| Previous changeset 0:c386fe82db82 (2013-09-25) Next changeset 2:293927a46697 (2013-09-25) |
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Commit message:
Deleted selected files |
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removed:
sra_tools-04cc8176e86f/datatypes_conf.xml sra_tools-04cc8176e86f/fastq_dump.xml sra_tools-04cc8176e86f/sam_dump.xml sra_tools-04cc8176e86f/sra.py sra_tools-04cc8176e86f/sra_pileup.xml sra_tools-04cc8176e86f/tool_dependencies.xml |
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| diff -r c386fe82db82 -r da2dbe22f80b sra_tools-04cc8176e86f/datatypes_conf.xml --- a/sra_tools-04cc8176e86f/datatypes_conf.xml Wed Sep 25 21:00:05 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,9 +0,0 @@ -<?xml version="1.0"?> -<datatypes> - <datatype_files> - <datatype_file name="sra.py"/> - </datatype_files> - <registration> - <datatype extension="sra" type="galaxy.datatypes.sra:sra" display_in_upload="true"/> - </registration> -</datatypes> |
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| diff -r c386fe82db82 -r da2dbe22f80b sra_tools-04cc8176e86f/fastq_dump.xml --- a/sra_tools-04cc8176e86f/fastq_dump.xml Wed Sep 25 21:00:05 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,123 +0,0 @@ -<tool id="fastq_dump" name="Extract reads" version="1.1.1"> - <description> from NCBI SRA.</description> - <command> - fastq-dump --log-level fatal - #if $input.input_select == "file": - --accession '${input.file.name}' - #else: - --accession $input.accession - #end if - --defline-seq '@\$sn[_\$rn]/\$ri' - --stdout - #if $split == "yes": - --split-spot - #end if - #if str( $alignments ) == "aligned": - --aligned - #end if - #if str( $alignments ) == "unaligned": - --unaligned - #end if - #if str( $minID ) != "": - --minSpotId $minID - #end if - #if str( $maxID ) != "": - --maxSpotId $maxID - #end if - #if str( $minlen ) != "": - --minReadLen $minlen - #end if - #if str( $readfilter ) != "": - --read-filter $readfilter - #end if - #if str( $region ) != "": - --aligned-region $region - #end if - #if str( $spotgroups ) != "": - --spot-groups $spotgroups - #end if - #if str( $matepairDist ) != "": - --matepair-distance $matepairDist - #end if - #if $clip == "yes": - --clip - #end if - #if str( $outputformat ) == "fasta": - --fasta - #end if - #if $input.input_select=="file": - $input.file - #else: - $input.accession - #end if - > $output - </command> - <version_string>fastq-dump --version</version_string> - <inputs> - <conditional name="input"> - <param name="input_select" type="select" label="select input type"> - <option value="accession_number">SRR accession</option> - <option value="file">SRA archive in current history</option> - </param> - <when value="file"> - <param format="sra" name="file" type="data" label="sra archive"/> - </when> - <when value="accession_number"> - <param format="text" name="accession" type="text" label="accession"/> - </when> - </conditional> - <param format="text" name="minID" type="text" label="minimum spot ID"/> - <param format="text" name="maxID" type="text" label="maximum spot ID"/> - <param format="text" name="minlen" type="text" label="minimum read length"/> - <param format="text" name="split" type="select" value="yes"> - <label>split spot by read pairs</label> - <option value="yes">Yes</option> - <option value="no">No</option> - </param> - <param format="text" name="alignments" type="select" value="both"> - <label>aligned or unaligned reads</label> - <option value="both">both</option> - <option value="aligned">aligned only</option> - <option value="unaligned">unaligned only</option> - </param> - <param format="text" name="region" type="text" label="aligned region"/> - <param format="text" name="matepairDist" type="text" label="mate-pair distance (from-to|unknown)"/> - <param format="text" name="readfilter" type="select" value=""> - <label>filter by value</label> - <option value="">None</option> - <option value="pass">pass</option> - <option value="reject">reject</option> - <option value="criteria">criteria</option> - <option value="redacted">redacted</option> - </param> - <param name="outputformat" type="select" label="select output format"> - <option value="fastqsanger">fastq</option> - <option value="fasta">fasta</option> - </param> - <param format="text" name="spotgroups" type="text" label="filter by spot-groups"/> - <param format="text" name="clip" type="select" value="no"> - <label>apply left and right clips</label> - <option value="no">No</option> - <option value="yes">Yes</option> - </param> - </inputs> - <outputs> - <data format="fastq" name="output"> - <change_format> - <when input="outputformat" value="fasta" format="fasta" /> - </change_format> - </data> - </outputs> - <stdio> - <exit_code range="127" level="fatal" description="Could not locate fastq-dump binary"/> - </stdio> - <requirements> - <requirement type="package" version="2.3.3-3">sra_toolkit</requirement> - </requirements> - <help> - This tool extracts reads from SRA archives using fastq-dump. - Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies. - The fastq-dump program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software. - Contact Matt Shirley at mdshw5@gmail.com for support and bug reports. - </help> -</tool> |
