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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sra-tools commit 70fadb7e8972b1db550d0e067584930ce1ec8673-dirty |
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LICENSE README.md README.txt datatypes_conf.xml fastq_dump.xml sam_dump.xml sra.py sra_macros.xml sra_pileup.xml test-data/bam_dump_result.bam test-data/fastq_dump_result.fastq test-data/sam_dump_result.sam test-data/sra_pileup_result.pileup tool_dependencies.xml |
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| diff -r 000000000000 -r 9f74a22d2060 LICENSE --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/LICENSE Wed Nov 04 06:57:32 2015 -0500 |
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| @@ -0,0 +1,60 @@ +CONTENTS + + Public Domain Notice + Exceptions (for bundled 3rd-party code) + Copyright F.A.Q. + + +============================================================== + PUBLIC DOMAIN NOTICE + National Center for Biotechnology Information + +With the exception of certain third-party files summarized below, this +software is a "United States Government Work" under the terms of the +United States Copyright Act. It was written as part of the authors' +official duties as United States Government employees and thus cannot +be copyrighted. This software is freely available to the public for +use. The National Library of Medicine and the U.S. Government have not +placed any restriction on its use or reproduction. + +Although all reasonable efforts have been taken to ensure the accuracy +and reliability of the software and data, the NLM and the U.S. +Government do not and cannot warrant the performance or results that +may be obtained by using this software or data. The NLM and the U.S. +Government disclaim all warranties, express or implied, including +warranties of performance, merchantability or fitness for any +particular purpose. + +Please cite the authors in any work or product based on this material. + + +============================================================== +Copyright F.A.Q. + + +-------------------------------------------------------------- +Q. Our product makes use of the NCBI source code, and we made changes + and additions to that version of the NCBI code to better fit it to + our needs. Can we copyright the code, and how? + +A. You can copyright only the *changes* or the *additions* you made to the + NCBI source code. You should identify unambiguously those sections of + the code that were modified, e.g. by commenting any changes you made + in the code you distribute. Therefore, your license has to make clear + to users that your product is a combination of code that is public domain + within the U.S. (but may be subject to copyright by the U.S. in foreign + countries) and code that has been created or modified by you. + +-------------------------------------------------------------- +Q. Can we (re)license all or part of the NCBI source code? + +A. No, you cannot license or relicense the source code written by NCBI + since you cannot claim any copyright in the software that was developed + at NCBI as a 'government work' and consequently is in the public domain + within the U.S. + +-------------------------------------------------------------- +Q. What if these copyright guidelines are not clear enough or are not + applicable to my particular case? + +A. Contact us. Send your questions to 'sra-tools@ncbi.nlm.nih.gov'. |
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| diff -r 000000000000 -r 9f74a22d2060 README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Wed Nov 04 06:57:32 2015 -0500 |
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| @@ -0,0 +1,32 @@ +[](https://travis-ci.org/mdshw5/sra-tools-galaxy) + +The Galaxy tool wrappers contained in this tool shed repository rely on software developed by +the NCBI: http://github.com/ncbi/sra-tools. + +# INSTALLATION + +Please use the Galaxy admin interface to install from the toolshed: https://toolshed.g2.bx.psu.edu/view/matt-shirley/ncbi_sra_toolkit + +This software release was designed to install using the Galaxy toolshed under Linux and MacOS operating systems on Intel x86-compatible 32/64 bit architectures. + +*Build Requirements* + +- bash +- git +- make +- gcc +- g++ +- perl +- libxml2 + +On a Debian OS use: + + apt-get install build-essential libxml2-dev git + +On a Mac with [command line tools](https://developer.apple.com/downloads/index.action) installed: + + brew install git libxml2 + +CONTROLLED-ACCESS DATA + +Encrypted, controlled-access data is not supported. |
