changeset 0:b723c120161a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
author iuc
date Sun, 06 Dec 2015 09:04:37 -0500
parents
children 462ee06c9358
files LICENSE README.rst fastq_dump.xml sam_dump.xml 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
diffstat 11 files changed, 610 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/LICENSE	Sun Dec 06 09:04:37 2015 -0500
@@ -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'.
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Sun Dec 06 09:04:37 2015 -0500
@@ -0,0 +1,68 @@
+The Galaxy tool wrappers contained in this tool shed repository rely on software developed by
+the NCBI: http://github.com/ncbi/sra-tools.
+
+NCBI Sequence Read Archive: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software.
+Use of SRA Toolkit software herein 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 install using the Galaxy toolshed under Linux and MacOS operating systems on Intel x86-compatible 32/64 bit architectures.
+
+*Build Requirements*
+
+- bash
+- make
+- gcc
+- g++
+- libxml2
+
+On a Debian OS use:
+
+    apt-get install build-essential libxml2-dev
+
+On a Mac with [command line tools](https://developer.apple.com/downloads/index.action) installed:
+
+    brew install libxml2
+
+# Installation of Aspera connect ascp binary
+
+The sra-tools suite is ready to benefit from increased transfer speed and reliability by using Aspera Connect ascp.
+To benefit, download the ascp commandline client, and place ascp and the required ssh keys into a PATH accessible to galaxys job handler.
+
+A convenience package for linux and OS X is available at https://toolshed.g2.bx.psu.edu/view/mvdbeek/package_ascp_3/e109f0ec22c3 .
+It suffices to copy the contents of the $INSTALL_DIR/bin into PATH.
+
+Alternatively go to http://downloads.asperasoft.com/connect2/ .
+
+Aspera connect is not provided by the IUC due to its closed-source nature.
+
+# Firewall settings for highspeed transfer
+
+To benefit from increased transfer speeds using ascp3 your local firewall must permit UDP data transfer in both
+directions on ports 33001-33009 for the following IP ranges:
+
+    130.14.*.*
+
+    165.112.*.*
+
+The firewall must also allow ssh traffic outbound to NCBI.
+The wrapper will fall back to http download if these requirements are not met.
+
+CONTROLLED-ACCESS DATA
+
+Encrypted, controlled-access data is not supported.
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastq_dump.xml	Sun Dec 06 09:04:37 2015 -0500
@@ -0,0 +1,149 @@
+<tool id="fastq_dump" name="Extract reads" version="1.2.5">
+    <description>in FASTQ/A format from NCBI SRA.</description>
+    <macros>
+        <import>sra_macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <stdio>
+        <exit_code range="127" level="fatal" description="Could not locate fastq-dump binary"/>
+    </stdio>
+    <version_command>fastq-dump --version</version_command>
+    <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=`command -v ascp` &&
+            ASCP_KEY=`dirname \$ASCP_PATH`/asperaweb_id_dsa.openssh || true &&
+            prefetch --ascp-path "\$ASCP_PATH|\$ASCP_KEY" $input.accession &&
+            ## Duplicate vdb-config, in case settings changed between prefetch and
+            ## dump command.
