Mercurial > repos > devteam > cufflinks
changeset 2:da11bfc10e81
Update to the new data table specification.
| author | Dave Bouvier <dave@bx.psu.edu> |
|---|---|
| date | Wed, 04 Dec 2013 13:24:49 -0500 |
| parents | b01956f26c36 |
| children | 398329a94c99 |
| files | cufflinks_wrapper.py cufflinks_wrapper.xml tool-data/fasta_indexes.loc.sample tool-data/sam_fa_indices.loc.sample tool_data_table_conf.xml.sample |
| diffstat | 5 files changed, 54 insertions(+), 65 deletions(-) [+] |
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--- a/cufflinks_wrapper.py Tue Oct 01 15:12:55 2013 -0400 +++ b/cufflinks_wrapper.py Wed Dec 04 13:24:49 2013 -0500 @@ -10,20 +10,6 @@ sys.stderr.write( "%s\n" % msg ) sys.exit() -# Copied from sam_to_bam.py: -def check_seq_file( dbkey, cached_seqs_pointer_file ): - seq_path = '' - for line in open( cached_seqs_pointer_file ): - line = line.rstrip( '\r\n' ) - if line and not line.startswith( '#' ) and line.startswith( 'index' ): - fields = line.split( '\t' ) - if len( fields ) < 3: - continue - if fields[1] == dbkey: - seq_path = fields[2].strip() - break - return seq_path - def __main__(): #Parse Command Line parser = optparse.OptionParser() @@ -53,8 +39,7 @@ # Bias correction options. parser.add_option( '-b', dest='do_bias_correction', action="store_true", help='Providing Cufflinks with a multifasta file via this option instructs it to run our new bias detection and correction algorithm which can significantly improve accuracy of transcript abundance estimates.') - parser.add_option( '', '--dbkey', dest='dbkey', help='The build of the reference dataset' ) - parser.add_option( '', '--index_dir', dest='index_dir', help='GALAXY_DATA_INDEX_DIR' ) + parser.add_option( '', '--index', dest='index', help='The path of the reference genome' ) parser.add_option( '', '--ref_file', dest='ref_file', help='The reference dataset from the history' ) # Global model. @@ -83,22 +68,16 @@ # If doing bias correction, set/link to sequence file. if options.do_bias_correction: - if options.ref_file != 'None': + if options.ref_file: # Sequence data from history. # Create symbolic link to ref_file so that index will be created in working directory. seq_path = "ref.fa" os.symlink( options.ref_file, seq_path ) else: - # Sequence data from loc file. - cached_seqs_pointer_file = os.path.join( options.index_dir, 'sam_fa_indices.loc' ) - if not os.path.exists( cached_seqs_pointer_file ): - stop_err( 'The required file (%s) does not exist.' % cached_seqs_pointer_file ) - # If found for the dbkey, seq_path will look something like /galaxy/data/equCab2/sam_index/equCab2.fa, - # and the equCab2.fa file will contain fasta sequences. - seq_path = check_seq_file( options.dbkey, cached_seqs_pointer_file ) - if seq_path == '': - stop_err( 'No sequence data found for dbkey %s, so bias correction cannot be used.' % options.dbkey ) - + if not os.path.exists( options.index ): + stop_err( 'Reference genome %s not present, request it by reporting this error.' % options.index ) + seq_path = options.index + # Build command. # Base; always use quiet mode to avoid problems with storing log output.