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| diff -r 000000000000 -r 9f74a22d2060 README.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.txt Wed Nov 04 06:57:32 2015 -0500 |
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| @@ -0,0 +1,39 @@ +The Galaxy tool wrappers contained in this tool shed repository rely on software developed by +the NCBI Sequence Read Archive: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software. +Use of SRA Toolkit software herin should comply with the GPL v2 or greater. + +Copyright (C) 2013 Matthew Shirley + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 2 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + +INSTALLATION + +This software release was designed to run under Linux, MacOSX operating systems on Intel x86-compatible 64 bit architectures. + +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 + +CONTROLLED-ACCESS DATA + +Encrypted, controlled-access data is not supported in this version of the SRA Toolkit Galaxy tool shed. \ No newline at end of file |
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| diff -r 000000000000 -r 9f74a22d2060 datatypes_conf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/datatypes_conf.xml Wed Nov 04 06:57:32 2015 -0500 |
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| @@ -0,0 +1,12 @@ +<?xml version="1.0"?> +<datatypes> + <datatype_files> + <datatype_file name="sra.py"/> + </datatype_files> + <registration> + <datatype extension="sra" type="galaxy.datatypes.sra:Sra" mimetype="application/octet-stream" display_in_upload="true"/> + </registration> + <sniffers> + <sniffer type="galaxy.datatypes.sra:Sra"/> + </sniffers> +</datatypes> |
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| diff -r 000000000000 -r 9f74a22d2060 fastq_dump.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fastq_dump.xml Wed Nov 04 06:57:32 2015 -0500 |
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| @@ -0,0 +1,142 @@ +<tool id="fastq_dump" name="Extract reads" version="1.2.4"> + <description>in FASTQ/A format from NCBI SRA.</description> + <macros> + <import>sra_macros.xml</import> + </macros> + <expand macro="requirements"/> + <command> + <![CDATA[ + ## Need to set the home directory to the current working directory, + ## else the tool tries to write to home/.ncbi and fails when used + ## with a cluster manager. + export HOME=\$PWD; + vdb-config --restore-defaults; + #if $input.input_select == "file": + fastq-dump --log-level fatal --accession '${input.file.name}' + #else: + vdb-config -s "/repository/user/main/public/root=\$PWD"; + ## Do not use prefetch if region is specified, to avoid downloading + ## the complete sra file. + #if ( str( $adv.region ) == "" ) and ( str( $adv.minID ) == "" ) and ( str( $adv.maxID ) == "" ): + ASCP_PATH=`which ascp`; + ASCP_KEY=`dirname \$ASCP_PATH`/asperaweb_id_dsa.openssh; + prefetch --ascp-path "\$ASCP_PATH|\$ASCP_KEY" $input.accession; + #end if + ## Duplicate vdb-config, in case settings changed between prefetch and + ## dump command. + vdb-config -s "/repository/user/main/public/root=\$PWD"; + fastq-dump --accession "$input.accession" + #end if + --defline-seq '@\$sn[_\$rn]/\$ri' + --stdout + #if str( $adv.split ) == "yes": + --split-spot + #end if + #if str( $adv.alignments ) == "aligned": + --aligned + #end if + #if str( $adv.alignments ) == "unaligned": + --unaligned + #end if + #if str( $adv.minID ) != "": + --minSpotId "$adv.minID" + #end if + #if str( $adv.maxID ) != "": + --maxSpotId "$adv.maxID" + #end if + #if str( $adv.minlen ) != "": + --minReadLen "$adv.minlen" + #end if + #if str( $adv.readfilter ) != "": + --read-filter "$adv.readfilter" + #end if + #if str( $adv.region ) != "": + --aligned-region "$adv.region" + #end if + #if str( $adv.spotgroups ) != "": + --spot-groups "$adv.spotgroups" + #end