+            vdb-config -s "/repository/user/main/public/root=\$PWD" &&
+            #end if
+        fastq-dump --accession "$input.accession"
+    #end if
+    --defline-seq '@\$sn[_\$rn]/\$ri'
+    --stdout
+    $adv.split
+    #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
+    $adv.clip
+    $adv.skip_technical
+    #if str( $outputformat ) == "fasta":
+        --fasta
+    #end if
+    #if $input.input_select=="file":
+        "$input.file" > "$output_file"
+    #else:
+        "$input.accession" > "$output_accession"
+    #end if
+    ]]>
+    </command>
+    <inputs>
+        <expand macro="input_conditional"/>
+        <param name="outputformat" type="select" label="select output format">
+            <option value="fastqsanger">fastq</option>
+            <option value="fasta">fasta</option>
+        </param>
+        <section name="adv" title="Advanced Options" expanded="False">
+            <param name="minID" type="integer" label="minimum spot ID" optional="true"/>
+            <param name="maxID" type="integer" label="maximum spot ID" optional="true"/>
+            <param name="minlen" type="integer" label="minimum read length" optional="true"/>
+            <param name="split" type="boolean" checked="true" truevalue="--split-spot" falsevalue="">
+                <label>split spot by read pairs</label>
+            </param>
+            <expand macro="alignments"/>
+            <expand macro="region"/>
+            <expand macro="matepairDist"/>
+            <param name="readfilter" type="select" value="">
+                <label>filter by value</label>
+                <option value="">None</option>
+                <option value="pass">pass</option>
+                <option value="reject">reject</option>
+                <option value="criteria">criteria</option>
+                <option value="redacted">redacted</option>
+            </param>
+            <param name="spotgroups" type="text" label="filter by spot-groups" optional="true"/>
+            <param name="clip" type="boolean" truevalue="--clip" falsevalue="">
+                <label>apply left and right clips</label>
+            </param>
+            <param name="skip_technical" type="boolean" truevalue="--skip-technical" falsevalue="" checked="False" label="Dump only biological reads"/>
+        </section>
+    </inputs>
+    <outputs>
+        <data format="fastq" name="output_accession" label="${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>
+    <tests>
+        <test>
+            <param name="input_select" value="accession_number"/>
+            <param name="outputformat" value="fastqsanger"/>
+            <param name="accession" value="SRR044777"/>
+            <param name="skip_technical" value="True"/>
+            <output name="output_accession">
+                <assert_contents>
+                    <not_has_text text="rRNA_primer"/>
+                    <has_text text="F47USSH02GNP1D" />
+                </assert_contents>
+            </output>
+        </test>
+        <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>
+    <expand macro="citation"/>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sam_dump.xml	Sun Dec 06 09:04:37 2015 -0500
@@ -0,0 +1,118 @@
+<tool id="sam_dump" name="Extract reads" version="1.2.5">
+    <description>in SAM or BAM format from NCBI SRA.</description>
+    <macros>
+        <import>sra_macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <version_command>sam-dump --version</version_command>
+    <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( $adv.region ) == "" ):
+            ASCP_PATH=`command -v ascp` &&
+            ASCP_KEY=`dirname \$ASCP_PATH`/asperaweb_id_dsa.openssh || true &&
+            prefetch --ascp-path "\$ASCP_PATH|\$ASCP_KEY" "$input.accession" &&
+            ## Duplicate vdb-config, in case settings changed between prefetch and
+            ## dump command.
+            vdb-config -s "/repository/user/main/public/root=\$PWD" &&
+        #end if
+        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>
+    <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" compare="contains" 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>
+    <expand macro="citation"/>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sra_macros.xml	Sun Dec 06 09:04:37 2015 -0500
@@ -0,0 +1,52 @@
+<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="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="SRR accession" help="Must start with SRR, e.g. SRR925743"/>
+            </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. Can be either accession.version (ex: NC_000001.10), chromosome name (ex:chr1 or 1) or 1-based coordinates (ex: chr1:1-101)."/>
+    </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>
+    <macro name="citation">
+        <citations>
+            <citation type="doi">10.1093/nar/gkq1019</citation>
+        </citations>
+    </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/galaxyproject/tools-iuc.</token>
+</macros>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sra_pileup.xml	Sun Dec 06 09:04:37 2015 -0500
@@ -0,0 +1,88 @@
+<tool id="sra_pileup" name="Generate pileup format" version="1.2.5">
+    <description>from NCBI sra.</description>
+    <macros>
+        <import>sra_macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <version_command>sra-pileup --version</version_command>
+    <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( $adv.region ) == "" ):
+            ASCP_PATH=`command -v ascp` &&
+            ASCP_KEY=`dirname \$ASCP_PATH`/asperaweb_id_dsa.openssh || true &&
+            prefetch --ascp-path "\$ASCP_PATH|\$ASCP_KEY" "$input.accession" &&
+            ## Duplicate vdb-config, in case settings changed between prefetch and
+            ## sra-pileup command.
