| Previous changeset 3:aa209d311ece (2013-12-04) Next changeset 5:9dd40f0bbfde (2014-01-08) |
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Commit message:
Merge heads. |
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modified:
cuffmerge_wrapper.py cuffmerge_wrapper.xml tool_data_table_conf.xml.sample |
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added:
tool-data/fasta_indexes.loc.sample |
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removed:
tool-data/sam_fa_indices.loc.sample |
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| diff -r aa209d311ece -r 9cfc0b970015 cuffmerge_wrapper.py --- a/cuffmerge_wrapper.py Wed Dec 04 16:21:38 2013 -0500 +++ b/cuffmerge_wrapper.py Wed Jan 08 09:16:08 2014 -0500 |
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| @@ -8,20 +8,6 @@ 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() @@ -31,8 +17,7 @@ # Wrapper / Galaxy options. - 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' ) # Outputs. @@ -61,21 +46,15 @@ # Set/link to sequence file. if options.use_seq_data: - 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 sequence data 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. |
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| diff -r aa209d311ece -r 9cfc0b970015 cuffmerge_wrapper.xml --- a/cuffmerge_wrapper.xml Wed Dec 04 16:21:38 2013 -0500 +++ b/cuffmerge_wrapper.xml Wed Jan 08 09:16:08 2014 -0500 |
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| @@ -1,4 +1,4 @@ -<tool id="cuffmerge" name="Cuffmerge" version="0.0.5"> +<tool id="cuffmerge" name="Cuffmerge" version="0.0.6"> <!-- Wrapper supports Cuffmerge versions 1.3 and newer --> <description>merge together several Cufflinks assemblies</description> <requirements> @@ -20,10 +20,8 @@ #if $seq_data.seq_source.index_source == "history": --ref_file=$seq_data.seq_source.ref_file #else: - --ref_file="None" + --index=${bias_correction.seq_source.index.fields.path} #end if - --dbkey=${first_input.metadata.dbkey} - --index_dir=${GALAXY_DATA_INDEX_DIR} #end if ## Outputs. @@ -64,7 +62,14 @@ <option value="cached">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> |
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| diff -r aa209d311ece -r 9cfc0b970015 tool-data/fasta_indexes.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/fasta_indexes.loc.sample Wed Jan 08 09:16:08 2014 -0500 |
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| @@ -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 |
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| diff -r aa209d311ece -r 9cfc0b970015 tool-data/sam_fa_indices.loc.sample --- a/tool-data/sam_fa_indices.loc.sample Wed Dec 04 16:21:38 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -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 |