if + #if str( $adv.matepairDist ) != "": + --matepair-distance "$adv.matepairDist" + #end if + #if $adv.clip == "yes": + --clip + #end if + #if str( $outputformat ) == "fasta": + --fasta + #end if + #if $input.input_select=="file": + "$input.file" > "$output_file" + #else: + "$input.accession" > "$output_accession" + #end if + ]]> + </command> + <version_string>fastq-dump --version</version_string> + <inputs> + <expand macro="input_conditional"/> + <param name="outputformat" type="select" label="select output format"> + <option value="fastqsanger">fastq</option> + <option value="fasta">fasta</option> + </param> + <section name="adv" title="Advanced Options" expanded="False"> + <param name="minID" type="integer" label="minimum spot ID" optional="true"/> + <param name="maxID" type="integer" label="maximum spot ID" optional="true"/> + <param name="minlen" type="integer" label="minimum read length" optional="true"/> + <param name="split" type="select" value="yes"> + <label>split spot by read pairs</label> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <expand macro="alignments"/> + <expand macro="region"/> + <expand macro="matepairDist"/> + <param name="readfilter" type="select" value=""> + <label>filter by value</label> + <option value="">None</option> + <option value="pass">pass</option> + <option value="reject">reject</option> + <option value="criteria">criteria</option> + <option value="redacted">redacted</option> + </param> + <param name="spotgroups" type="text" label="filter by spot-groups" optional="true"/> + <param name="clip" type="select" value="no"> + <label>apply left and right clips</label> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + </section> + </inputs> + <outputs> + <data format="fastq" name="output_accession" label="${input.accession}.${outputformat}"> + <filter>input['input_select'] == "accession_number"</filter> + <change_format> + <when input="outputformat" value="fasta" format="fasta"/> + </change_format> + </data> + <data format="fastq" name="output_file" label="${input.file.name}.${outputformat}"> + <filter>input['input_select'] == "file"</filter> + <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> + <tests> + <test> + <param name="input_select" value="accession_number"/> + <param name="outputformat" value="fastqsanger"/> + <param name="accession" value="SRR925743"/> + <param name="maxID" value="5"/> + <output name="output_accession" file="fastq_dump_result.fastq" ftype="fastq"/> + </test> + </tests> + <help> + This tool extracts reads from SRA archives using fastq-dump. + The fastq-dump program is developed at NCBI, and is available at + http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software. + @SRATOOLS_ATTRRIBUTION@ + </help> +</tool> |
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| diff -r 000000000000 -r 9f74a22d2060 sam_dump.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sam_dump.xml Wed Nov 04 06:57:32 2015 -0500 |
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| @@ -0,0 +1,117 @@ +<tool id="sam_dump" name="Extract reads" version="1.2.4"> + <description>in SAM or BAM format from NCBI SRA.</description> + <macros> + <import>sra_macros.xml</import> + </macros> + <expand macro="requirements"/> + <command> + <![CDATA[ + ## Need to set the home directory to the current working directory, + ## else the tool tries to write to home/.ncbi and fails when used + ## with a cluster manager. + export HOME=\$PWD; + vdb-config --restore-defaults; + vdb-config -s "/repository/user/main/public/root=\$PWD"; + ## Do not use prefetch if region is specified, to avoid downloading + ## the complete sra file. + #if ( str( $adv.region ) == "" ): + ASCP_PATH=`which ascp`; + ASCP_KEY=`dirname \$ASCP_PATH`/asperaweb_id_dsa.openssh; + prefetch --ascp-path "\$ASCP_PATH|\$ASCP_KEY" "$input.accession"; + ##Duplicate vdb-config, in case settings changed between prefetch and + ##dump command. + #end if + vdb-config -s "/repository/user/main/public/root=\$PWD"; + sam-dump --log-level fatal --disable-multithreading + #if str( $adv.region ) != "": + --aligned-region "$adv.region" + #end if + #if str( $adv.matepairDist ) != "": + --matepair-distance "$adv.matepairDist" + #end if + #if str( $adv.minMapq ) != "": + --min-mapq "$adv.minMapq" + #end if + #if str( $adv.header ) == "yes": + --header + #else: + --no-header + #end if + #if str( $adv.alignments ) == "both": + --unaligned + #end if + #if str( $adv.alignments ) == "unaligned": + --unaligned-spots-only + #end if + #if (str( $adv.primary ) == "yes") and (str ( $adv.alignments != "unaligned") ): + --primary + #end if + #if $input.input_select == "file": + "$input.file" + #elif $input.input_select == "accession_number": + "$input.accession" + #end if + #if str( $outputformat ) == "bam": + | samtools view -Sb - 2> /dev/null + #end if + #if $input.input_select == "file": + > "$output_file" + #elif $input.input_select == "accession_number": + > "$output_accession" + #end if + ]]> + </command> + <version_string>sam-dump --version</version_string> + <inputs> + <expand macro="input_conditional"/> + <param name="outputformat" type="select" label="select output format"> + <option value="bam">bam</option> + <option value="sam">sam</option> + </param> + <section name="adv" title="Advanced Options" expanded="False"> + <param name="header" type="select" value="yes"> + <label>output header</label> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <expand macro="alignments"/> + <expand macro="region"/> + <expand macro="matepairDist"/> + <param name="primary" type="select" value="no"> + <label>only primary aligments</label> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <expand macro="minMapq"></expand> + </section> + </inputs> + <outputs> + <data name="output_accession" format="bam" label="${input.accession}.${outputformat}"> + <filter>input['input_select'] == "accession_number"</filter> + <change_format> + <when input="outputformat" value="sam" format="sam"/> + </change_format> + </data> + <data name="output_file" format="bam" label="${input.file.name}.${outputformat}"> + <filter>input['input_select'] == "file"</filter> + <change_format> + <when input="outputformat" value="sam" format="sam"/> + </change_format> + </data> + </outputs> + <tests> + <test> + <param name="input_select" value="accession_number"/> + <param name="accession" value="SRR925743"/> + <param name="outputformat" value="sam"/> + <param name="region" value="17:41243452-41277500"/> + <output name="output_accession" file="sam_dump_result.sam" ftype="sam"/> + </test> + </tests> + <help> + This tool extracts reads from sra archives using sam-dump. + The sam-dump program is developed at NCBI, and is available at + http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software. + @SRATOOLS_ATTRRIBUTION@ + </help> +</tool> |
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| diff -r 000000000000 -r 9f74a22d2060 sra.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sra.py Wed Nov 04 06:57:32 2015 -0500 |
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| @@ -0,0 +1,45 @@ +""" +NCBI sra class +""" +import logging +import binascii +from galaxy.datatypes.data import nice_size +from galaxy.datatypes.binary import Binary + +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 'NCBI.sra', and the file is binary. + 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 = 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)' % (nice_size(dataset.get_size())) + +Binary.register_sniffable_binary_format('sra', 'sra', Sra) |
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| diff -r 000000000000 -r 9f74a22d2060 sra_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sra_macros.xml Wed Nov 04 06:57:32 2015 -0500 |
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| @@ -0,0 +1,48 @@ +<macros> + <macro name="requirements"> + <requirements> + <requirement type="package" version="1.1.3">ngs_sdk</requirement> + <requirement type="package" version="2.5.2">ncbi_vdb</requirement> + <requirement type="package" version="2.5.2">sra_toolkit</requirement> + <requirement type="package" version="3">ascp</requirement> + <requirement type="package" version="5.18.1">perl</requirement> + </requirements> + </macro> + <macro name="input_conditional"> + <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="accession_number"> + <param name="accession" type="text" label="accession"/> + </when> + <when