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