mirror of
https://github.com/galaxyproject/galaxy.git
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A bit of code cleanup in genetics.py, and add all rgenetics data types to datatypes_conf.xml.sample. Also include the new Sff data type in the upload config help section.
This commit is contained in:
Greg Von Kuster
+221
-210
@@ -1,213 +1,224 @@
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<?xml version="1.0"?>
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<datatypes>
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<registration converters_path="lib/galaxy/datatypes/converters">
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<datatype extension="ab1" type="galaxy.datatypes.binary:Ab1" mimetype="application/octet-stream" display_in_upload="true"/>
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<datatype extension="axt" type="galaxy.datatypes.sequence:Axt" display_in_upload="true"/>
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<datatype extension="bam" type="galaxy.datatypes.binary:Bam" mimetype="application/octet-stream"/>
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<datatype extension="bed" type="galaxy.datatypes.interval:Bed" display_in_upload="true">
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<converter file="bed_to_gff_converter.xml" target_datatype="gff"/>
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<converter file="interval_to_coverage.xml" target_datatype="coverage"/>
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<converter file="bed_to_interval_index_converter.xml" target_datatype="interval_index"/>
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</datatype>
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<datatype extension="binseq.zip" type="galaxy.datatypes.binary:Binseq" mimetype="application/zip" display_in_upload="true"/>
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<datatype extension="len" type="galaxy.datatypes.chrominfo:ChromInfo" display_in_upload="true">
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<!-- no converters yet -->
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</datatype>
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<datatype extension="coverage" type="galaxy.datatypes.coverage:LastzCoverage" display_in_upload="true">
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<indexer file="coverage.xml" />
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</datatype>
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<datatype extension="customtrack" type="galaxy.datatypes.interval:CustomTrack"/>
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<datatype extension="csfasta" type="galaxy.datatypes.sequence:csFasta" display_in_upload="true"/>
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<datatype extension="data" type="galaxy.datatypes.data:Data" mimetype="application/octet-stream"/>
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<datatype extension="fasta" type="galaxy.datatypes.sequence:Fasta" display_in_upload="true">
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<converter file="fasta_to_tabular_converter.xml" target_datatype="tabular"/>
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</datatype>
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<datatype extension="fastq" type="galaxy.datatypes.sequence:Fastq" display_in_upload="true"/>
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<datatype extension="fastqsanger" type="galaxy.datatypes.sequence:FastqSanger" display_in_upload="true"/>
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<datatype extension="genetrack" type="galaxy.datatypes.tracks:GeneTrack"/>
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<datatype extension="gff" type="galaxy.datatypes.interval:Gff" display_in_upload="true">
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<converter file="gff_to_bed_converter.xml" target_datatype="bed"/>
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</datatype>
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<datatype extension="gff3" type="galaxy.datatypes.interval:Gff3" display_in_upload="true"/>
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<datatype extension="gif" type="galaxy.datatypes.images:Image" mimetype="image/gif"/>
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<datatype extension="gmaj.zip" type="galaxy.datatypes.images:Gmaj" mimetype="application/zip"/>
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<datatype extension="html" type="galaxy.datatypes.images:Html" mimetype="text/html"/>
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<datatype extension="interval" type="galaxy.datatypes.interval:Interval" display_in_upload="true">
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<converter file="interval_to_bed_converter.xml" target_datatype="bed"/>
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<indexer file="interval_awk.xml" />
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</datatype>
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<datatype extension="jpg" type="galaxy.datatypes.images:Image" mimetype="image/jpeg"/>
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<datatype extension="laj" type="galaxy.datatypes.images:Laj"/>
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<datatype extension="lav" type="galaxy.datatypes.sequence:Lav" display_in_upload="true"/>
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<datatype extension="maf" type="galaxy.datatypes.sequence:Maf" display_in_upload="true">
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<converter file="maf_to_fasta_converter.xml" target_datatype="fasta"/>
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<converter file="maf_to_interval_converter.xml" target_datatype="interval"/>
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</datatype>
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<datatype extension="pdf" type="galaxy.datatypes.images:Image" mimetype="application/pdf"/>
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<datatype extension="png" type="galaxy.datatypes.images:Image" mimetype="image/png"/>
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<datatype extension="qualsolexa" type="galaxy.datatypes.qualityscore:QualityScoreSolexa" display_in_upload="true"/>
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<datatype extension="qualsolid" type="galaxy.datatypes.qualityscore:QualityScoreSOLiD" display_in_upload="true"/>
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<datatype extension="qual454" type="galaxy.datatypes.qualityscore:QualityScore454" display_in_upload="true"/>
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<datatype extension="sam" type="galaxy.datatypes.tabular:Sam" display_in_upload="true"/>
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<datatype extension="scf" type="galaxy.datatypes.binary:Scf" mimetype="application/octet-stream" display_in_upload="true"/>
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<datatype extension="sff" type="galaxy.datatypes.binary:Sff" mimetype="application/octet-stream" display_in_upload="true"/>
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<datatype extension="taxonomy" type="galaxy.datatypes.tabular:Taxonomy" display_in_upload="true"/>
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<datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular" display_in_upload="true"/>
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<datatype extension="txt" type="galaxy.datatypes.data:Text" display_in_upload="true"/>
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<datatype extension="blastxml" type="galaxy.datatypes.xml:BlastXml" display_in_upload="true"/>
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<datatype extension="txtseq.zip" type="galaxy.datatypes.data:Txtseq" mimetype="application/zip" display_in_upload="true"/>
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<datatype extension="wig" type="galaxy.datatypes.interval:Wiggle" display_in_upload="true">
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<converter file="wiggle_to_array_tree_converter.xml" target_datatype="array_tree"/>
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</datatype>
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<datatype extension="array_tree" type="galaxy.datatypes.data:Data" />