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| diff -r c386fe82db82 -r da2dbe22f80b sra_tools-04cc8176e86f/sam_dump.xml --- a/sra_tools-04cc8176e86f/sam_dump.xml Wed Sep 25 21:00:05 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,99 +0,0 @@ -<tool id="sam_dump" name="Extract reads" version="1.1.1"> - <description> in SAM format from NCBI SRA.</description> - <command> - sam-dump --log-level fatal - #if str( $region ) != "": - --aligned-region $region - #end if - #if str( $matepairDist ) != "": - --matepair-distance $matepairDist - #end if - #if str( $minMapq ) != "": - --minmapq $minMapq - #end if - #if $header == "yes": - --header - #else: - --no-header - #end if - #if str( $alignments ) == "both": - --unaligned - #end if - #if str( $alignments ) == "unaligned": - --unaligned-spots-only - #end if - #if (str( $primary ) == "yes") and (str ( $alignments != "unaligned") ): - --primary - #end if - #if str( $fastq ) == "yes": - --fastq - #end if - #if $input.input_select == "file": - $input.file - #elif $input.input_select == "accession_number": - $input.accession - #elif $input.input_select == "text": - `cat $input.text` - #end if - > $output - </command> - <version_string>sam-dump --version</version_string> - <inputs> - <conditional name="input"> - <param name="input_select" type="select" label="select input type"> - <option value="accession_number">SRR accession</option> - <option value="file">SRA archive in current history</option> - <option value="text">text file containing SRR accession</option> - </param> - <when value="file"> - <param format="sra" name="file" type="data" label="sra archive"/> - </when> - <when value="accession_number"> - <param format="text" name="accession" type="text" label="accession"/> - </when> - <when value="text"> - <param format="txt" name="text" type="data" label="text file"/> - </when> - </conditional> - <param format="text" name="region" type="text" label="aligned region"/> - <param format="text" name="matepairDist" type="text" label="mate-pair distance (from-to|unknown)"/> - <param format="text" name="header" type="select" value="yes"> - <label>output SAM header</label> - <option value="yes">Yes</option> - <option value="no">No</option> - </param> - <param format="text" name="alignments" type="select" value="both"> - <label>aligned or unaligned reads</label> - <option value="both">both</option> - <option value="aligned">aligned only</option> - <option value="unaligned">unaligned only</option> - </param> - <param format="text" name="primary" type="select" value="no"> - <label>only primary aligments</label> - <option value="no">No</option> - <option value="yes">Yes</option> - </param> - <param format="text" name="minMapq" type="text" label="minimum mapping quality"/> - <param format="text" name="fastq" type="select" value="no"> - <label>output fastq</label> - <option value="no">No</option> - <option value="yes">Yes</option> - </param> - </inputs> - <outputs> - <data name="output" format="sam"> - <change_format> - <when input="fastq" value="yes" format="fastq"/> - </change_format> - </data> - </outputs> - <requirements> - <requirement type="package" version="2.3.3-3">sra_toolkit</requirement> - </requirements> - <help> - This tool extracts reads from sra archives using sam-dump. - Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies. - The sam-dump program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software. - Contact Matt Shirley at mdshw5@gmail.com for support and bug reports. - </help> -</tool> \ No newline at end of file |
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| diff -r c386fe82db82 -r da2dbe22f80b sra_tools-04cc8176e86f/sra.py --- a/sra_tools-04cc8176e86f/sra.py Wed Sep 25 21:00:05 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,46 +0,0 @@ -""" -NCBI sra class -""" -import logging -import binascii -from galaxy.datatypes.data import * -from galaxy.datatypes.sniff import * -from galaxy.datatypes.binary import * -from galaxy.datatypes.metadata import * - -log = logging.getLogger(__name__) - -class sra( Binary ): - """ Sequence Read Archive (SRA) """ - file_ext = 'sra' - - def __init__( self, **kwd ): - Binary.