value="file"> + <param format="sra" name="file" type="data" label="sra archive"/> + </when> + </conditional> + </macro> + <macro name="alignments"> + <param 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> + </macro> + <macro name="minMapq"> + <param name="minMapq" type="integer" min="0" max="42" label="minimum mapping quality" optional="true"/> + </macro> + <macro name="region"> + <param format="text" name="region" type="text" label="aligned region" optional="true" + help="Filter by position on genome. Name can either be accession.version (ex: NC_000001.10) or file specific name (ex:chr1 or 1). from and to are 1-based coordinates"/> + </macro> + <macro name="matepairDist"> + <param name="matepairDist" type="text" label="mate-pair distance (from-to|unknown)" optional="true" + help="Filter by distance between matepairs. Use unknown to find matepairs split between the references. Use from-to (inclusive) to limit matepair distance on the same reference"/> + </macro> + <token name="@SRATOOLS_ATTRRIBUTION@">Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies. + Galaxy tool wrapper originally written by Matt Shirley (mdshw5 at gmail.com). + Tool dependencies, clean-up and bug-fixes by Marius van den Beek (m.vandenbeek at gmail.com). + For support and bug reports contact Matt Shirley or Marius van den Beek or go to https://github.com/mdshw5/sra-tools-galaxy.</token> +</macros> |
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| diff -r 000000000000 -r 9f74a22d2060 sra_pileup.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sra_pileup.xml Wed Nov 04 06:57:32 2015 -0500 |
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| @@ -0,0 +1,89 @@ +<tool id="sra_pileup" name="Generate pileup format" version="1.2.4"> + <description>from NCBI sra.</description> + <macros> + <import>sra_macros.xml</import> + </macros> + <expand macro="requirements"/> + <command> + <![CDATA[ + ## Need to set the home directory to the current working directory, + ## else the tool tries to write to home/.ncbi and fails when used + ## with a cluster manager. + export HOME=\$PWD; + vdb-config --restore-defaults; + vdb-config -s "/repository/user/main/public/root=\$PWD"; + #if ( str( $adv.region ) == "" ): + ASCP_PATH=`which ascp`; + ASCP_KEY=`dirname \$ASCP_PATH`/asperaweb_id_dsa.openssh; + prefetch --ascp-path "\$ASCP_PATH|\$ASCP_KEY" "$input.accession"; + ##Duplicate vdb-config, in case settings changed between prefetch and + ##dump command. + #end if + vdb-config -s "/repository/user/main/public/root=\$PWD"; + sra-pileup --log-level fatal + #if str( $adv.region ) != "": + + --aligned-region "$adv.region" + + #end if + #if str( $adv.minMapq ) != "": + --minmapq "$adv.minMapq" + #end if + #if $input.input_select == "file": + "$input.file" > "$output_file" + #elif $input.input_select == "accession_number": + "$input.accession" > "$output_accession" + #elif $input.input_select == "text": + `cat $input.text` > "$output_text" + #end if + ]]> + </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> + <section name="adv" title="Advanced Options" expanded="False"> + <expand macro="region"/> + <expand macro="minMapq"/> + </section> + </inputs> + <outputs> + <data format="pileup" name="output_accession" label="${input.accession}.pileup"> + <filter>input['input_select'] == "accession_number"</filter> + </data> + <data format="pileup" name="output_file" label="${input.file.name}.pileup"> + <filter>input['input_select'] == "file"</filter> + </data> + <data format="pileup" name="output_text" label="${input.text.name}.pileup"> + <filter>input['input_select'] == "text"</filter> + </data> + </outputs> + <tests> + <test> + <param name="input_select" value="accession_number"/> + <param name="accession" value="SRR925743"/> + <param name="region" value="17:41243452-41277500"/> + <output name="output_accession" file="sra_pileup_result.pileup" ftype="pileup"/> + </test> + </tests> + <help> + This tool produces pileup format from sra archives using sra-pileup. + The sra-pileup program is developed at NCBI, and is available at + http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software. + @SRATOOLS_ATTRRIBUTION@ + </help> +</tool> |
