Repository 'sra_tools'
hg clone https://toolshed.g2.bx.psu.edu/repos/mvdbeek/sra_tools

Changeset 0:9f74a22d2060 (2015-11-04)
Commit message:
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sra-tools commit 70fadb7e8972b1db550d0e067584930ce1ec8673-dirty
added:
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
b
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
b
@@ -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'.
b
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
[
@@ -0,0 +1,32 @@
+[![Build Status](https://travis-ci.org/mdshw5/sra-tools-galaxy.svg?branch=master)](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.
b
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
b
@@ -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
b
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
b
@@ -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>
b
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
[
@@ -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>
b
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
[
@@ -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>
b
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
b
@@ -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)
b
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
b
@@ -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>
b
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
[
@@ -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>
b
diff -r 000000000000 -r 9f74a22d2060 test-data/bam_dump_result.bam
b
Binary file test-data/bam_dump_result.bam has changed
b
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 @@\n+CM000679.1\t41243452\tC\t22\t..,,,.............,,,,\tEHEHHDHHHHHHHHHHHHGGHC\n+CM000679.1\t41243453\tT\t22\t..,,,.............,,,,\tEFDGGHHHHHHHHHHHHHHDGG\n+CM000679.1\t41243454\tA\t22\t..,,,.............,,,,\tDAABHHHHCHHHHHHHHEHFFG\n+CM000679.1\t41243455\tA\t22\t..,,,.............,,,,\tBF.DHHFFHHHDHHHHHEEFCG\n+CM000679.1\t41243456\tG\t22\t..,,,.............,,,,\t?FDFHDHHHHHHHFHHHHHHEG\n+CM000679.1\t41243457\tT\t22\t..,,,.............,,,,\t1D@EFHHFHHHHFHHHHFHHB@\n+CM000679.1\t41243458\tT\t22\t..,,,.............,,,,\t4FEEHHHHHHHHHHHHHHDCFE\n+CM000679.1\t41243459\tT\t22\t..,,,.............,,,,\t1GHHHHFHHHHHHHGHHGFHFF\n+CM000679.1\t41243460\tG\t22\t..,,,.............,,,,\t;FHHHEHHHHHHFHHGHGHFHH\n+CM000679.1\t41243461\tA\t22\t..,,,.............,,,,\t/:FGHBHHHHHHFHHHHGHHGH\n+CM000679.1\t41243462\tA\t22\t..,,,.............,,,,\t:EHFHDHHHHHHFHHHHEHHHG\n+CM000679.1\t41243463\tT\t22\t..,,,.............,,,,\t3EFHHFFFHHFHFHHHHHHFFH\n+CM000679.1\t41243464\tC\t22\t..,,,.............,,,,\t*?FHHFHFHHHHHHHHHHGHFH\n+CM000679.1\t41243465\tC\t22\t..,,,.............,,,,\t7FFHHHFHHHHHHHHHHHHHHF\n+CM000679.1\t41243466\tA\t22\t..,,,.............,,,,\t7?FEDHHHHHFHHHHHHHFHHH\n+CM000679.1\t41243467\tT\t22\t..,,,.............,,,,\t3CHHFHFHHHHHHHHHHHGHHH\n+CM000679.1\t41243468\tG\t22\t..,,,.............,,,,\t5EAHH=HHHHHHHHHHHHHHHB\n+CM000679.1\t41243469\tC\t22\t..,,,.............,,,,\t;FHHGGHHHHHHHHHHHHGHEH\n+CM000679.1\t41243470\tT\t22\t..,,,.............,,,,\t3E?GHGHHEHHHHHHHHHGHHH\n+CM000679.1\t41243471\tT\t22\t..,,,.............,,,,\t9EDFHHHHHHHHHHHHHHFHFD\n+CM000679.1\t41243472\tT\t24\t..,,,.............,,,,^>.^>.\t2FHHHDHHHHHHFHHHHHHHHHHH\n+CM000679.1\t41243473\tG\t24\t..,,,.............,,,,..\t0HHHH/HHHGHHHHHHHGGHHHHH\n+CM000679.1\t41243474\tC\t24\t..,,,.............,,,,TT\t>FHFHFHHHHHHHHHHHHFHHHHH\n+CM000679.1\t41243475\tT\t24\t..,,,.............,,,,..\t;FHHFGHHHHHHHHHFHHBHBGHH\n+CM000679.1\t41243476\tC\t24\t..,,,.............,,,,..\t<HFHHGEHHHHHFHHHHHHHDFHH\n+CM000679.1\t41243477\tT\t25\t..,,,.............,,,,..^].\t>FHHHGGHHHHHHHHHHHHHHHHHH\n+CM000679.1\t41243478\tT\t25\t..,,,.............,,,,...\t:HHHFEGHHHHHHHHHHHHHHHHHH\n+CM000679.1\t41243479\tC\t28\t..,,,.............,,,,...^].^].^].\tBHEHHEHHHHHHHHHHHHFHHHHHHHHH\n+CM000679.1\t41243480\tT\t28\t..,,,.............,,,,......\tCHHHHFFHHHHHHHHHHHHHHHHHHHHH\n+CM000679.1\t41243481\tT\t28\t..,,,.............,,,,......\tFHFHHGHHHHHHHHHHHHEHHHHHHHHH\n+CM000679.1\t41243482\tG\t31\t..,,,.............,,,,......^].^].^].\tCFHHHEHHEHHGHHHHHHHFHHHHHHHHHBF\n+CM000679.1\t41243483\tA\t32\t.$.,,,.............,,,,......CCC^F.\t#9HHHDHHHHEHHEHHBHEGHHHHHHHHH@GH\n+CM000679.1\t41243484\tT\t35\t.,,,.............,,,,..........^>.^>.^>.^>.\tFHHHGHHHHHHHFHHHEHHHHHHHHHHHDFHGHHH\n+CM000679.1\t41243485\tT\t35\t.,,,.............,,,,..............\tFHHHHFHHHHHHHHHHHHHHHHHHHHHHEFHGHHH\n+CM000679.1\t41243486\tA\t35\t.,,,.............,,,,......GGG.GGGG\tDFHHDFHHHEFHFHHHFHGGHHDHHHHHFFHGHHH\n+CM000679.1\t41243487\tT\t35\t.,,,.............,,,,..............\tEHHHGHHHHHHHHHHHHGHHFGHHHHHHEEHGHHH\n+CM000679.1\t41243488\tT\t41\t.,,,.............,,,,..............^]G^]G^]G^]G^]G^]G\tCHHHHHHFHHHHGHHHGHHEHHHHHHHHFGHFHHHHHHHHH\n+CM000679.1\t41243489\tT\t46\t.,,,$.............,$,$,$,$....................^>.^>.^>.^>.^>.\t/HHEFHHHHHHGHHHHHGHHGHHHHHHHEGHGHHHHHHHFHHHCHH\n+CM000679.1\t41243490\tT\t41\t.,,......................................\tBBGDGEHHHHHHHHHHHHHHHHHFHHFGHHHHHHHHHHIHH\n+CM000679.1\t41243491\tC\t41\t.,,......................................\tBFHEHFHHHHHHHHHHGEHHHHGEGHEHHHHHHHHHHHGHH\n+CM000679.1\t41243492\tT\t41\t.,,......................................