| Next changeset 1:da2dbe22f80b (2013-09-25) |
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Commit message:
Initial commit, moving from test tool shed. |
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added:
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 000000000000 -r c386fe82db82 sra_tools-04cc8176e86f/datatypes_conf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sra_tools-04cc8176e86f/datatypes_conf.xml Wed Sep 25 21:00:05 2013 -0400 |
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| @@ -0,0 +1,9 @@ +<?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 000000000000 -r c386fe82db82 sra_tools-04cc8176e86f/fastq_dump.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sra_tools-04cc8176e86f/fastq_dump.xml Wed Sep 25 21:00:05 2013 -0400 |
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| @@ -0,0 +1,123 @@ +<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 000000000000 -r c386fe82db82 sra_tools-04cc8176e86f/sam_dump.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sra_tools-04cc8176e86f/sam_dump.xml Wed Sep 25 21:00:05 2013 -0400 |
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| @@ -0,0 +1,99 @@ +<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 000000000000 -r c386fe82db82 sra_tools-04cc8176e86f/sra.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sra_tools-04cc8176e86f/sra.py Wed Sep 25 21:00:05 2013 -0400 |
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| @@ -0,0 +1,46 @@ +""" +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 000000000000 -r c386fe82db82 sra_tools-04cc8176e86f/sra_pileup.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sra_tools-04cc8176e86f/sra_pileup.xml Wed Sep 25 21:00:05 2013 -0400 |
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| @@ -0,0 +1,51 @@ +<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 000000000000 -r c386fe82db82 sra_tools-04cc8176e86f/tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sra_tools-04cc8176e86f/tool_dependencies.xml Wed Sep 25 21:00:05 2013 -0400 |
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| @@ -0,0 +1,37 @@ +<?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> |