+            vdb-config -s "/repository/user/main/public/root=\$PWD" &&
+        #end if
+        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"` > "$output_text"
+        #end if
+        ]]>
+    </command>
+    <inputs>
+        <conditional name="input">
+            <param name="input_select" type="select" label="select input type">
+                <option value="accession_number">SRR accession</option>
+                <option value="file">SRA archive in current history</option>
+                <option value="text">text file containing SRR accession</option>
+            </param>
+            <when value="file">
+                <param format="sra" name="file" type="data" label="sra archive"/>
+            </when>
+            <when value="accession_number">
+                <param format="text" name="accession" type="text" label="SRR accession" help="Must start with SRR, e.g. SRR925743"/>
+            </when>
+            <when value="text">
+                <param format="txt" name="text" type="data" label="text file"/>
+            </when>
+        </conditional>
+        <section name="adv" title="Advanced Options" expanded="False">
+            <expand macro="region"/>
+          <expand macro="minMapq"/>
+        </section>
+    </inputs>
+    <outputs>
+        <data format="pileup" name="output_accession" label="${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" compare="contains" 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>
+    <expand macro="citation"/>
+</tool>
Binary file test-data/bam_dump_result.bam has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastq_dump_result.fastq	Sun Dec 06 09:04:37 2015 -0500
@@ -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@########
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sam_dump_result.sam	Sun Dec 06 09:04:37 2015 -0500
@@ -0,0 +1,10 @@
+44155511	165	*	0	0	*	17	41275978	0	CATTAATGCTATGCAGATAATCATAGGAATCCCAAATTAATACACTCTTGTGCTGACTTACCAGATGGGACACTCTAAGATTTTCTGCATAGCATTAATG	HHHHHHHHHHHHHHHHHGHDHHHHHHHHHHHHHEHHHHHHHGHHHGHHHHHHHHHHHHHHHHHHHGFHHFHHHHHFHEBGHHHHHD<EFGBBBCAGFGE;	RG:Z:0
+44155516	165	*	0	0	*	17	41275988	0	CATTAATGCTATGCAGATAATCATAGGAATCCCAAATTAATACACTCTTGTGCTGACTTACCAGATGGGACACTCTAAGATTTTCTGCATAGCATTAATG	HHHHHHHHHHHHHHHHFGHHHHHHGHHHHHHHHGHFHHHHHHHEHHHHHFHHHHHFHHHHHHHHHFCCDDHFFHGFHHHBBHFHHFFF@FEFCCBBEE=:	RG:Z:0
+44155520	133	*	0	0	*	17	41276001	0	ATCCCAAATTAATACACTCTTAGAGTGTCCCATCTGGTAAGTCAGCACAAGAGTGTATTAATTTGGGATAGATCGGAAGAGCGTCGTGTAGGGAAAGAGG	HHHHHHHHHHHHHHHHHHHHHGHFHDHFHFHHHHHHHFHBHEHHFHHHHHGGGBGEHGGIHHHHHDHEHHEHHHHBHHHHHFFFFFEHEECHEBDEFEF#	RG:Z:0
+44155522	133	*	0	0	*	17	41276005	0	CAAATTAATACACTCTTCGCGTTGAAGAAGTACAAAATGTCATTAATGCTATGCAGAAAATCTTAGAGTGTCCCATCTGGTAAGTCAGCACAAGAGTGTA	HHHHHHHHHHHGHHHGHHHHGHHHFHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEHFHEHGHHHHGHHHBHEHFHHHEF3FF######	RG:Z:0