\t=HHGGEHHGHGGHHHHHHHHHHHGHHDHHHHHHHHHHHEHH\n+CM000679.1\t41243493\tT\t45\t.,,......................................^],^],^],^],\tEFHDHHHGGHHHHHHHHGHHHHHFHHGHHHHHHHHHHHGHH@<<D\n+CM000679.1\t41243494\tC\t45\t.,,......................................,,,,\t<HHGFHFEHGEHHHHHHHHHHHHHHHGHHHHHHHGHHHGHH75:D\n+CM000679.1\t41243495\tC\t45\t.,,......................................,,,,\tDHHCGBHHHHFHHHHHHHHHHHHFHHGHHHHHHHHHHHHHHB<9D\n+CM000679.1\t41243496\tA\t47\t.$,,......................................,,,,^F,^F,\tDHHBEHHGBEGHHHHHHHHHHHEHEFFHHHHHHHEHHHFHHB>6D5#\n+CM000679.1\t41243497\tA\t46\t,,......................................,,,,,,\t'..b'1277359\tT\t2\t,,\tHE\n+CM000679.1\t41277360\tC\t2\t,,\tHG\n+CM000679.1\t41277361\tC\t2\t,,\tHE\n+CM000679.1\t41277362\tC\t2\t,,\tHH\n+CM000679.1\t41277363\tC\t2\t,,\tHG\n+CM000679.1\t41277364\tC\t2\t,,\tHH\n+CM000679.1\t41277365\tG\t2\t,,\tHH\n+CM000679.1\t41277366\tT\t2\t,,\tHH\n+CM000679.1\t41277367\tC\t2\t,,\tHH\n+CM000679.1\t41277368\tC\t2\t,,\tHF\n+CM000679.1\t41277369\tA\t2\t,,\tHH\n+CM000679.1\t41277370\tG\t2\t,,\tHH\n+CM000679.1\t41277371\tG\t2\t,,\tHH\n+CM000679.1\t41277372\tA\t2\t,,\tHE\n+CM000679.1\t41277373\tA\t2\t,,\tHH\n+CM000679.1\t41277374\tG\t2\t,,\tGH\n+CM000679.1\t41277375\tT\t2\t,,\tHH\n+CM000679.1\t41277376\tC\t2\t,,\tHH\n+CM000679.1\t41277377\tT\t2\t,,\tFH\n+CM000679.1\t41277378\tC\t2\t,,\tHH\n+CM000679.1\t41277379\tA\t2\t,,\tHH\n+CM000679.1\t41277380\tG\t2\t,,\tHH\n+CM000679.1\t41277381\tC\t2\t,,\tHH\n+CM000679.1\t41277382\tG\t2\t,,\tHH\n+CM000679.1\t41277383\tA\t2\t,,\tHH\n+CM000679.1\t41277384\tG\t2\t,,\tHH\n+CM000679.1\t41277385\tC\t2\t,,\tHH\n+CM000679.1\t41277386\tT\t2\t,$,$\tHG\n+CM000679.1\t41277419\tT\t4\t^].^].^].^].\tHGHH\n+CM000679.1\t41277420\tA\t4\t....\tHGHH\n+CM000679.1\t41277421\tA\t4\t....\tHEHH\n+CM000679.1\t41277422\tT\t4\t....\tHGHH\n+CM000679.1\t41277423\tT\t4\t....\tH=HH\n+CM000679.1\t41277424\tC\t4\t....\tHGHH\n+CM000679.1\t41277425\tC\t4\t....\tHGHH\n+CM000679.1\t41277426\tC\t4\t....\tHGHH\n+CM000679.1\t41277427\tG\t4\t....\tHGHH\n+CM000679.1\t41277428\tC\t4\t....\tHGHH\n+CM000679.1\t41277429\tG\t4\t....\tHFHH\n+CM000679.1\t41277430\tC\t4\t....\tHFGH\n+CM000679.1\t41277431\tT\t4\t....\tHGHH\n+CM000679.1\t41277432\tT\t4\t....\tHGHH\n+CM000679.1\t41277433\tT\t4\t....\tHGHH\n+CM000679.1\t41277434\tT\t4\t....\tHGHH\n+CM000679.1\t41277435\tC\t4\t....\tHGHH\n+CM000679.1\t41277436\tC\t4\t....\tHGHH\n+CM000679.1\t41277437\tG\t4\t....\tHGHH\n+CM000679.1\t41277438\tT\t4\t....\tHFHH\n+CM000679.1\t41277439\tT\t4\t....\tHGHH\n+CM000679.1\t41277440\tG\t4\t....\tHGHH\n+CM000679.1\t41277441\tC\t4\t....\tHGHH\n+CM000679.1\t41277442\tC\t4\t....\tHGHH\n+CM000679.1\t41277443\tA\t4\t....