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| diff -r 000000000000 -r 9f74a22d2060 test-data/bam_dump_result.bam |
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| Binary file test-data/bam_dump_result.bam has changed |
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| diff -r 000000000000 -r 9f74a22d2060 test-data/fastq_dump_result.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastq_dump_result.fastq Wed Nov 04 06:57:32 2015 -0500 |
| b |
| @@ -0,0 +1,40 @@ +@1/1 +AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGT ++SRR925743.1 1 length=100 +EGGEGGGDFGEEEAEECGDEGGFEEGEFGBEEDDECFEFDD@CDD<EDDE?2@?AEEDEED=D+C?5@A=6:>BA8:>@:4+36945&4354445>/B>@ +@1/2 +CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTA ++SRR925743.1 1 length=100 +GHHHDFDFGFGEGFBGEGGEGEGGGHGFGHFHFHHHHHHHEF?EFEFF?EHGGHHHGHFHEHDEHGHFFEEE9BDDBEBAD.AD:ACBBC=4@>?5>=+? +@2/1 +AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGGTAGGGTTAGGGT ++SRR925743.2 2 length=100 +HHHHHHEGFHEEFEEHEEHHGGEGGGGEFGFGGGGHHHHFBEEEEEFGGEEAEEEDD0ADDBD9BDBDDA@6?BA;?CD=:-7<<::)1;5,6-6A@?=9 +@2/2 +CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTA ++SRR925743.2 2 length=100 +HHHHHHHHHHHHHGHHHHHHGHHHHHHHHHHHFHHHFHHHHHHHHHHHHHHHHHHHGHHHGHHBHGHHFDBDDED5FCFCEEGF<@>>>@,<5<@@?>;D +@3/1 +CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCA ++SRR925743.3 3 length=100 +HHHHFHHHHHHHHHHHFHHHHHHHHHHHHHHHHHHHHHHHGEFHGEGGFGGGGGGHHHHEFEIDDEEEEEDD4DD;??:6>6<@.<==@?.@@<?##### +@3/2 +ATGGATGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGT ++SRR925743.3 3 length=100 +HHHHHHHHHFIEGFHFHDHHHHGFFHGEGDIGGEGGHHHAGEGGGDHHHHHHHHHHHFGDGGGEGDFFF>BEEEE3B;BB;>B7C@DA=DFBDD.BEE=9 +@4/1 +CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACACTAACCCTAACCCTAACCCTAACCCTA ++SRR925743.4 4 length=100 +HHGBHHHHGFHHHHHFDHHFHGEHHHHHEFHHHHEGEGEFFFAFFFDCFGF?@GCDFGFEFHHEFDF*F6DC4DD:A8>@D@CD8->=>=<@CB@##### +@4/2 +ATGGATGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGT ++SRR925743.4 4 length=100 +GFFFHHFFHHHFHHFEFGGBGEEEE?<9?6=>>:=DDDD@DBGDB;DBDBA.ADD8<2<>6A@=A5>550=>>>>BE;EEEDEEE79+336<68=BCEB@ +@5/1 +CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACACTAACCCTCACACTCACCCTA ++SRR925743.5 5 length=100 +GGGFGFFGGGFBGGEGGFFGGGCFFGGGGGEGFFFFFGFFGFFFDFFB+FGGFEE?FCF::7B5A?+BB############################### +@5/2 +ATGGATGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGGTAGGGTTAGGGTTAGGGTTAGGGGTAGGGT ++SRR925743.5 5 length=100 +479<.>><:<A7BABBE8@=:<<:@BB?C75:2?;.5<<3FEFGEEC88FEDEE=AB><AA@B<ABDC8.27<9:58.58??6<:@>+?=9@######## |
| b |
| diff -r 000000000000 -r 9f74a22d2060 test-data/sam_dump_result.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sam_dump_result.sam Wed Nov 04 06:57:32 2015 -0500 |
| b |
| b'@@ -0,0 +1,3025 @@\n+@HD\tVN:1.3\n+@SQ\tSN:1\tAS:CM000663.1\tLN:249250621\n+@SQ\tSN:2\tAS:CM000664.1\tLN:243199373\n+@SQ\tSN:3\tAS:CM000665.1\tLN:198022430\n+@SQ\tSN:4\tAS:CM000666.1\tLN:191154276\n+@SQ\tSN:5\tAS:CM000667.1\tLN:180915260\n+@SQ\tSN:6\tAS:CM000668.1\tLN:171115067\n+@SQ\tSN:7\tAS:CM000669.1\tLN:159138663\n+@SQ\tSN:8\tAS:CM000670.1\tLN:146364022\n+@SQ\tSN:9\tAS:CM000671.1\tLN:141213431\n+@SQ\tSN:10\tAS:CM000672.1\tLN:135534747\n+@SQ\tSN:11\tAS:CM000673.1\tLN:135006516\n+@SQ\tSN:12\tAS:CM000674.1\tLN:133851895\n+@SQ\tSN:13\tAS:CM000675.1\tLN:115169878\n+@SQ\tSN:14\tAS:CM000676.1\tLN:107349540\n+@SQ\tSN:15\tAS:CM000677.1\tLN:102531392\n+@SQ\tSN:16\tAS:CM000678.1\tLN:90354753\n+@SQ\tSN:17\tAS:CM000679.1\tLN:81195210\n+@SQ\tSN:18\tAS:CM000680.1\tLN:78077248\n+@SQ\tSN:19\tAS:CM000681.1\tLN:59128983\n+@SQ\tSN:20\tAS:CM000682.1\tLN:63025520\n+@SQ\tSN:21\tAS:CM000683.1\tLN:48129895\n+@SQ\tSN:22\tAS:CM000684.1\tLN:51304566\n+@SQ\tSN:X\tAS:CM000685.1\tLN:155270560\n+@SQ\tSN:Y\tAS:CM000686.1\tLN:59373566\n+@SQ\tSN:M\tAS:J01415.2\tLN:16569\n+@SQ\tSN:1_gl000191_random\tAS:NT_113878.1\tLN:106433\n+@SQ\tSN:4_gl000193_random\tAS:NT_113885.1\tLN:189789\n+@SQ\tSN:4_gl000194_random\tAS:NT_113888.1\tLN:191469\n+@SQ\tSN:Un_gl000218\tAS:NT_113889.1\tLN:161147\n+@SQ\tSN:6_cox_hap2\tAS:NT_113891.2\tLN:4795371\n+@SQ\tSN:7_gl000195_random\tAS:NT_113901.1\tLN:182896\n+@SQ\tSN:8_gl000197_random\tAS:NT_113907.1\tLN:37175\n+@SQ\tSN:8_gl000196_random\tAS:NT_113909.1\tLN:38914\n+@SQ\tSN:9_gl000