat_type_missing"/>
-                <option name="Ignore invalid strands (bad_strand)" value="bad_strand"/>
-                <option name="Ignore Invalid scores (bad_score)" value="bad_score"/>
-                <option name="Bad color specification (color_format)" value="color_format"/>
-                <option name="use Score shading is not yet supported (score_shading)" value="score_shading"/>
-                <option name="Ignoring malformed URLs (bad_url)" value="bad_url"/>
-              </option>
-              <option name="Red Flags" value="red">
-                <option name="Sequence name in annotation file does not match (seqname_mismatch)" value="seqname_mismatch"/>
-                <option name="Start or end &lt; 1" value="lessthanone">
-                  <option name="BED (bed_coord)" value="bed_coord"/>
-                  <option name="GFF (gff_coord)" value="gff_coord"/>
-                </option>
-                <option name="Missing item name for URL substitution (url_subst)" value="url_subst"/>
-              </option>
-            </option>
-            <option name="Miscellaneous" value="miscellaneous">
-              <option name="Tokens end with an escaped quote (escaped_quote)" value="escaped_quote"/>
-              <option name="Draggable panel dividers cannot be made sticky (no_sticky)" value="no_sticky"/>
-            </option>
-          </option>
-        </options>
-      </param>
       <repeat name="annotations" title="Annotations">
         <param name="species" type="select" label="Species of Annotation" multiple="False">
           <options>
@@ -66,6 +17,53 @@
         <param name="links_file" type="data" format="bed,gff" label="Links File" optional="True"/>
         <param name="offset" label="Offset" value="0" type="integer"/>
       </repeat>
+      <param name="nowarn" type="drill_down" display="checkbox" hierarchy="recurse" multiple="true" label="Choose Warnings to Suppress" separator=" " help="These do not affect behavior, only suppress warning messages.">
+        <options>    
+          <option name="All" value="all">
+            <option name="MAF File" value="maf">
+              <option name="Invalid MAF version (maf_version)" value="maf_version"/>
+              <option name="Skipping unsupported paragraph (maf_paragraph)" value="maf_paragraph"/>
+              <option name="Skipping all reconstruction scores: no species specified (recon_noseq)" value="recon_noseq"/>
+              <option name="Skipping reconstruction scores in blocks with missing row (recon_missing)" value="recon_missing"/>
+              <option name="Skipping extra MAF File (unused_maf)" value="unused_maf"/>
+            </option>
+            <option name="Annotation Files" value="annotations">
+              <option name="Semantic Assumptions" value="semantics">
+                <option name="BED Format" value = "bed">
+                  <option name="BED12 blocks are exons (bed_blocks)" value="bed_blocks"/>
+                  <option name="BED thickstart/thickend designate CDS (bed_thick)" value="bed_thick"/>
+                  <option name="BED name is gene name when loading exons from BED12 (bed_name)" value="bed_name"/>
+                  <option name="BED name is gene name when loading exons from exon BED (bed_name_full)" value="bed_name_full"/>
+                  <option name="BED name's prefix is gene name when loading exons from exon BED (bed_name_prefix)" value="bed_name_prefix"/>
+                </option>
+                <option name="GFF group is gene name (gff_group)" value="gff_group"/>
+              </option>
+              <option name="Skipped Items" value="skipped">
+                <option name="Skipping lines in unrecognized format (annot_format)" value="annot_format"/>
+                <option name="Skipping lines with no gene name when loading exons (gene_missing)" value="gene_missing"/>
+                <option name="Skipping lone CDS start/stop codons when strand is unknown (ambiguous_codon)" value="ambiguous_codon"/>
+                <option name="Skipping lines with invalid repeat types (unrec_repeat)" value="unrec_repeat"/>
+                <option name="Using 'Other' for missing or incomplete repeat types (repeat_type_missing)" value="repeat_type_missing"/>
+                <option name="Ignoring invalid strand fields (bad_strand)" value="bad_strand"/>
+                <option name="Ignoring invalid score fields (bad_score)" value="bad_score"/>
+                <option name="Ignoring invalid color fields (color_format)" value="color_format"/>
+                <option name="Ignoring malformed URLs (bad_url)" value="bad_url"/>
+                <option name="Score shading is not yet supported (score_shading)" value="score_shading"/>
+              </option>
+              <option name="Red Flags" value="red">
+                <option name="Sequence name in annotation file does not match name in MAF (seqname_mismatch)" value="seqname_mismatch"/>
+                <option name="BED Start or end &lt; (bed_coord)" value="bed_coord"/>
+                <option name="GFF Start or end &lt; (gff_coord)" value="gff_coord"/>
+                <option name="Missing item name for URL substitution (url_subst)" value="url_subst"/>
+              </option>
+            </option>
+            <option name="Miscellaneous" value="miscellaneous">
+              <option name="Possible parse error: token ends with an escaped quote (escaped_quote)" value="escaped_quote"/>
+              <option name="Draggable panel dividers will not be sticky (no_sticky)" value="no_sticky"/>
+            </option>
+          </option>
+        </options>
+      </param>
   </inputs>
   <configfiles>
     <configfile name="gmaj_file">#:gmaj