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<datatype extension="interval_index" type="galaxy.datatypes.data:Data" />
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<!-- EMBOSS TOOLS -->
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<datatype extension="acedb" type="galaxy.datatypes.data:Text"/>
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<datatype extension="asn1" type="galaxy.datatypes.data:Text"/>
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<datatype extension="btwisted" type="galaxy.datatypes.data:Text"/>
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<datatype extension="cai" type="galaxy.datatypes.data:Text"/>
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<datatype extension="charge" type="galaxy.datatypes.data:Text"/>
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<datatype extension="checktrans" type="galaxy.datatypes.data:Text"/>
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<datatype extension="chips" type="galaxy.datatypes.data:Text"/>
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<datatype extension="clustal" type="galaxy.datatypes.data:Text"/>
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<datatype extension="codata" type="galaxy.datatypes.data:Text"/>
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<datatype extension="codcmp" type="galaxy.datatypes.data:Text"/>
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<datatype extension="coderet" type="galaxy.datatypes.data:Text"/>
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<datatype extension="compseq" type="galaxy.datatypes.data:Text"/>
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<datatype extension="cpgplot" type="galaxy.datatypes.data:Text"/>
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<datatype extension="cpgreport" type="galaxy.datatypes.data:Text"/>
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<datatype extension="cusp" type="galaxy.datatypes.data:Text"/>
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<datatype extension="cut" type="galaxy.datatypes.data:Text"/>
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<datatype extension="dan" type="galaxy.datatypes.data:Text"/>
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<datatype extension="dbmotif" type="galaxy.datatypes.data:Text"/>
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<datatype extension="diffseq" type="galaxy.datatypes.data:Text"/>
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<datatype extension="digest" type="galaxy.datatypes.data:Text"/>
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<datatype extension="dreg" type="galaxy.datatypes.data:Text"/>
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<datatype extension="einverted" type="galaxy.datatypes.data:Text"/>
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<datatype extension="embl" type="galaxy.datatypes.data:Text"/>
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<datatype extension="epestfind" type="galaxy.datatypes.data:Text"/>
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<datatype extension="equicktandem" type="galaxy.datatypes.data:Text"/>
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<datatype extension="est2genome" type="galaxy.datatypes.data:Text"/>
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<datatype extension="etandem" type="galaxy.datatypes.data:Text"/>
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<datatype extension="excel" type="galaxy.datatypes.data:Text"/>
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<datatype extension="feattable" type="galaxy.datatypes.data:Text"/>
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<datatype extension="fitch" type="galaxy.datatypes.data:Text"/>
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<datatype extension="freak" type="galaxy.datatypes.data:Text"/>
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<datatype extension="fuzznuc" type="galaxy.datatypes.data:Text"/>
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<datatype extension="fuzzpro" type="galaxy.datatypes.data:Text"/>
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<datatype extension="fuzztran" type="galaxy.datatypes.data:Text"/>
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<datatype extension="garnier" type="galaxy.datatypes.data:Text"/>
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<datatype extension="gcg" type="galaxy.datatypes.data:Text"/>
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<datatype extension="geecee" type="galaxy.datatypes.data:Text"/>
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<datatype extension="genbank" type="galaxy.datatypes.data:Text"/>
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<datatype extension="helixturnhelix" type="galaxy.datatypes.data:Text"/>
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<datatype extension="hennig86" type="galaxy.datatypes.data:Text"/>
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<datatype extension="hmoment" type="galaxy.datatypes.data:Text"/>
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<datatype extension="ig" type="galaxy.datatypes.data:Text"/>
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<datatype extension="isochore" type="galaxy.datatypes.data:Text"/>
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<datatype extension="jackknifer" type="galaxy.datatypes.data:Text"/>
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<datatype extension="jackknifernon" type="galaxy.datatypes.data:Text"/>
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<datatype extension="markx10" type="galaxy.datatypes.data:Text"/>
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<datatype extension="markx1" type="galaxy.datatypes.data:Text"/>
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<datatype extension="markx0" type="galaxy.datatypes.data:Text"/>
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<datatype extension="markx3" type="galaxy.datatypes.data:Text"/>
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<datatype extension="markx2" type="galaxy.datatypes.data:Text"/>
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<datatype extension="match" type="galaxy.datatypes.data:Text"/>
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<datatype extension="mega" type="galaxy.datatypes.data:Text"/>
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<datatype extension="meganon" type="galaxy.datatypes.data:Text"/>
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<datatype extension="motif" type="galaxy.datatypes.data:Text"/>
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<datatype extension="msf" type="galaxy.datatypes.data:Text"/>
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<datatype extension="nametable" type="galaxy.datatypes.data:Text"/>
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<datatype extension="ncbi" type="galaxy.datatypes.data:Text"/>
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<datatype extension="needle" type="galaxy.datatypes.data:Text"/>
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<datatype extension="newcpgreport" type="galaxy.datatypes.data:Text"/>
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<datatype extension="newcpgseek" type="galaxy.datatypes.data:Text"/>
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<datatype extension="nexus" type="galaxy.datatypes.data:Text"/>
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<datatype extension="nexusnon" type="galaxy.datatypes.data:Text"/>
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<datatype extension="noreturn" type="galaxy.datatypes.data:Text"/>
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<datatype extension="pair" type="galaxy.datatypes.data:Text"/>
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<datatype extension="palindrome" type="galaxy.datatypes.data:Text"/>
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<datatype extension="pepcoil" type="galaxy.datatypes.data:Text"/>
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<datatype extension="pepinfo" type="galaxy.datatypes.data:Text"/>
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<datatype extension="pepstats" type="galaxy.datatypes.data:Text"/>
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<datatype extension="phylip" type="galaxy.datatypes.data:Text"/>