201_random\tAS:NT_113911.1\tLN:36148\n+@SQ\tSN:9_gl000198_random\tAS:NT_113914.1\tLN:90085\n+@SQ\tSN:9_gl000200_random\tAS:NT_113915.1\tLN:187035\n+@SQ\tSN:9_gl000199_random\tAS:NT_113916.2\tLN:169874\n+@SQ\tSN:11_gl000202_random\tAS:NT_113921.2\tLN:40103\n+@SQ\tSN:Un_gl000212\tAS:NT_113923.1\tLN:186858\n+@SQ\tSN:17_gl000205_random\tAS:NT_113930.1\tLN:174588\n+@SQ\tSN:17_gl000203_random\tAS:NT_113941.1\tLN:37498\n+@SQ\tSN:17_gl000204_random\tAS:NT_113943.1\tLN:81310\n+@SQ\tSN:17_gl000206_random\tAS:NT_113945.1\tLN:41001\n+@SQ\tSN:18_gl000207_random\tAS:NT_113947.1\tLN:4262\n+@SQ\tSN:19_gl000208_random\tAS:NT_113948.1\tLN:92689\n+@SQ\tSN:19_gl000209_random\tAS:NT_113949.1\tLN:159169\n+@SQ\tSN:21_gl000210_random\tAS:NT_113950.2\tLN:27682\n+@SQ\tSN:Un_gl000211\tAS:NT_113961.1\tLN:166566\n+@SQ\tSN:1_gl000192_random\tAS:NT_167207.1\tLN:547496\n+@SQ\tSN:Un_gl000213\tAS:NT_167208.1\tLN:164239\n+@SQ\tSN:Un_gl000214\tAS:NT_167209.1\tLN:137718\n+@SQ\tSN:Un_gl000215\tAS:NT_167210.1\tLN:172545\n+@SQ\tSN:Un_gl000216\tAS:NT_167211.1\tLN:172294\n+@SQ\tSN:Un_gl000217\tAS:NT_167212.1\tLN:172149\n+@SQ\tSN:Un_gl000219\tAS:NT_167213.1\tLN:179198\n+@SQ\tSN:Un_gl000220\tAS:NT_167214.1\tLN:161802\n+@SQ\tSN:Un_gl000221\tAS:NT_167215.1\tLN:155397\n+@SQ\tSN:Un_gl000222\tAS:NT_167216.1\tLN:186861\n+@SQ\tSN:Un_gl000223\tAS:NT_167217.1\tLN:180455\n+@SQ\tSN:Un_gl000224\tAS:NT_167218.1\tLN:179693\n+@SQ\tSN:Un_gl000225\tAS:NT_167219.1\tLN:211173\n+@SQ\tSN:Un_gl000226\tAS:NT_167220.1\tLN:15008\n+@SQ\tSN:Un_gl000227\tAS:NT_167221.1\tLN:128374\n+@SQ\tSN:Un_gl000228\tAS:NT_167222.1\tLN:129120\n+@SQ\tSN:Un_gl000229\tAS:NT_167223.1\tLN:19913\n+@SQ\tSN:Un_gl000230\tAS:NT_167224.1\tLN:43691\n+@SQ\tSN:Un_gl000231\tAS:NT_167225.1\tLN:27386\n+@SQ\tSN:Un_gl000232\tAS:NT_167226.1\tLN:40652\n+@SQ\tSN:Un_gl000233\tAS:NT_167227.1\tLN:45941\n+@SQ\tSN:Un_gl000234\tAS:NT_167228.1\tLN:40531\n+@SQ\tSN:Un_gl000235\tAS:NT_167229.1\tLN:34474\n+@SQ\tSN:Un_gl000236\tAS:NT_167230.1\tLN:41934\n+@SQ\tSN:Un_gl000237\tAS:NT_167231.1\tLN:45867\n+@SQ\tSN:Un_gl000238\tAS:NT_167232.1\tLN:39939\n+@SQ\tSN:Un_gl000239\tAS:NT_167233.1\tLN:33824\n+@SQ\tSN:Un_gl000240\tAS:NT_167234.1\tLN:41933\n+@SQ\tSN:Un_gl000241\tAS:NT_167235.1\tLN:42152\n+@SQ\tSN:Un_gl000242\tAS:NT_167236.1\tLN:43523\n+@SQ\tSN:Un_gl000243\tAS:NT_167237.1\tLN:43341\n+@SQ\tSN:Un_gl000244\tAS:NT_167238.1\tLN:39929\n+@SQ\tSN:Un_gl000245\tAS:NT_167239.1\tLN:36651\n+@SQ\tSN:Un_gl000246\tAS:NT_167240.1\tLN:38154\n+@SQ\tSN:Un_gl000247\tAS:NT_167241.1\tLN:36422\n+@SQ\tSN:Un_gl000248\tAS:NT_167242.1\tLN:39786\n+@SQ\tSN:Un_gl000249\tAS:NT_167243.1\tLN:38502\n+@SQ\tSN:6_apd_hap1\tAS:NT_167244.1\tLN:4622290\n+@SQ\tSN:6_dbb_hap3\tAS:NT_167245.1\tLN:4610396\n+@SQ\tSN:6_mann_hap4\tAS:NT_167246.1\tLN:4683263\n+@SQ\tSN:6_mcf_hap5\tAS:NT_167247.1\tLN:4833398\n+@SQ\tSN:6_qbl_hap6\tAS:NT_167248.1\tLN:4611984\n+@SQ\tSN:6_ssto_hap7\tAS:'..b'HHHHHHHHHHHHHHHHHHHHHHGHHHHHHHHGEHDHHHHHHHHHEHFGE=BHIGEGGEDHEHHHHDFGBGG\tRG:Z:0\n+44155476\t133\t*\t0\t0\t*\t17\t41267696\t0\tCAAAAACAAAAGCTAGTCTGGAGTTGATCAAGGAACCTGTCTCCACAAAGTGTGACCACATATTTTGCAAGTAAGTTTGAATGTGTTATGTGGCTCCATT\tHHHHHHHHHHHHHHHHHHHHHBHFGHHHHHHHHHHHHHHHHHHHHHHHHHHHFHBHHHHHHGHGHGDHDGHHHHHHHEHHHHHFHFHHHGBFFHFHG8HG\tRG:Z:0\n+44155477\t133\t*\t0\t0\t*\t17\t41267696\t0\tCAAAAACAAAAGCTAGTCTGGAGTTGATCAAGGAACCTGTCTCCACAAAGTGTGACCACATATTTTGCAAGTAAGTTTGAATGTGTTATGTGGCTCCATT\tHHHHHHHHHHGHHHFHHHHHHFHHHHHHHHHHHHHHHHHHHHFHGHHHHHHHFHHHHHHHHHHHHHHHEHHHHHHHHHHHFHHHFHHFBHHHFGHHH<EG\tRG:Z:0\n+44155502\t133\t*\t0\t0\t*\t17\t41275955\t0\tTATGTAAGGTCAATTCTGTTCATTAATGCTATGCAGAAAATCTTAGAGTGTCCCATCTGGTAAGTCAGCACAAGAGTGTATTAATTTGGGATTCCTATGA\tHHHHHGHHHFHHHHHHHGFHHHHHHHHHHHHFBHHHHHHEHHHHHHF>DHHFHHFHHHHHFHCHFHGGHHHHHFHHFF;HBFFD?GFDFAACCAFEEFE?