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Update GMAJ tool to allow the specifying of annotations in two styles.
This commit is contained in:
Daniel Blankenberg
@@ -1,21 +1,40 @@
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<tool id="gmaj_1" name="GMAJ" Version="2.0.0">
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<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" value="" type="text" help="Leave empty to allow interactive selection."/>
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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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<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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<param name="offset" label="Offset" value="0" type="integer"/>
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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 of Annotation" 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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<param name="offset" label="Offset" value="0" type="integer"/>
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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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@@ -81,52 +100,59 @@ nowarn = $nowarn
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#end if
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#set $seq_count = 0
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#for $spec_count, $annotation in $enumerate( $annotations ):
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#if $maf_input.metadata.species_chromosomes and $annotation['species'].value in $maf_input.metadata.species_chromosomes and $maf_input.metadata.species_chromosomes[$annotation['species'].value]:
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#set $seq_names = [ "%s.%s" % ( $annotation['species'].value, $chrom ) for $chrom in $maf_input.metadata.species_chromosomes[$annotation['species'].value]]
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#else
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#set $seq_names = [$annotation['species'].value]
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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.metadata.species_chromosomes and $annotation.annotation_style['species'].value in $maf_input.metadata.species_chromosomes and $maf_input.metadata.species_chromosomes[$annotation.annotation_style['species'].value]:
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#set $seq_names = [ "%s.%s" % ( $annotation.annotation_style['species'].value, $chrom ) for $chrom in $maf_input.metadata.species_chromosomes[$annotation.annotation_style['species'].value]]
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#set $aliases = [ " %s" % $chrom for $chrom in $maf_input.metadata.species_chromosomes[$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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#set $aliases = [""]
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#end if
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#for $seq_name in $seq_names:
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#else:
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#set $seq_names = [$annotation.annotation_style['seq_name']]
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#set $aliases = [""]
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#end if
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#for $seq_name, $alias in $zip( $seq_names, $aliases ):
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seq ${seq_count}:
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seqname = $seq_name
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#if $annotation['exons_file'].dataset:
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exons = ${spec_count}.exons.${annotation['exons_file'].extension}
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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}$alias
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#end if
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#if $annotation['repeats_file'].dataset:
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repeats = ${spec_count}.repeats.${annotation['repeats_file'].extension}
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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}$alias
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#end if
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#if $annotation['links_file'].dataset:
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links = ${spec_count}.links.${annotation['links_file'].extension}
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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}$alias
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#end if
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#if $annotation['underlays_file'].dataset:
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underlays = ${spec_count}.underlays.${annotation['underlays_file'].extension}
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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}$alias
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#end if
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#if $annotation['highlights_file'].dataset:
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highlights = ${spec_count}.highlights.${annotation['highlights_file'].extension}
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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}$alias
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#end if
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offset = $annotation['offset']
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offset = $annotation.annotation_style['offset']
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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 $spec_count, $annotation in $enumerate( $annotations ):
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#if $annotation['exons_file'].dataset:
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$annotation['exons_file'] = ${spec_count}.exons.${annotation['exons_file'].extension}
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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 $annotation['repeats_file'].dataset:
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$annotation['repeats_file'] = ${spec_count}.repeats.${annotation['repeats_file'].extension}
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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 $annotation['links_file'].dataset:
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$annotation['links_file'] = ${spec_count}.links.${annotation['links_file'].extension}
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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 $annotation['underlays_file'].dataset:
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$annotation['underlays_file'] = ${spec_count}.underlays.${annotation['underlays_file'].extension}
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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 $annotation['highlights_file'].dataset:
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$annotation['highlights_file'] = ${spec_count}.highlights.${annotation['highlights_file'].extension}
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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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