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174 lines
11 KiB
XML
174 lines
11 KiB
XML
<tool id="gmaj_1" name="GMAJ" Version="2.0.1">
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<description>Multiple Alignment Viewer</description>
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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="refseq" label="Reference Sequence" type="select">
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<option value="first" selected="true">First sequence in each block</option>
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<option value="any">Any sequence</option>
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</param>
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<repeat name="annotations" title="Annotations">
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<conditional name="annotation_style">
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<param name="style" type="select" label="Annotation Style" help="If your data is not in a style similar to what is available from Galaxy (and the UCSC table browser), choose 'Basic'.">
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<option value="galaxy" selected="true">Galaxy</option>
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<option value="basic">Basic</option>
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</param>
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<when value="galaxy">
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<param name="species" type="select" label="Species" multiple="False">
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<options>
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<filter type="data_meta" ref="maf_input" key="species" />
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</options>
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</param>
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<param name="exons_file" type="data" format="bed,gff" label="Exons File" optional="True"/>
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<param name="highlights_file" type="data" format="bed,gff" label="Highlights File" optional="True"/>
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<param name="underlays_file" type="data" format="bed,gff" label="Underlays File" optional="True"/>
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<param name="repeats_file" type="data" format="bed,gff" label="Repeats File" optional="True"/>
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<param name="links_file" type="data" format="bed,gff" label="Links File" optional="True"/>
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</when>
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<when value="basic">
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<param name="seq_name" label="Full Sequence Name" value="" type="text">
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<validator type="empty_field" message="You must supply the sequence name"/>
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</param>
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<param name="exons_file" type="data" format="bed,gff" label="Exons File" optional="True"/>
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<param name="highlights_file" type="data" format="bed,gff" label="Highlights File" optional="True"/>
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<param name="underlays_file" type="data" format="bed,gff" label="Underlays File" optional="True"/>
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<param name="repeats_file" type="data" format="bed,gff" label="Repeats File" optional="True"/>
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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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</when>
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</conditional>
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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="The first row in some blocks is not the specified reference sequence (refseq_not_first)" value="refseq_not_first"/>
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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 < 0 (bed_coord)" value="bed_coord"/>
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<option name="GFF start or end < 1 (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="No refseq specified; assuming 'first' (default_refseq)" value="default_refseq"/>
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<option name="One or more bundle entries are not used in parameters file(unused_entry)" value="unused_entry"/>
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<option name="Skipping blocks for export where reference sequence is hidden or all gaps (export_skip)" value="export_skip"/>
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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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title = "Galaxy: $maf_input.name"
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alignfile = input.maf
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refseq = $refseq
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tabext = .bed .gff .gtf
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#if $nowarn.value:
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nowarn = $nowarn
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#end if
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#set $seq_count = 0
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#for $annotation_count, $annotation in $enumerate( $annotations ):
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#if $annotation.annotation_style.style == "galaxy":
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#if $maf_input.dataset.metadata.species_chromosomes and $annotation.annotation_style['species'].value in $maf_input.dataset.metadata.species_chromosomes and $maf_input.dataset.metadata.species_chromosomes[$annotation.annotation_style['species'].value]:
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#set $seq_names = [ "%s.%s" % ( $annotation.annotation_style['species'].value, $chrom ) for $chrom in $maf_input.dataset.metadata.species_chromosomes[$annotation.annotation_style['species'].value]]
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#else:
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#set $seq_names = [$annotation.annotation_style['species']]
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#end if
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#else:
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#set $seq_names = [$annotation.annotation_style['seq_name']]
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#end if
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#for $seq_name in $seq_names:
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seq ${seq_count}:
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seqname = $seq_name
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#if $annotation.annotation_style['exons_file'].dataset:
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exons = ${annotation_count}.exons.${annotation.annotation_style['exons_file'].extension}
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#end if
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#if $annotation.annotation_style['repeats_file'].dataset:
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repeats = ${annotation_count}.repeats.${annotation.annotation_style['repeats_file'].extension}
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#end if
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#if $annotation.annotation_style['links_file'].dataset:
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links = ${annotation_count}.links.${annotation.annotation_style['links_file'].extension}
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#end if
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#if $annotation.annotation_style['underlays_file'].dataset:
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underlays = ${annotation_count}.underlays.${annotation.annotation_style['underlays_file'].extension}
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#end if
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#if $annotation.annotation_style['highlights_file'].dataset:
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highlights = ${annotation_count}.highlights.${annotation.annotation_style['highlights_file'].extension}
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#end if
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#if $annotation.annotation_style.style == "basic":
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offset = $annotation.annotation_style['offset']
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#end if
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#set $seq_count = $seq_count + 1
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#end for
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#end for
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</configfile>
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<configfile name="filenames_file">
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#for $annotation_count, $annotation in $enumerate( $annotations ):
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#if $annotation.annotation_style['exons_file'].dataset:
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$annotation.annotation_style['exons_file'] = ${annotation_count}.exons.${annotation.annotation_style['exons_file'].extension}
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#end if
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#if $annotation.annotation_style['repeats_file'].dataset:
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$annotation.annotation_style['repeats_file'] = ${annotation_count}.repeats.${annotation.annotation_style['repeats_file'].extension}
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#end if
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#if $annotation.annotation_style['links_file'].dataset:
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$annotation.annotation_style['links_file'] = ${annotation_count}.links.${annotation.annotation_style['links_file'].extension}
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#end if
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#if $annotation.annotation_style['underlays_file'].dataset:
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$annotation.annotation_style['underlays_file'] = ${annotation_count}.underlays.${annotation.annotation_style['underlays_file'].extension}
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#end if
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#if $annotation.annotation_style['highlights_file'].dataset:
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$annotation.annotation_style['highlights_file'] = ${annotation_count}.highlights.${annotation.annotation_style['highlights_file'].extension}
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#end if
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#end for
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</configfile>
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</configfiles>
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<outputs>
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<data name="out_file1" format="gmaj.zip"/>
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</outputs>
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<help>
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You can use this tool to view a set of MAF alignments. You may also include optional annotation data for one or more of the organisms.
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For detailed information on GMAJ, click here_.
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.. _here: /static/gmaj/docs/gmaj_readme.html
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Gmaj is a tool for viewing and manipulating Generalized Multiple Alignments (GMAs) produced by programs such as TBA (though it can also be used with maf-format alignments from other sources). It can display interactive graphical and text representations of the alignments, a diagram showing the locations of exons and repeats, and other annotations -- all with the user's choice of reference sequence.
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</help>
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</tool> |