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<datatype extension="phylipnon" type="galaxy.datatypes.data:Text"/>
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<datatype extension="pir" type="galaxy.datatypes.data:Text"/>
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<datatype extension="polydot" type="galaxy.datatypes.data:Text"/>
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<datatype extension="preg" type="galaxy.datatypes.data:Text"/>
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<datatype extension="prettyseq" type="galaxy.datatypes.data:Text"/>
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<datatype extension="primersearch" type="galaxy.datatypes.data:Text"/>
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<datatype extension="regions" type="galaxy.datatypes.data:Text"/>
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<datatype extension="score" type="galaxy.datatypes.data:Text"/>
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<datatype extension="selex" type="galaxy.datatypes.data:Text"/>
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<datatype extension="seqtable" type="galaxy.datatypes.data:Text"/>
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<datatype extension="showfeat" type="galaxy.datatypes.data:Text"/>
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<datatype extension="showorf" type="galaxy.datatypes.data:Text"/>
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<datatype extension="simple" type="galaxy.datatypes.data:Text"/>
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<datatype extension="sixpack" type="galaxy.datatypes.data:Text"/>
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<datatype extension="srs" type="galaxy.datatypes.data:Text"/>
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<datatype extension="srspair" type="galaxy.datatypes.data:Text"/>
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<datatype extension="staden" type="galaxy.datatypes.data:Text"/>
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<datatype extension="strider" type="galaxy.datatypes.data:Text"/>
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<datatype extension="supermatcher" type="galaxy.datatypes.data:Text"/>
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<datatype extension="swiss" type="galaxy.datatypes.data:Text"/>
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<datatype extension="syco" type="galaxy.datatypes.data:Text"/>
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<datatype extension="table" type="galaxy.datatypes.data:Text"/>
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<datatype extension="textsearch" type="galaxy.datatypes.data:Text"/>
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<datatype extension="vectorstrip" type="galaxy.datatypes.data:Text"/>
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<datatype extension="wobble" type="galaxy.datatypes.data:Text"/>
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<datatype extension="wordcount" type="galaxy.datatypes.data:Text"/>
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<datatype extension="tagseq" type="galaxy.datatypes.data:Text"/>
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<!-- Start RGenetics Datatypes -->
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<!-- genome graphs ucsc file - first col is always marker then numeric values to plot -->
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<datatype extension="gg" type="galaxy.datatypes.genetics:GenomeGraphs"/>
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<datatype extension="rgenetics" type="galaxy.datatypes.genetics:Rgenetics"/>
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<!-- linkage format pedigree (separate .map file) -->
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<datatype extension="lped" type="galaxy.datatypes.genetics:Lped" display_in_upload="true"/>
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<!-- plink compressed file - has bed extension unfortunately -->
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<datatype extension="pbed" type="galaxy.datatypes.genetics:Pbed" display_in_upload="true"/>
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<!-- eigenstrat pedigree input file -->
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<datatype extension="eigenstratgeno" type="galaxy.datatypes.genetics:Eigenstratgeno"/>
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<!-- eigenstrat pca output file for adjusted eigenQTL eg -->
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<datatype extension="eigenstratpca" type="galaxy.datatypes.genetics:Eigenstratpca"/>
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<!-- fbat/pbat format pedigree (header row of marker names) -->
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<datatype extension="fped" type="galaxy.datatypes.genetics:Fped"/>
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<!-- part of linkage format pedigree -->
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<datatype extension="lmap" type="galaxy.datatypes.genetics:Lmap"/>
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<!-- phenotype file - fbat format -->
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<datatype extension="fphe" type="galaxy.datatypes.genetics:Fphe"/>
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<!-- phenotype file - plink format -->
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<datatype extension="pphe" type="galaxy.datatypes.genetics:Pphe"/>
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<datatype extension="snptest" type="galaxy.datatypes.genetics:Snptest"/>
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<datatype extension="snpmatrix" type="galaxy.datatypes.genetics:SNPMatrix"/>
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<datatype extension="xls" type="galaxy.datatypes.tabular:Tabular"/>
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<!-- End RGenetics Datatypes -->
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</registration>
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<sniffers>
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<!--
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The order in which Galaxy attempts to determine data types is
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important because some formats are much more loosely defined
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than others. The following list should be the most rigidly
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defined format first, followed by next-most rigidly defined,
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and so on.
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-->
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<sniffer type="galaxy.datatypes.binary:Sff"/>
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<sniffer type="galaxy.datatypes.xml:BlastXml"/>
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<sniffer type="galaxy.datatypes.sequence:Maf"/>
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<sniffer type="galaxy.datatypes.sequence:Lav"/>
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<sniffer type="galaxy.datatypes.sequence:csFasta"/>
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<sniffer type="galaxy.datatypes.qualityscore:QualityScoreSOLiD"/>
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<sniffer type="galaxy.datatypes.qualityscore:QualityScore454"/>
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<sniffer type="galaxy.datatypes.sequence:Fasta"/>
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<sniffer type="galaxy.datatypes.sequence:Fastq"/>
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<sniffer type="galaxy.datatypes.interval:Wiggle"/>
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<sniffer type="galaxy.datatypes.images:Html"/>
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<sniffer type="galaxy.datatypes.sequence:Axt"/>
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<sniffer type="galaxy.datatypes.interval:Bed"/>
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<sniffer type="galaxy.datatypes.interval:CustomTrack"/>
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<sniffer type="galaxy.datatypes.interval:Gff"/>
