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Add a new metadata type of Metadata Files.

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These are now used to store the list of chromosomes for species as well as the index for MAF files.

MAF tools have been enhanced to make use of index files when available.

TODO: When datasets are purged from disk, these files should also be purged.
This commit is contained in:
Daniel Blankenberg
2008-10-22 13:49:22 -04:00
parent 53008a413d
commit b9e242e4eb
23 changed files with 222 additions and 61 deletions
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tools/visualization/GMAJ.xml
+17 -5
View File
@@ -2,7 +2,9 @@
<description>Multiple Alignment Viewer</description>
<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="maf_input" type="data" format="maf" label="Alignment File" optional="False">
<validator type="metadata" check="species_chromosomes" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/>
</param>
<param name="refseq" label="Reference Sequence" type="select">
<option value="first" selected="true">First sequence in each block</option>
<option value="any">Any sequence</option>
@@ -103,9 +105,19 @@ nowarn = $nowarn
#set $seq_count = 0
#for $annotation_count, $annotation in $enumerate( $annotations ):
#if $annotation.annotation_style.style == "galaxy":
#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]:
#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]]
#if $annotation.annotation_style.style == "galaxy":
#set $species_chromosomes = {}
#if $maf_input.dataset.metadata.species_chromosomes:
#for $line in open( $maf_input.dataset.metadata.species_chromosomes.file_name ):
#set $fields = $line.split( "\t" )
#if $fields:
#set $spec = $fields.pop( 0 )
#set $species_chromosomes[spec] = $fields
#end if
#end for
#end if
#if $species_chromosomes and $annotation.annotation_style['species'].value in $species_chromosomes and $species_chromosomes[$annotation.annotation_style['species'].value]:
#set $seq_names = [ "%s.%s" % ( $annotation.annotation_style['species'].value, $chrom ) for $chrom in $species_chromosomes[$annotation.annotation_style['species'].value]]
#else:
#set $seq_names = [$annotation.annotation_style['species']]
#end if
@@ -171,4 +183,4 @@ For detailed information on GMAJ, click here_.
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.
</help>
</tool>
</tool>