\tHGHH\n+CM000679.1\t41277444\tC\t4\t....\tHGHH\n+CM000679.1\t41277445\tG\t4\t....\tHGHH\n+CM000679.1\t41277446\tG\t4\t....\tHGHG\n+CM000679.1\t41277447\tA\t4\t....\tHGBH\n+CM000679.1\t41277448\tA\t4\t....\tHEHH\n+CM000679.1\t41277449\tA\t4\t....\tGGHG\n+CM000679.1\t41277450\tC\t4\t....\tHFHH\n+CM000679.1\t41277451\tC\t4\t....\tHGHH\n+CM000679.1\t41277452\tA\t4\t....\tHFBH\n+CM000679.1\t41277453\tA\t4\t....\tHFFH\n+CM000679.1\t41277454\tG\t4\t....\tHFHG\n+CM000679.1\t41277455\tG\t4\t....\tFEEH\n+CM000679.1\t41277456\tG\t4\t....\tHEFH\n+CM000679.1\t41277457\tG\t4\t....\tHCGH\n+CM000679.1\t41277458\tC\t5\t....^],\tHGHH#\n+CM000679.1\t41277459\tT\t5\t....,\tHFEG@\n+CM000679.1\t41277460\tA\t5\t....,\tGGHH;\n+CM000679.1\t41277461\tC\t5\t....,\tHCDHD\n+CM000679.1\t41277462\tC\t5\t....,\tHFEH=\n+CM000679.1\t41277463\tG\t5\t....,\tGGFHA\n+CM000679.1\t41277464\tC\t5\t....,\tHEGH5\n+CM000679.1\t41277465\tT\t5\t....,\tHEHH:\n+CM000679.1\t41277466\tA\t5\t....,\t=.BH7\n+CM000679.1\t41277467\tA\t5\t....,\tHDHH?\n+CM000679.1\t41277468\tG\t5\t....,\tHEHH?\n+CM000679.1\t41277469\tC\t7\t....,^],^],\tH@FHD##\n+CM000679.1\t41277470\tA\t7\t....,,,\tFAEHECA\n+CM000679.1\t41277471\tG\t7\t....,,,\tE;EEBA:\n+CM000679.1\t41277472\tC\t7\t....,,,\tH;FHGEE\n+CM000679.1\t41277473\tA\t7\t....,,,\tF.FHFFH\n+CM000679.1\t41277474\tG\t7\t....,,,\tFCHEEGH\n+CM000679.1\t41277475\tC\t7\t....,,,\tH@CFGHG\n+CM000679.1\t41277476\tC\t7\t....,,,\tHCFHEHE\n+CM000679.1\t41277477\tT\t7\t....,,,\tF@HGFHF\n+CM000679.1\t41277478\tC\t7\t....,,,\tHCEH?>B\n+CM000679.1\t41277479\tT\t7\t....,,,\t4FGDHFF\n+CM000679.1\t41277480\tC\t8\t....,,,^],\tDEGHDFG#\n+CM000679.1\t41277481\tA\t8\t....,,,,\tCBGHHGG?\n+CM000679.1\t41277482\tG\t8\t....,,,,\tAFGFHGGA\n+CM000679.1\t41277483\tA\t8\t....,,,,\t0@?HHHG=\n+CM000679.1\t41277484\tA\t8\t....,,,,\tCBGGHHHF\n+CM000679.1\t41277485\tT\t8\t....,,,,\t>CEDHHEF\n+CM000679.1\t41277486\tA\t8\t....,,,,\tCCEDHFHH\n+CM000679.1\t41277487\tC\t8\t....,,,,\tCCGDHHHH\n+CM000679.1\t41277488\tG\t8\t....,,,,\tC8GDGGHG\n+CM000679.1\t41277489\tA\t8\t....,,,,\tH.HHHHHG\n+CM000679.1\t41277490\tA\t8\t....,,,,\tD9EHHHHG\n+CM000679.1\t41277491\tA\t8\t....,,,,\tE4BHHHHG\n+CM000679.1\t41277492\tT\t8\t....,,,,\tG<FHCHEF\n+CM000679.1\t41277493\tC\t8\t....,,,,\tH7HGHEE8\n+CM000679.1\t41277494\tA\t8\t....,,,,\tECGFHHHG\n+CM000679.1\t41277495\tA\t8\t....,,,,\tF@GGHHHE\n+CM000679.1\t41277496\tG\t8\t....,,,,\tDAGFHHHG\n+CM000679.1\t41277497\tG\t8\t....,,,,\t=AE@HHHF\n+CM000679.1\t41277498\tT\t8\t....,,,,\tF.?GFGFG\n+CM000679.1\t41277499\tA\t8\t....,,,,\tG:EGHGH=\n+CM000679.1\t41277500\tC\t8\t....,,,,\tE:EGHGGE\n'
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>