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<sniffer type="galaxy.datatypes.interval:Gff3"/>
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<sniffer type="galaxy.datatypes.interval:Interval"/>
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<sniffer type="galaxy.datatypes.tabular:Sam"/>
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</sniffers>
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<registration converters_path="lib/galaxy/datatypes/converters">
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<datatype extension="ab1" type="galaxy.datatypes.binary:Ab1" mimetype="application/octet-stream" display_in_upload="true"/>
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<datatype extension="axt" type="galaxy.datatypes.sequence:Axt" display_in_upload="true"/>
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<datatype extension="bam" type="galaxy.datatypes.binary:Bam" mimetype="application/octet-stream"/>
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<datatype extension="bed" type="galaxy.datatypes.interval:Bed" display_in_upload="true">
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<converter file="bed_to_gff_converter.xml" target_datatype="gff"/>
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<converter file="interval_to_coverage.xml" target_datatype="coverage"/>
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<converter file="bed_to_interval_index_converter.xml" target_datatype="interval_index"/>
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</datatype>
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<datatype extension="binseq.zip" type="galaxy.datatypes.binary:Binseq" mimetype="application/zip" display_in_upload="true"/>
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<datatype extension="len" type="galaxy.datatypes.chrominfo:ChromInfo" display_in_upload="true">
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<!-- no converters yet -->
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</datatype>
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<datatype extension="coverage" type="galaxy.datatypes.coverage:LastzCoverage" display_in_upload="true">
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<indexer file="coverage.xml" />
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</datatype>
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<datatype extension="customtrack" type="galaxy.datatypes.interval:CustomTrack"/>
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<datatype extension="csfasta" type="galaxy.datatypes.sequence:csFasta" display_in_upload="true"/>
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<datatype extension="data" type="galaxy.datatypes.data:Data" mimetype="application/octet-stream"/>
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<datatype extension="fasta" type="galaxy.datatypes.sequence:Fasta" display_in_upload="true">
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<converter file="fasta_to_tabular_converter.xml" target_datatype="tabular"/>
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</datatype>
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<datatype extension="fastq" type="galaxy.datatypes.sequence:Fastq" display_in_upload="true"/>
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<datatype extension="fastqsanger" type="galaxy.datatypes.sequence:FastqSanger" display_in_upload="true"/>
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<datatype extension="genetrack" type="galaxy.datatypes.tracks:GeneTrack"/>
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<datatype extension="gff" type="galaxy.datatypes.interval:Gff" display_in_upload="true">
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<converter file="gff_to_bed_converter.xml" target_datatype="bed"/>
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</datatype>
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<datatype extension="gff3" type="galaxy.datatypes.interval:Gff3" display_in_upload="true"/>
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<datatype extension="gif" type="galaxy.datatypes.images:Image" mimetype="image/gif"/>
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<datatype extension="gmaj.zip" type="galaxy.datatypes.images:Gmaj" mimetype="application/zip"/>
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<datatype extension="html" type="galaxy.datatypes.images:Html" mimetype="text/html"/>
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<datatype extension="interval" type="galaxy.datatypes.interval:Interval" display_in_upload="true">
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<converter file="interval_to_bed_converter.xml" target_datatype="bed"/>
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<indexer file="interval_awk.xml" />
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</datatype>
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<datatype extension="jpg" type="galaxy.datatypes.images:Image" mimetype="image/jpeg"/>
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<datatype extension="laj" type="galaxy.datatypes.images:Laj"/>
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<datatype extension="lav" type="galaxy.datatypes.sequence:Lav" display_in_upload="true"/>
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<datatype extension="maf" type="galaxy.datatypes.sequence:Maf" display_in_upload="true">
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<converter file="maf_to_fasta_converter.xml" target_datatype="fasta"/>
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<converter file="maf_to_interval_converter.xml" target_datatype="interval"/>
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</datatype>
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<datatype extension="pdf" type="galaxy.datatypes.images:Image" mimetype="application/pdf"/>
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<datatype extension="png" type="galaxy.datatypes.images:Image" mimetype="image/png"/>
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<datatype extension="qualsolexa" type="galaxy.datatypes.qualityscore:QualityScoreSolexa" display_in_upload="true"/>
|
||||
<datatype extension="qualsolid" type="galaxy.datatypes.qualityscore:QualityScoreSOLiD" display_in_upload="true"/>
|
||||
<datatype extension="qual454" type="galaxy.datatypes.qualityscore:QualityScore454" display_in_upload="true"/>
|
||||
<datatype extension="sam" type="galaxy.datatypes.tabular:Sam" display_in_upload="true"/>
|
||||
<datatype extension="scf" type="galaxy.datatypes.binary:Scf" mimetype="application/octet-stream" display_in_upload="true"/>
|
||||
<datatype extension="sff" type="galaxy.datatypes.binary:Sff" mimetype="application/octet-stream" display_in_upload="true"/>
|
||||
<datatype extension="taxonomy" type="galaxy.datatypes.tabular:Taxonomy" display_in_upload="true"/>
|
||||
<datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular" display_in_upload="true"/>
|
||||
<datatype extension="txt" type="galaxy.datatypes.data:Text" display_in_upload="true"/>
|
||||
<datatype extension="blastxml" type="galaxy.datatypes.xml:BlastXml" display_in_upload="true"/>
|
||||
<datatype extension="txtseq.zip" type="galaxy.datatypes.data:Txtseq" mimetype="application/zip" display_in_upload="true"/>
|
||||
<datatype extension="wig" type="galaxy.datatypes.interval:Wiggle" display_in_upload="true">
|
||||
<converter file="wiggle_to_array_tree_converter.xml" target_datatype="array_tree"/>
|
||||
</datatype>
|
||||
<datatype extension="array_tree" type="galaxy.datatypes.data:Data" />
|
||||
<datatype extension="interval_index" type="galaxy.datatypes.data:Data" />
|
||||
<!-- Start EMBOSS tools -->
|
||||