__init__( self, **kwd ) - def sniff( self, filename ): - """ The first 8 bytes of any NCBI sra file is 'NCIB.sra', and the file is binary. EBI and DDBJ files may differ, though EBI and DDBJ - submissions through NCBI (ERR and DRR accessions) read 'NCBI.sra'. - For details about the format, see http://www.ncbi.nlm.nih.gov/books/n/helpsra/SRA_Overview_BK/#SRA_Overview_BK.4_SRA_Data_Structure - """ - try: - header = open(filename).read(8) - if binascii.b2a_hex(header) == binascii.hexlify('NCBI.sra'): - return True - else: - return False - except: - return False - def set_peek(self, dataset, is_multi_byte=False): - if not dataset.dataset.purged: - dataset.peek = 'Binary sra file' - dataset.blurb = data.nice_size(dataset.get_size()) - else: - dataset.peek = 'file does not exist' - dataset.blurb = 'file purged from disk' - def display_peek(self, dataset): - try: - return dataset.peek - except: - return 'Binary sra file (%s)' % ( data.nice_size(dataset.get_size())) - -if hasattr(Binary, 'register_sniffable_binary_format'): - Binary.register_sniffable_binary_format('sra', 'sra', sra) |
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| diff -r c386fe82db82 -r da2dbe22f80b sra_tools-04cc8176e86f/sra_pileup.xml --- a/sra_tools-04cc8176e86f/sra_pileup.xml Wed Sep 25 21:00:05 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,51 +0,0 @@ -<tool id="sra_pileup" name="Generate pileup format" version="1.1.1"> - <description> from NCBI sra.</description> - <command>sra-pileup --log-level fatal - #if str( $region ) != "": - --aligned-region $region - #end if - #if str( $minMapq ) != "": - --minmapq $minMapq - #end if - #if $input.input_select == "file": - $input.file - #elif $input.input_select == "accession_number": - $input.accession - #elif $input.input_select == "text": - `cat $input.text` - #end if - > $output</command> - <version_string>sra-pileup --version</version_string> - <inputs> - <conditional name="input"> - <param name="input_select" type="select" label="select input type"> - <option value="accession_number">SRR accession</option> - <option value="file">SRA archive in current history</option> - <option value="text">text file containing SRR accession</option> - </param> - <when value="file"> - <param format="sra" name="file" type="data" label="sra archive"/> - </when> - <when value="accession_number"> - <param format="text" name="accession" type="text" label="accession"/> - </when> - <when value="text"> - <param format="txt" name="text" type="data" label="text file"/> - </when> - </conditional> - <param format="text" name="region" type="text" label="aligned region"/> - <param format="text" name="minMapq" type="text" label="minimum mapping quality"/> - </inputs> - <outputs> - <data format="pileup" name="output"/> - </outputs> - <requirements> - <requirement type="package" version="2.3.3-3">sra_toolkit</requirement> - </requirements> - <help> - This tool produces pileup format from sra archives using sra-pileup. - Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies. - The sra-pileup program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software. - Contact Matt Shirley at mdshw5@gmail.com for support and bug reports. - </help> -</tool> |
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| diff -r c386fe82db82 -r da2dbe22f80b sra_tools-04cc8176e86f/tool_dependencies.xml --- a/sra_tools-04cc8176e86f/tool_dependencies.xml Wed Sep 25 21:00:05 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,37 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="sra_toolkit" version="2.3.3-3"> - <install version="1.0"> - <actions> - <action type="download_by_url">http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.3.3-3/sra_sdk-2.3.3-3.tar.gz</action> - <action type="shell_command">make release</action> - <action type="shell_command">make static</action> - <action type="shell_command">make</action> - <action type="make_directory">$INSTALL_DIR/bin</action> - <action type="make_directory">$INSTALL_DIR/ncbi</action> - <action type="make_directory">$INSTALL_DIR/ncbi/public</action> - <action type="shell_command">sed -i -e "s|\$(HOME)|$INSTALL_DIR|g" -e "s|cache-enabled = \"true\"|cache-enabled = \"false\"|" bin64/ncbi/default.kfg</action> - <action type="shell_command">cp --recursive --dereference bin64/* $INSTALL_DIR/bin</action> - <action type="set_environment"><environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable></action> - </actions> - </install> - <readme>Tools from NCBI SRA Toolkit for extracting FASTQ and SAM format reads from SRA format archives. -This software release was designed to run under Linux, MacOSX operating systems on Intel x86-compatible 64 bit architectures. -When running on Amazon EC2, be sure to keep in mind the size limitation of EBS storage devices when requesting a -download of a large SRA data set. - -Build Requirements: - ar - bash - make - gcc, g++ - libxml2 - libcurl4 - zlib - -On a debian based Linux OS use: - - apt-get install build-essential libxml2-dev libcurl4-openssl-dev zlib-dev - </readme> - </package> -</tool_dependency> |