+44155523	133	*	0	0	*	17	41276005	0	CAAATTAATACACTCTTCGCGTTGAAGAAGTACAAAATGTCATTAATGCTATGCAGAAAATCTTAGAGTGTCCCATCTGGTAAGTCAGCACAAGAGTGTA	FGDBGEFFDGGDEFGFFGFG=EACE>CBDDFCFBBDBCCDEGGFEEEE=ECADDFFGD@BGFFEEC8EEE=EEGDBDDDEGBDFG7@B>BAGBADGDEEB	RG:Z:0
+44155531	165	*	0	0	*	17	41276036	0	AAGTTCATTGGGACACTCTAAGATTTTCTGCATAGCATTAATGACATTTTGTACTTCTTCAACGCGAAGAGCAGATAAATCCATTTCTTTCTGTTCCAAT	HFHHEHHHHHHHHHFHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEHHHHHACFIFGIGHHHFHFGHHHHHFHHFF5HH	RG:Z:0
+44155532	165	*	0	0	*	17	41276056	0	AGAAAGAAATGGATTTTCTGCATAGCATTAATGACATTTTGTACTTCTTCAACGCGAAGAGCAGATAAATCCATTTCTTTCTAGATCGGAAGAGCGTCGT	HHHHHHHHHHHHHHHHHGHHHHHHHHHHHFHHHHHHGHHHHFGHHGHHHHHHHHHHHHHHHEHHFGBGGGFHHHHHHDHHHHHHFGHHC:EA9BEEDDGB	RG:Z:0
+44155533	165	*	0	0	*	17	41276058	0	AGAAAGAAATGGATTTTCTGCATAGCATTAATGACATTTTGTACTTCTTCAACGCGAAGAGCAGATAAATCCATTTCTTTCTAGATCGGAAGAGCGTCGT	HHHHHHHHHHHHHHHHHHHHHHDEHEHHHHEHHHHHHHHHHHHHHHHHHHHHHHGHHHHHHHHHGHEHHEHHHHHHHHHHHHEHHHHHFHHFHHHEEHF9	RG:Z:0
+44155535	165	*	0	0	*	17	41276061	0	AGAAAGAAATGGATTTTCTGCATAGCATTAATGACATTTTGTACTTCTTCAACGCGAAGAGCAGATAAATCCATTTCTTTCTAGATCGGAAGAGCGTCGT	HHHHHHFHHHHHHHHHHHHGHHHFHHHHHFHHHHHFHHHHHHHHHHFHHHGFHHFGHHHHHHHHHEFHHHHHGHHGGHHGHHHHEGH=CHG@E<G@CEA?	RG:Z:0
+44155536	165	*	0	0	*	17	41276063	0	AACAGAAAGAAATGGATTTTCTGCATAGCATTAATGACATTTTGTACTTCTTCAACGCGAAGAGCAGATAAATCCATTTCTTTCTGTTAGATCGGAAGAG	HHHHHHHHHFHHHHHHHHHHHHHHHFHHHHHHHHHHHHHHHHHHHHHHHFHHHHEHEHHHEHGHHHFEHFHHHHHHHHHFHEHHGHFHHHHFBFHHHHHF	RG:Z:0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sra_pileup_result.pileup	Sun Dec 06 09:04:37 2015 -0500
@@ -0,0 +1,10 @@
+CM000679.1	41277491	A	8	....,,,,	E4BHHHHG
+CM000679.1	41277492	T	8	....,,,,	G<FHCHEF
+CM000679.1	41277493	C	8	....,,,,	H7HGHEE8
+CM000679.1	41277494	A	8	....,,,,	ECGFHHHG
+CM000679.1	41277495	A	8	....,,,,	F@GGHHHE
+CM000679.1	41277496	G	8	....,,,,	DAGFHHHG
+CM000679.1	41277497	G	8	....,,,,	=AE@HHHF
+CM000679.1	41277498	T	8	....,,,,	F.?GFGFG
+CM000679.1	41277499	A	8	....,,,,	G:EGHGH=
+CM000679.1	41277500	C	8	....,,,,	E:EGHGGE
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Sun Dec 06 09:04:37 2015 -0500
@@ -0,0 +1,15 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="ncbi_vdb" version="2.5.2">
+        <repository changeset_revision="b980182ad267" name="package_ncbi_vdb_2_5_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="ngs_sdk" version="1.1.3">
+        <repository changeset_revision="1197d3c98375" name="package_ngs_sdk_1_1_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="sra_toolkit" version="2.5.2">
+        <repository changeset_revision="ab06c0240705" name="package_sra_toolkit_2_5_2" owner="iuc" 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>