<datatype extension="acedb" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="asn1" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="btwisted" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="cai" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="charge" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="checktrans" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="chips" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="clustal" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="codata" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="codcmp" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="coderet" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="compseq" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="cpgplot" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="cpgreport" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="cusp" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="cut" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="dan" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="dbmotif" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="diffseq" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="digest" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="dreg" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="einverted" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="embl" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="epestfind" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="equicktandem" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="est2genome" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="etandem" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="excel" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="feattable" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="fitch" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="freak" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="fuzznuc" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="fuzzpro" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="fuzztran" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="garnier" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="gcg" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="geecee" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="genbank" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="helixturnhelix" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="hennig86" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="hmoment" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="ig" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="isochore" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="jackknifer" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="jackknifernon" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="markx10" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="markx1" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="markx0" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="markx3" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="markx2" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="match" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="mega" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="meganon" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="motif" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="msf" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="nametable" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="ncbi" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="needle" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="newcpgreport" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="newcpgseek" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="nexus" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="nexusnon" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="noreturn" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="pair" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="palindrome" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="pepcoil" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="pepinfo" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="pepstats" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="phylip" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="phylipnon" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="pir" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="polydot" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="preg" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="prettyseq" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="primersearch" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="regions" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="score" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="selex" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="seqtable" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="showfeat" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="showorf" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="simple" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="sixpack" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="srs" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="srspair" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="staden" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="strider" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="supermatcher" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="swiss" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="syco" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="table" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="textsearch" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="vectorstrip" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="wobble" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="wordcount" type="galaxy.datatypes.data:Text"/>
|
||||
<datatype extension="tagseq" type="galaxy.datatypes.data:Text"/>
|
||||
<!-- End EMBOSS tools -->
|
||||
<!-- Start RGenetics Datatypes -->
|
||||
<datatype extension="affybatch" type="galaxy.datatypes.genetics:Affybatch" display_in_upload="true"/>
|
||||
<!-- eigenstrat pedigree input file -->
|
||||
<datatype extension="eigenstratgeno" type="galaxy.datatypes.genetics:Eigenstratgeno"/>
|
||||
<!-- eigenstrat pca output file for adjusted eigenQTL eg -->
|
||||
<datatype extension="eigenstratpca" type="galaxy.datatypes.genetics:Eigenstratpca"/>
|
||||
<datatype extension="eset" type="galaxy.datatypes.genetics:Eset" display_in_upload="true" />
|
||||
<!-- fbat/pbat format pedigree (header row of marker names) -->
|
||||
<datatype extension="fped" type="galaxy.datatypes.genetics:Fped" display_in_upload="true"/>
|
||||
<!-- phenotype file - fbat format -->
|
||||
<datatype extension="fphe" type="galaxy.datatypes.genetics:Fphe" display_in_upload="true" mimetype="text/html"/>
|
||||
<!-- genome graphs ucsc file - first col is always marker then numeric values to plot -->
|
||||
<datatype extension="gg" type="galaxy.datatypes.genetics:GenomeGraphs"/>
|
||||
<!-- part of linkage format pedigree -->
|
||||
<datatype extension="lmap" type="galaxy.datatypes.genetics:Lmap" display_in_upload="true"/>
|
||||
<datatype extension="malist" type="galaxy.datatypes.genetics:MAlist" display_in_upload="true"/>
|
||||
<!-- linkage format pedigree (separate .map file) -->
|
||||
<datatype extension="lped" type="galaxy.datatypes.genetics:Lped" display_in_upload="true">
|
||||
<converter file="lped_to_fped_converter.xml" target_datatype="fped"/>
|
||||
<converter file="lped_to_pbed_converter.xml" target_datatype="pbed"/>
|
||||
</datatype>
|
||||
<!-- plink compressed file - has bed extension unfortunately -->
|
||||
<datatype extension="pbed" type="galaxy.datatypes.genetics:Pbed" display_in_upload="true">
|
||||
<converter file="pbed_to_lped_converter.xml" target_datatype="lped"/>
|
||||
</datatype>
|
||||
<datatype extension="pheno" type="galaxy.datatypes.genetics:Pheno"/>
|
||||
<!-- phenotype file - plink format -->
|
||||
<datatype extension="pphe" type="galaxy.datatypes.genetics:Pphe" display_in_upload="true" mimetype="text/html"/>
|
||||
<datatype extension="rexpbase" type="galaxy.datatypes.genetics:RexpBase"/>
|
||||
<datatype extension="rgenetics" type="galaxy.datatypes.genetics:Rgenetics"/>
|
||||
<datatype extension="snptest" type="galaxy.datatypes.genetics:Snptest" display_in_upload="true"/>
|
||||
<datatype extension="snpmatrix" type="galaxy.datatypes.genetics:SNPMatrix" display_in_upload="true"/>
|
||||
<datatype extension="xls" type="galaxy.datatypes.tabular:Tabular"/>
|
||||
<!-- End RGenetics Datatypes -->
|
||||
</registration>
|
||||
<sniffers>
|
||||
<!--
|
||||
The order in which Galaxy attempts to determine data types is
|
||||
important because some formats are much more loosely defined
|
||||
than others. The following list should be the most rigidly
|
||||
defined format first, followed by next-most rigidly defined,
|
||||
and so on.
