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Add additional nowarn parameter options to GMAJ.

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Daniel Blankenberg
2008-05-22 17:20:09 +00:00
parent 094790f164
commit 69116c95b1
1 changed files with 45 additions and 8 deletions
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tools/visualization/GMAJ.xml
+45 -8
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@@ -3,15 +3,52 @@
<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=" ">
<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" selected="True">
<option name="seqname_mismatch" value="seqname_mismatch"/>
<option name="bed_blocks" value="bed_blocks"/>
<option name="bed_thick" value="bed_thick"/>
<option name="bed_name" value="bed_name"/>
<option name="repeat_type_missing" value="repeat_type_missing"/>
<option name="bed_name_prefix" value="bed_name_prefix"/>
<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>