--- a/cufflinks_wrapper.xml Tue Oct 01 15:12:55 2013 -0400 +++ b/cufflinks_wrapper.xml Wed Dec 04 13:24:49 2013 -0500 @@ -1,4 +1,4 @@ -<tool id="cufflinks" name="Cufflinks" version="0.0.6"> +<tool id="cufflinks" name="Cufflinks" version="0.0.7"> <!-- Wrapper supports Cufflinks versions v1.3.0 and newer --> <description>transcript assembly and FPKM (RPKM) estimates for RNA-Seq data</description> <requirements> @@ -30,14 +30,12 @@ ## Bias correction? #if $bias_correction.do_bias_correction == "Yes": - -b + -b #if $bias_correction.seq_source.index_source == "history": --ref_file=$bias_correction.seq_source.ref_file #else: - --ref_file="None" + --index=${bias_correction.seq_source.index.fields.path} #end if - --dbkey=${input.metadata.dbkey} - --index_dir=${GALAXY_DATA_INDEX_DIR} #end if ## Multi-read correct? @@ -68,15 +66,15 @@ <when value="No"></when> <when value="Use reference annotation"> <param format="gff3,gtf" name="reference_annotation_file" type="data" label="Reference Annotation" help="Gene annotation dataset in GTF or GFF3 format."/> - </when> - <when value="Use reference annotation guide"> + </when> + <when value="Use reference annotation guide"> <param format="gff3,gtf" name="reference_annotation_guide_file" type="data" label="Reference Annotation" help="Gene annotation dataset in GTF or GFF3 format."/> - </when> + </when> </conditional> <conditional name="bias_correction"> <param name="do_bias_correction" type="select" label="Perform Bias Correction" help="Bias detection and correction can significantly improve accuracy of transcript abundance estimates."> <option value="No" selected="true">No</option> - <option value="Yes">Yes</option> + <option value="Yes">Yes</option> </param> <when value="Yes"> <conditional name="seq_source"> @@ -84,7 +82,14 @@ <option value="cached" selected="true">Locally cached</option> <option value="history">History</option> </param> - <when value="cached"></when> + <when value="cached"> + <param name="index" type="select" label="Using reference genome"> + <options from_data_table="fasta_indexes"> + <filter type="data_meta" ref="input" key="dbkey" column="1" /> + <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" /> + </options> + </param> + </when> <when value="history"> <param name="ref_file" type="data" format="fasta" label="Using reference file" /> </when>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/fasta_indexes.loc.sample Wed Dec 04 13:24:49 2013 -0500 @@ -0,0 +1,29 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of Samtools indexed sequences data files. You will need +#to create these data files and then create a sam_fa_new_indices.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The sam_fa_new_indices.loc +#file has this format (white space characters are TAB characters): +# +# <unique_build_id> <dbkey> <display_name> <file_base_path> +# +#So, for example, if you had hg19 Canonical indexed stored in +# +# /depot/data2/galaxy/hg19/sam/, +# +#then the sam_fa_new_indices.loc entry would look like this: +# +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +# +#and your /depot/data2/galaxy/hg19/sam/ directory +#would contain hg19canon.fa and hg19canon.fa.fai files. +# +#Your sam_fa_new_indices.loc file should include an entry per line for +#each index set you have stored. The file in the path does actually +#exist, but it should never be directly used. Instead, the name serves +#as a prefix for the index file. For example: +# +#hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa +#hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa
--- a/tool-data/sam_fa_indices.loc.sample Tue Oct 01 15:12:55 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,28 +0,0 @@ -#This is a sample file distributed with Galaxy that enables tools -#to use a directory of Samtools indexed sequences data files. You will need -#to create these data files and then create a sam_fa_indices.loc file -#similar to this one (store it in this directory) that points to -#the directories in which those files are stored. The sam_fa_indices.loc -#file has this format (white space characters are TAB characters): -# -#index <seq> <location> -# -#So, for example, if you had hg18 indexed stored in -#/depot/data2/galaxy/sam/, -#then the sam_fa_indices.loc entry would look like this: -# -#index hg18 /depot/data2/galaxy/sam/hg18.fa -# -#and your /depot/data2/galaxy/sam/ directory -#would contain hg18.fa and hg18.fa.fai files: -# -#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.fa -#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.fa.fai -# -#Your sam_fa_indices.loc file should include an entry per line for -#each index set you have stored. The file in the path does actually -#exist, but it should never be directly used. Instead, the name serves -#as a prefix for the index file. For example: -# -#index hg18 /depot/data2/galaxy/sam/hg18.fa -#index hg19 /depot/data2/galaxy/sam/hg19.fa