|
||||
-->
|
||||
<sniffer type="galaxy.datatypes.binary:Sff"/>
|
||||
<sniffer type="galaxy.datatypes.xml:BlastXml"/>
|
||||
<sniffer type="galaxy.datatypes.sequence:Maf"/>
|
||||
<sniffer type="galaxy.datatypes.sequence:Lav"/>
|
||||
<sniffer type="galaxy.datatypes.sequence:csFasta"/>
|
||||
<sniffer type="galaxy.datatypes.qualityscore:QualityScoreSOLiD"/>
|
||||
<sniffer type="galaxy.datatypes.qualityscore:QualityScore454"/>
|
||||
<sniffer type="galaxy.datatypes.sequence:Fasta"/>
|
||||
<sniffer type="galaxy.datatypes.sequence:Fastq"/>
|
||||
<sniffer type="galaxy.datatypes.interval:Wiggle"/>
|
||||
<sniffer type="galaxy.datatypes.images:Html"/>
|
||||
<sniffer type="galaxy.datatypes.sequence:Axt"/>
|
||||
<sniffer type="galaxy.datatypes.interval:Bed"/>
|
||||
<sniffer type="galaxy.datatypes.interval:CustomTrack"/>
|
||||
<sniffer type="galaxy.datatypes.interval:Gff"/>
|
||||
<sniffer type="galaxy.datatypes.interval:Gff3"/>
|
||||
<sniffer type="galaxy.datatypes.interval:Interval"/>
|
||||
<sniffer type="galaxy.datatypes.tabular:Sam"/>
|
||||
</sniffers>
|
||||
</datatypes>
|
||||
|
||||
@@ -1,6 +1,5 @@
|
||||
"""
|
||||
rgenetics datatypes
|
||||
Use at your peril
|
||||
Ross Lazarus
|
||||
for the rgenetics and galaxy projects
|
||||
|
||||
@@ -11,7 +10,6 @@ subsequent row values are all numeric ! Will fail if any non numeric (eg '+' or
|
||||
ross lazarus for rgenetics
|
||||
august 20 2007
|
||||
"""
|
||||
|
||||
import logging, os, sys, time, tempfile, shutil, string, glob
|
||||
import data
|
||||
from galaxy import util
|
||||
@@ -26,8 +24,7 @@ from galaxy.datatypes.images import Html
|
||||
from galaxy.datatypes.interval import Interval
|
||||
from galaxy.util.hash_util import *
|
||||
|
||||
gal_Log = logging.getLogger(__name__)
|
||||
verbose = False
|
||||
log = logging.getLogger(__name__)
|
||||
|
||||
class GenomeGraphs(Interval):
|
||||
|
||||
@@ -154,7 +151,7 @@ class GenomeGraphs(Interval):
|
||||
link = '%s?redirect_url=%s&display_url=%s' % ( internal_url, redirect_url, display_url )
|
||||
ret_val.append( (site_name, link) )
|
||||
else:
|
||||
gal_Log.debug('@@@ gg ucsc_links - no viewport_tuple')
|
||||
log.debug('@@@ gg ucsc_links - no viewport_tuple')
|
||||
return ret_val
|
||||
def sniff( self, filename ):
|
||||
"""
|
||||
@@ -195,7 +192,8 @@ class GenomeGraphs(Interval):
|
||||
return False
|
||||
|
||||
class rgTabList(Tabular):
|
||||
""" for sampleid and for featureid lists of exclusions or inclusions in the clean tool
|
||||
"""
|
||||
for sampleid and for featureid lists of exclusions or inclusions in the clean tool
|
||||
featureid subsets on statistical criteria -> specialized display such as gg
|
||||
"""
|
||||
file_ext = "rgTList"
|
||||
@@ -225,16 +223,19 @@ class rgTabList(Tabular):
|
||||
return out
|
||||
|
||||
class rgSampleList(rgTabList):
|
||||
""" for sampleid exclusions or inclusions in the clean tool
|
||||
output from QC eg excess het, gender error, ibd pair member,eigen outlier,excess mendel errors,...
|
||||
since they can be uploaded, should be flexible
|
||||
but they are persistent at least
|
||||
same infrastructure for expression?
|
||||
"""
|
||||
for sampleid exclusions or inclusions in the clean tool
|
||||
output from QC eg excess het, gender error, ibd pair member,eigen outlier,excess mendel errors,...
|
||||
since they can be uploaded, should be flexible
|
||||
but they are persistent at least
|
||||
same infrastructure for expression?
|
||||
"""
|
||||
file_ext = "rgSList"
|
||||
|
||||
def __init__(self, **kwd):
|
||||
"""Initialize samplelist datatype"""
|
||||
"""
|
||||
Initialize samplelist datatype
|
||||
"""
|
||||
rgTabList.__init__( self, **kwd )
|
||||
self.column_names[0] = 'FID'
|
||||
self.column_names[1] = 'IID'
|
||||
@@ -250,10 +251,11 @@ class rgSampleList(rgTabList):
|
||||
return False
|
||||
|
||||
class rgFeatureList( rgTabList ):
|
||||
""" for featureid lists of exclusions or inclusions in the clean tool
|
||||
output from QC eg low maf, high missingness, bad hwe in controls, excess mendel errors,...
|
||||
featureid subsets on statistical criteria -> specialized display such as gg
|
||||
same infrastructure for expression?
|
||||
"""
|
||||
for featureid lists of exclusions or inclusions in the clean tool
|
||||
output from QC eg low maf, high missingness, bad hwe in controls, excess mendel errors,...
|
||||
featureid subsets on statistical criteria -> specialized display such as gg
|
||||
same infrastructure for expression?
|
||||
"""
|
||||
file_ext = "rgFList"
|
||||
|
||||
@@ -264,8 +266,9 @@ class rgFeatureList( rgTabList ):
|
||||
self.column_names[i] = s
|
||||
|
||||
class Rgenetics(Html):
|
||||
"""class to use for rgenetics"""
|
||||
|
||||
"""
|
||||
class to use for rgenetics
|
||||
"""
|
||||
MetadataElement( name="base_name", desc="base name for all transformed versions of this genetic dataset", default="rgenetics", readonly=True, set_in_upload=True)
|
||||
|
||||
composite_type = 'auto_primary_file'
|
||||
@@ -289,7 +292,8 @@ class Rgenetics(Html):
|
||||
rval.append( '</ul></div></html>' )
|
||||
return "\n".join( rval )
|
||||
def regenerate_primary_file(self,dataset):
|
||||
"""cannot do this until we are setting metadata
|
||||
"""
|
||||
cannot do this until we are setting metadata
|
||||
"""
|
||||
def fix(oldpath,newbase):
|
||||
old,e = os.path.splitext(oldpath)
|
||||
@@ -314,26 +318,24 @@ class Rgenetics(Html):
|
||||
f.write('\n')
|
||||
f.close()
|
||||
def set_meta( self, dataset, **kwd ):
|
||||
"""for lped/pbed eg"""
|
||||
"""
|
||||
for lped/pbed eg
|
||||
"""
|
||||
if kwd.get('overwrite') == False:
|
||||
if verbose:
|
||||
gal_Log.debug('@@@ rgenetics set_meta called with overwrite = False')
|
||||
#log.debug('@@@ rgenetics set_meta called with overwrite = False')
|
||||
return True
|
||||
try:
|
||||
efp = dataset.extra_files_path
|
||||
except:
|
||||
if verbose:
|
||||
gal_Log.debug('@@@rgenetics set_meta failed %s - dataset %s has no efp ?' % (sys.exc_info()[0], dataset.name))
|
||||
#log.debug('@@@rgenetics set_meta failed %s - dataset %s has no efp ?' % (sys.exc_info()[0], dataset.name))
|
||||
return False
|
||||
try:
|
||||
flist = os.listdir(efp)
|
||||
except:
|
||||
if verbose:
|
||||
gal_Log.debug('@@@rgenetics set_meta failed %s - dataset %s has no efp ?' % (sys.exc_info()[0],dataset.name))
|
||||
#log.debug('@@@rgenetics set_meta failed %s - dataset %s has no efp ?' % (sys.exc_info()[0],dataset.name))
|
||||
return False
|
||||
if len(flist) == 0:
|
||||
if verbose:
|
||||
gal_Log.debug('@@@rgenetics set_meta failed - %s efp %s is empty?' % (dataset.name,efp))
|
||||
#log.debug('@@@rgenetics set_meta failed - %s efp %s is empty?' % (dataset.name,efp))
|
||||
return False
|
||||
bn = None
|
||||
for f in flist:
|
||||
@@ -351,7 +353,8 @@ class Rgenetics(Html):
|
||||
return True
|
||||
|
||||
class SNPMatrix(Rgenetics):
|
||||
"""fake class to distinguish different species of Rgenetics data collections
|
||||
"""
|
||||
fake class to distinguish different species of Rgenetics data collections
|
||||
"""
|
||||
file_ext="snpmatrix"
|
||||
|
||||
@@ -363,7 +366,8 @@ class SNPMatrix(Rgenetics):
|
||||
dataset.peek = 'file does not exist'
|
||||
dataset.blurb = 'file purged from disk'
|
||||
def sniff(self,filename):
|
||||
""" need to check the file header hex code
|
||||
"""
|
||||
need to check the file header hex code
|
||||
"""
|
||||
infile = open(dataset.file_name, "b")
|
||||
head = infile.read(16)
|
||||
@@ -374,7 +378,8 @@ class SNPMatrix(Rgenetics):
|
||||
return True
|
||||
|
||||
class Lped(Rgenetics):
|
||||
"""fake class to distinguish different species of Rgenetics data collections
|
||||
"""
|
||||
fake class to distinguish different species of Rgenetics data collections
|
||||
"""
|
||||
file_ext="lped"
|
||||
|
||||
@@ -384,7 +389,8 @@ class Lped(Rgenetics):
|
||||
self.add_composite_file( '%s.map', description = 'Map File', substitute_name_with_metadata = 'base_name', is_binary = True )
|
||||
|
||||
class Pphe(Rgenetics):
|
||||
"""fake class to distinguish different species of Rgenetics data collections
|
||||
"""
|
||||
fake class to distinguish different species of Rgenetics data collections
|
||||
"""
|
||||
file_ext="pphe"
|
||||
|
||||
@@ -393,12 +399,14 @@ class Pphe(Rgenetics):
|
||||
self.add_composite_file( '%s.pphe', description = 'Plink Phenotype File', substitute_name_with_metadata = 'base_name' )
|
||||
|
||||
class Lmap(Rgenetics):
|
||||
"""fake class to distinguish different species of Rgenetics data collections
|
||||
"""
|
||||
fake class to distinguish different species of Rgenetics data collections
|
||||
"""
|
||||
file_ext="lmap"
|
||||
|
||||
class Fphe(Rgenetics):
|
||||
"""fake class to distinguish different species of Rgenetics data collections
|
||||
"""
|
||||
fake class to distinguish different species of Rgenetics data collections
|
||||
"""
|
||||
file_ext="fphe"
|
||||
|
||||
@@ -407,7 +415,8 @@ class Fphe(Rgenetics):
|
||||
self.add_composite_file( '%s.fphe', description = 'FBAT Phenotype File', substitute_name_with_metadata = 'base_name' )
|
||||
|
||||
class Phe(Rgenetics):
|
||||
"""fake class to distinguish different species of Rgenetics data collections
|
||||
"""
|
||||
fake class to distinguish different species of Rgenetics data collections
|
||||
"""
|
||||
file_ext="phe"
|
||||
|
||||
@@ -416,7 +425,8 @@ class Phe(Rgenetics):
|
||||
self.add_composite_file( '%s.phe', description = 'Phenotype File', substitute_name_with_metadata = 'base_name' )
|
||||
|
||||
class Fped(Rgenetics):
|
||||
"""fake class to distinguish different species of Rgenetics data collections
|
||||
"""
|
||||
fake class to distinguish different species of Rgenetics data collections
|
||||
"""
|
||||
file_ext="fped"
|
||||
|
||||
@@ -425,7 +435,8 @@ class Fped(Rgenetics):
|
||||
self.add_composite_file( '%s.fped', description = 'FBAT format pedfile', substitute_name_with_metadata = 'base_name' )
|
||||
|
||||
class Pbed(Rgenetics):
|
||||
"""fake class to distinguish different species of Rgenetics data collections
|
||||
"""
|
||||
fake class to distinguish different species of Rgenetics data collections
|
||||
"""
|
||||
file_ext="pbed"
|
||||
|
||||
@@ -436,7 +447,8 @@ class Pbed(Rgenetics):
|
||||
self.add_composite_file( '%s.fam', substitute_name_with_metadata = 'base_name', is_binary = True )
|
||||
|
||||
class Eigenstratgeno(Rgenetics):
|
||||
"""fake class to distinguish different species of Rgenetics data collections
|
||||
"""
|
||||
fake class to distinguish different species of Rgenetics data collections
|
||||
"""
|
||||
file_ext="eigenstratgeno"
|
||||
|
||||
@@ -447,7 +459,8 @@ class Eigenstratgeno(Rgenetics):
|
||||
self.add_composite_file( '%s.map', substitute_name_with_metadata = 'base_name', is_binary = True )
|
||||
|
||||
class Eigenstratpca(Rgenetics):
|
||||
"""fake class to distinguish different species of Rgenetics data collections
|
||||
"""
|
||||
fake class to distinguish different species of Rgenetics data collections
|
||||
"""
|
||||
file_ext="eigenstratpca"
|
||||
|
||||
@@ -456,7 +469,8 @@ class Eigenstratpca(Rgenetics):
|
||||
self.add_composite_file( '%s.eigenstratpca', description = 'Eigenstrat PCA file', substitute_name_with_metadata = 'base_name' )
|
||||
|
||||
class Snptest(Rgenetics):
|
||||
"""fake class to distinguish different species of Rgenetics data collections
|
||||
"""
|
||||
fake class to distinguish different species of Rgenetics data collections
|
||||
"""
|
||||
file_ext="snptest"
|
||||
|
||||
@@ -467,7 +481,8 @@ class Pheno(Tabular):
|
||||
file_ext = 'pheno'
|
||||
|
||||
class RexpBase( Html ):
|
||||
"""base class for BioC data structures in Galaxy
|
||||
"""
|
||||
base class for BioC data structures in Galaxy
|
||||
must be constructed with the pheno data in place since that
|
||||
goes into the metadata for each instance
|
||||
"""
|
||||
@@ -488,7 +503,8 @@ class RexpBase( Html ):
|
||||
self.add_composite_file( '%s.pheno', description = 'Phenodata tab text file',
|
||||
substitute_name_with_metadata = 'base_name', is_binary=True)
|
||||
def generate_primary_file( self, dataset = None ):
|
||||
""" This is called only at upload to write the html file
|
||||
"""
|
||||
This is called only at upload to write the html file
|
||||
cannot rename the datasets here - they come with the default unfortunately
|
||||
"""
|
||||
return '<html><head></head><body>AutoGenerated Primary File for Composite Dataset</body></html>'
|
||||
@@ -517,7 +533,7 @@ class RexpBase( Html ):
|
||||
else:
|
||||
for col,code in enumerate(row): # keep column order correct
|
||||
if col >= totcols:
|
||||
gal_Log.warning('### get_phecols error in pheno file - row %d col %d (%s) longer than header %s' % (nrows, col, row, head))
|
||||
log.warning('### get_phecols error in pheno file - row %d col %d (%s) longer than header %s' % (nrows, col, row, head))
|
||||
else:
|
||||
concordance[col].setdefault(code,0) # first one is zero
|
||||
concordance[col][code] += 1
|
||||
@@ -564,7 +580,8 @@ class RexpBase( Html ):
|
||||
return res
|
||||
|
||||
def get_pheno(self,dataset):
|
||||
"""expects a .pheno file in the extra_files_dir - ugh
|
||||
"""
|
||||
expects a .pheno file in the extra_files_dir - ugh
|
||||
note that R is wierd and adds the row.name in
|
||||
the header so the columns are all wrong - unless you tell it not to.
|
||||
A file can be written as
|
||||
@@ -581,9 +598,11 @@ class RexpBase( Html ):
|
||||
p = []
|
||||
return '\n'.join(p)
|
||||
def set_peek( self, dataset ):
|
||||
"""expects a .pheno file in the extra_files_dir - ugh
|
||||
"""
|
||||
expects a .pheno file in the extra_files_dir - ugh
|
||||
note that R is wierd and does not include the row.name in
|
||||
the header. why?"""
|
||||
the header. why?
|
||||
"""
|
||||
if not dataset.dataset.purged:
|
||||
pp = os.path.join(dataset.extra_files_path,'%s.pheno' % dataset.metadata.base_name)
|
||||
try:
|
||||
@@ -596,8 +615,7 @@ class RexpBase( Html ):
|
||||
dataset.peek = 'file does not exist\n'
|
||||
dataset.blurb = 'file purged from disk'
|
||||
def get_peek( self, dataset ):
|
||||
"""expects a .pheno file in the extra_files_dir - ugh
|
||||
"""
|
||||
"""expects a .pheno file in the extra_files_dir - ugh"""
|
||||
pp = os.path.join(dataset.extra_files_path,'%s.pheno' % dataset.metadata.base_name)
|
||||
try:
|
||||
p = file(pp,'r').readlines()
|
||||
@@ -640,8 +658,7 @@ class RexpBase( Html ):
|
||||
try:
|
||||
flist = os.listdir(dataset.extra_files_path)
|
||||
except:
|
||||
if verbose:
|
||||
gal_Log.debug('@@@rexpression set_meta failed - no dataset?')
|
||||
#log.debug('@@@rexpression set_meta failed - no dataset?')
|
||||
return False
|
||||
bn = None
|
||||
for f in flist:
|
||||
@@ -711,7 +728,6 @@ class RexpBase( Html ):
|
||||
|
||||
class Affybatch( RexpBase ):
|
||||
"""derived class for BioC data structures in Galaxy """
|
||||
|
||||
file_ext = "affybatch"
|
||||
|
||||
def __init__( self, **kwd ):
|
||||
@@ -728,7 +744,6 @@ class Eset( RexpBase ):
|
||||
self.add_composite_file( '%s.eset', description = 'ESet R object saved to file',
|
||||
substitute_name_with_metadata = 'base_name', is_binary = True )
|
||||
|
||||
|
||||
class MAlist( RexpBase ):
|
||||
"""derived class for BioC data structures in Galaxy """
|
||||
file_ext = "malist"
|
||||
|
||||
@@ -181,6 +181,12 @@ A binary sequence file in 'scf' format with a '.scf' file extension. You must m
|
||||
|
||||
-----
|
||||
|
||||
**Sff**
|
||||
|
||||
A binary file in 'Standard Flowgram Format' with a '.sff' file extension.
|
||||
|
||||
-----
|
||||
|
||||
**Tabular (tab delimited)**
|
||||
|
||||
Any data in tab delimited format (tabular)
|
||||
|
||||
Reference in New Issue
Block a user