\tRG:Z:0\n+44155503\t133\t*\t0\t0\t*\t17\t41275955\t0\tTATGTAAGGTCAATTCTGTTCATTAATGCTATGCAGAAAATCTTAGAGTGTCCCATCTGGTAAGTCAGCACAAGAGTGTATTAATTTGGGATTCCTATGA\tHHHHHHHHHBFFFFGFHFFHEHGHGGFEFFFHFEF@EFEEHHHHFHFHDHFHHHHHHFHEHHHHFHHHHHHHHFBE:FAAFEFEFHDHHBCE?FF>ADA5\tRG:Z:0\n+44155504\t133\t*\t0\t0\t*\t17\t41275955\t0\tTATGTAAGGTCAATTCTGTTCATTAATGCTATGCAGAAAATCTTAGAGTGTCCCATCTGGTAAGTCAGCACAAGAGTGTATTAATTTGGGATTCCTATGA\tHHHHHGHHH:HHHHHHHH<HGFFGGHEHHHHHHHHHHHFHHHHHFHDGDHGGFGGHHHHHHHHHHFHHHBGF?IA@5A>B6;>??FGFA4>ACB5ECEE#\tRG:Z:0\n+44155505\t133\t*\t0\t0\t*\t17\t41275976\t0\tATTTGCATAGGAGAAAATCTTAGAGTGTCCCATCTGGTAAGTCAGCACAAGAGTGTATTAATTTGGGATTCCTATGATTATCTCCTATGCAAATAGATCG\tHHHHHHHHHFHHHHHHHHHHHHHHGFHFHHHHHHHHHFHHHHHHHHHHHFIGECIEIGGGHHHHHHGHHHHHFHGHHHHHHHHHHHHFEHFDDFFFFFCG\tRG:Z:0\n+44155511\t165\t*\t0\t0\t*\t17\t41275978\t0\tCATTAATGCTATGCAGATAATCATAGGAATCCCAAATTAATACACTCTTGTGCTGACTTACCAGATGGGACACTCTAAGATTTTCTGCATAGCATTAATG\tHHHHHHHHHHHHHHHHHGHDHHHHHHHHHHHHHEHHHHHHHGHHHGHHHHHHHHHHHHHHHHHHHGFHHFHHHHHFHEBGHHHHHD<EFGBBBCAGFGE;\tRG:Z:0\n+44155516\t165\t*\t0\t0\t*\t17\t41275988\t0\tCATTAATGCTATGCAGATAATCATAGGAATCCCAAATTAATACACTCTTGTGCTGACTTACCAGATGGGACACTCTAAGATTTTCTGCATAGCATTAATG\tHHHHHHHHHHHHHHHHFGHHHHHHGHHHHHHHHGHFHHHHHHHEHHHHHFHHHHHFHHHHHHHHHFCCDDHFFHGFHHHBBHFHHFFF@FEFCCBBEE=:\tRG:Z:0\n+44155520\t133\t*\t0\t0\t*\t17\t41276001\t0\tATCCCAAATTAATACACTCTTAGAGTGTCCCATCTGGTAAGTCAGCACAAGAGTGTATTAATTTGGGATAGATCGGAAGAGCGTCGTGTAGGGAAAGAGG\tHHHHHHHHHHHHHHHHHHHHHGHFHDHFHFHHHHHHHFHBHEHHFHHHHHGGGBGEHGGIHHHHHDHEHHEHHHHBHHHHHFFFFFEHEECHEBDEFEF#\tRG:Z:0\n+44155522\t133\t*\t0\t0\t*\t17\t41276005\t0\tCAAATTAATACACTCTTCGCGTTGAAGAAGTACAAAATGTCATTAATGCTATGCAGAAAATCTTAGAGTGTCCCATCTGGTAAGTCAGCACAAGAGTGTA\tHHHHHHHHHHHGHHHGHHHHGHHHFHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEHFHEHGHHHHGHHHBHEHFHHHEF3FF######\tRG:Z:0\n+44155523\t133\t*\t0\t0\t*\t17\t41276005\t0\tCAAATTAATACACTCTTCGCGTTGAAGAAGTACAAAATGTCATTAATGCTATGCAGAAAATCTTAGAGTGTCCCATCTGGTAAGTCAGCACAAGAGTGTA\tFGDBGEFFDGGDEFGFFGFG=EACE>CBDDFCFBBDBCCDEGGFEEEE=ECADDFFGD@BGFFEEC8EEE=EEGDBDDDEGBDFG7@B>BAGBADGDEEB\tRG:Z:0\n+44155531\t165\t*\t0\t0\t*\t17\t41276036\t0\tAAGTTCATTGGGACACTCTAAGATTTTCTGCATAGCATTAATGACATTTTGTACTTCTTCAACGCGAAGAGCAGATAAATCCATTTCTTTCTGTTCCAAT\tHFHHEHHHHHHHHHFHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEHHHHHACFIFGIGHHHFHFGHHHHHFHHFF5HH\tRG:Z:0\n+44155532\t165\t*\t0\t0\t*\t17\t41276056\t0\tAGAAAGAAATGGATTTTCTGCATAGCATTAATGACATTTTGTACTTCTTCAACGCGAAGAGCAGATAAATCCATTTCTTTCTAGATCGGAAGAGCGTCGT\tHHHHHHHHHHHHHHHHHGHHHHHHHHHHHFHHHHHHGHHHHFGHHGHHHHHHHHHHHHHHHEHHFGBGGGFHHHHHHDHHHHHHFGHHC:EA9BEEDDGB\tRG:Z:0\n+44155533\t165\t*\t0\t0\t*\t17\t41276058\t0\tAGAAAGAAATGGATTTTCTGCATAGCATTAATGACATTTTGTACTTCTTCAACGCGAAGAGCAGATAAATCCATTTCTTTCTAGATCGGAAGAGCGTCGT\tHHHHHHHHHHHHHHHHHHHHHHDEHEHHHHEHHHHHHHHHHHHHHHHHHHHHHHGHHHHHHHHHGHEHHEHHHHHHHHHHHHEHHHHHFHHFHHHEEHF9\tRG:Z:0\n+44155535\t165\t*\t0\t0\t*\t17\t41276061\t0\tAGAAAGAAATGGATTTTCTGCATAGCATTAATGACATTTTGTACTTCTTCAACGCGAAGAGCAGATAAATCCATTTCTTTCTAGATCGGAAGAGCGTCGT\tHHHHHHFHHHHHHHHHHHHGHHHFHHHHHFHHHHHFHHHHHHHHHHFHHHGFHHFGHHHHHHHHHEFHHHHHGHHGGHHGHHHHEGH=CHG@E<G@CEA?\tRG:Z:0\n+44155536\t165\t*\t0\t0\t*\t17\t41276063\t0\tAACAGAAAGAAATGGATTTTCTGCATAGCATTAATGACATTTTGTACTTCTTCAACGCGAAGAGCAGATAAATCCATTTCTTTCTGTTAGATCGGAAGAG\tHHHHHHHHHFHHHHHHHHHHHHHHHFHHHHHHHHHHHHHHHHHHHHHHHFHHHHEHEHHHEHGHHHFEHFHHHHHHHHHFHEHHGHFHHHHFBFHHHHHF\tRG:Z:0\n' |
| b |
| diff -r 000000000000 -r 9f74a22d2060 test-data/sra_pileup_result.pileup --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sra_pileup_result.pileup Wed Nov 04 06:57:32 2015 -0500 |
| b |
| b'@@ -0,0 +1,7349 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|
| b |
| diff -r 000000000000 -r 9f74a22d2060 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Nov 04 06:57:32 2015 -0500 |
| b |
| @@ -0,0 +1,18 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="ncbi_vdb" version="2.5.2"> + <repository changeset_revision="1d307129f4f2" name="package_ncbi_vdb_2_5_2" owner="mvdbeek" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="ngs_sdk" version="1.1.3"> + <repository changeset_revision="2cc3f1941cb5" name="package_ngs_sdk_1_1_3" owner="mvdbeek" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="sra_toolkit" version="2.5.2"> + <repository changeset_revision="88273fd00182" name="package_sra_toolkit_2_5_2" owner="mvdbeek" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="ascp" version="3"> + <repository changeset_revision="e109f0ec22c3" name="package_ascp_3" owner="mvdbeek" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="perl" version="5.18.1"> + <repository changeset_revision="8b3509930a44" name="package_perl_5_18" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |