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changeset 1:da2dbe22f80b

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Deleted selected files
author matt-shirley
date Wed, 25 Sep 2013 21:02:15 -0400
parents c386fe82db82
children 293927a46697
files sra_tools-04cc8176e86f/datatypes_conf.xml sra_tools-04cc8176e86f/fastq_dump.xml sra_tools-04cc8176e86f/sam_dump.xml sra_tools-04cc8176e86f/sra.py sra_tools-04cc8176e86f/sra_pileup.xml sra_tools-04cc8176e86f/tool_dependencies.xml
diffstat 6 files changed, 0 insertions(+), 365 deletions(-) [+]
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--- a/sra_tools-04cc8176e86f/datatypes_conf.xml	Wed Sep 25 21:00:05 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,9 +0,0 @@
-<?xml version="1.0"?>
-<datatypes>
-  <datatype_files>
-    <datatype_file name="sra.py"/>
-  </datatype_files>
-  <registration>
-    <datatype extension="sra" type="galaxy.datatypes.sra:sra" display_in_upload="true"/>
-  </registration>
-</datatypes>
--- a/sra_tools-04cc8176e86f/fastq_dump.xml	Wed Sep 25 21:00:05 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,123 +0,0 @@
-<tool id="fastq_dump" name="Extract reads" version="1.1.1">
-  <description> from NCBI SRA.</description>
-  <command>
-    fastq-dump --log-level fatal 
-    #if $input.input_select == "file":
-      --accession '${input.file.name}' 
-    #else:
-      --accession $input.accession 
-    #end if
-    --defline-seq '@\$sn[_\$rn]/\$ri' 
-    --stdout 
-    #if $split == "yes":
-      --split-spot
-    #end if
-    #if str( $alignments ) == "aligned":
-      --aligned
-    #end if
-    #if str( $alignments ) == "unaligned":
-      --unaligned
-    #end if
-    #if str( $minID ) != "":
-      --minSpotId $minID 
-    #end if
-    #if str( $maxID ) != "":
-      --maxSpotId $maxID 
-    #end if
-    #if str( $minlen ) != "":
-      --minReadLen $minlen 
-    #end if
-    #if str( $readfilter ) != "":
-      --read-filter $readfilter 
-    #end if
-    #if str( $region ) != "":
-      --aligned-region $region
-    #end if
-    #if str( $spotgroups ) != "":
-      --spot-groups $spotgroups
-    #end if
-    #if str( $matepairDist ) != "":
-      --matepair-distance $matepairDist
-    #end if
-    #if $clip == "yes":
-      --clip
-    #end if
-    #if str( $outputformat ) == "fasta":
-      --fasta
-    #end if
-    #if $input.input_select=="file":
-      $input.file
-    #else:
-        $input.accession 
-    #end if
-    > $output
-  </command>
-  <version_string>fastq-dump --version</version_string>
-  <inputs>
-    <conditional name="input">
-      <param name="input_select" type="select" label="select input type">
-        <option value="accession_number">SRR accession</option>
-        <option value="file">SRA archive in current history</option>
-      </param>
-      <when value="file">
-    <param format="sra" name="file" type="data" label="sra archive"/>
-      </when>
-      <when value="accession_number">
-    <param format="text" name="accession" type="text" label="accession"/>
-      </when>
-    </conditional>
-    <param format="text" name="minID" type="text" label="minimum spot ID"/>
-    <param format="text" name="maxID" type="text" label="maximum spot ID"/>
-    <param format="text" name="minlen" type="text" label="minimum read length"/>
-    <param format="text" name="split" type="select" value="yes">
-      <label>split spot by read pairs</label>
-      <option value="yes">Yes</option>
-      <option value="no">No</option>
-    </param>
-    <param format="text" name="alignments" type="select" value="both">
-      <label>aligned or unaligned reads</label>
-      <option value="both">both</option>
-      <option value="aligned">aligned only</option>
-        <option value="unaligned">unaligned only</option>
-    </param>
-    <param format="text" name="region" type="text" label="aligned region"/>
-    <param format="text" name="matepairDist" type="text" label="mate-pair distance (from-to|unknown)"/>
-    <param format="text" name="readfilter" type="select" value="">
-      <label>filter by value</label>
-      <option value="">None</option>
-      <option value="pass">pass</option>
-      <option value="reject">reject</option>
-      <option value="criteria">criteria</option>
-      <option value="redacted">redacted</option>
-    </param>
-    <param name="outputformat" type="select" label="select output format">
-      <option value="fastqsanger">fastq</option>
-      <option value="fasta">fasta</option>
-    </param>
-    <param format="text" name="spotgroups" type="text" label="filter by spot-groups"/>
-    <param format="text" name="clip" type="select" value="no">
-      <label>apply left and right clips</label>
-      <option value="no">No</option>
-      <option value="yes">Yes</option>
-    </param>
-  </inputs>
-  <outputs>
-    <data format="fastq" name="output">
-        <change_format>
-            <when input="outputformat" value="fasta" format="fasta" />
-        </change_format>
-    </data>
-  </outputs>
-  <stdio>
-    <exit_code range="127" level="fatal" description="Could not locate fastq-dump binary"/>
-  </stdio>
-  <requirements>
-    <requirement type="package" version="2.3.3-3">sra_toolkit</requirement>
-  </requirements>
-  <help>
-    This tool extracts reads from SRA archives using fastq-dump. 
-    Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies. 
-    The fastq-dump program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software.
-    Contact Matt Shirley at mdshw5@gmail.com for support and bug reports.
-  </help>
-</tool>
--- a/sra_tools-04cc8176e86f/sam_dump.xml	Wed Sep 25 21:00:05 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,99 +0,0 @@
-<tool id="sam_dump" name="Extract reads" version="1.1.1">
-  <description> in SAM format from NCBI SRA.</description>
-  <command>
-    sam-dump --log-level fatal 
-    #if str( $region ) != "":
-      --aligned-region $region
-    #end if
-    #if str( $matepairDist ) != "":
-      --matepair-distance $matepairDist
-    #end if
-    #if str( $minMapq ) != "":
-      --minmapq $minMapq
-    #end if
-    #if $header == "yes":
-      --header
-    #else:
-      --no-header 
-    #end if
-    #if str( $alignments ) == "both":
-      --unaligned
-    #end if
-    #if str( $alignments ) == "unaligned":
-      --unaligned-spots-only
-    #end if
-    #if (str( $primary ) == "yes") and (str ( $alignments != "unaligned") ):
-      --primary
-    #end if
-    #if str( $fastq ) == "yes":
-      --fastq
-    #end if
-    #if $input.input_select == "file":
-      $input.file
-    #elif $input.input_select == "accession_number":
-      $input.accession 
-    #elif $input.input_select == "text":
-      `cat $input.text`
-    #end if
-    > $output
-  </command>  
-  <version_string>sam-dump --version</version_string>
-  <inputs>
-    <conditional name="input">
-      <param name="input_select" type="select" label="select input type">
-        <option value="accession_number">SRR accession</option>
-        <option value="file">SRA archive in current history</option>
-        <option value="text">text file containing SRR accession</option>
-      </param>
-      <when value="file">
-        <param format="sra" name="file" type="data" label="sra archive"/>
-      </when>
-      <when value="accession_number">
-        <param format="text" name="accession" type="text" label="accession"/>
-      </when>
-      <when value="text">
-        <param format="txt" name="text" type="data" label="text file"/>
-      </when>
-    </conditional>
-    <param format="text" name="region" type="text" label="aligned region"/>
-    <param format="text" name="matepairDist" type="text" label="mate-pair distance (from-to|unknown)"/>
-    <param format="text" name="header" type="select" value="yes">
-      <label>output SAM header</label>
-      <option value="yes">Yes</option>
-      <option value="no">No</option>
-    </param>
-    <param format="text" name="alignments" type="select" value="both">
-      <label>aligned or unaligned reads</label>
-      <option value="both">both</option>
-      <option value="aligned">aligned only</option>
-        <option value="unaligned">unaligned only</option>
-    </param>
-    <param format="text" name="primary" type="select" value="no">
-      <label>only primary aligments</label>
-      <option value="no">No</option>
-      <option value="yes">Yes</option>
-    </param>
-    <param format="text" name="minMapq" type="text" label="minimum mapping quality"/>
-    <param format="text" name="fastq" type="select" value="no">
-      <label>output fastq</label>
-      <option value="no">No</option>
-      <option value="yes">Yes</option>
-    </param>
-  </inputs>
-  <outputs>
-    <data name="output" format="sam">
-      <change_format>
-        <when input="fastq" value="yes" format="fastq"/>
-      </change_format>
-    </data>
-  </outputs>
-  <requirements>
-    <requirement type="package" version="2.3.3-3">sra_toolkit</requirement>
-  </requirements>
-  <help>
-    This tool extracts reads from sra archives using sam-dump. 
-    Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies. 
-    The sam-dump program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software.
-    Contact Matt Shirley at mdshw5@gmail.com for support and bug reports.
-  </help>
-</tool>
\ No newline at end of file
--- a/sra_tools-04cc8176e86f/sra.py	Wed Sep 25 21:00:05 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,46 +0,0 @@
-"""
-NCBI sra class
-"""
-import logging
-import binascii
-from galaxy.datatypes.data import *
-from galaxy.datatypes.sniff import *
-from galaxy.datatypes.binary import *
-from galaxy.datatypes.metadata import *
-
-log = logging.getLogger(__name__)
-
-class sra( Binary ):
-    """ Sequence Read Archive (SRA) """
-    file_ext = 'sra'
-
-    def __init__( self, **kwd ):
-        Binary.__init__( self, **kwd )
-    def sniff( self, filename ):
-        """ The first 8 bytes of any NCBI sra file is 'NCIB.sra', and the file is binary. EBI and DDBJ files may differ, though EBI and DDBJ 
-        submissions through NCBI (ERR and DRR accessions) read 'NCBI.sra'.
-        For details about the format, see http://www.ncbi.nlm.nih.gov/books/n/helpsra/SRA_Overview_BK/#SRA_Overview_BK.4_SRA_Data_Structure 
-        """
-        try:
-            header = open(filename).read(8)
-            if binascii.b2a_hex(header) == binascii.hexlify('NCBI.sra'):
-                return True
-            else:
-                return False
-        except:
-            return False
-    def set_peek(self, dataset, is_multi_byte=False):
-        if not dataset.dataset.purged:
-            dataset.peek  = 'Binary sra file'
-            dataset.blurb = data.nice_size(dataset.get_size())
-        else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
-    def display_peek(self, dataset):
-        try:
-            return dataset.peek
-        except:
-            return 'Binary sra file (%s)' % ( data.nice_size(dataset.get_size()))
-
-if hasattr(Binary, 'register_sniffable_binary_format'):
-    Binary.register_sniffable_binary_format('sra', 'sra', sra)
--- a/sra_tools-04cc8176e86f/sra_pileup.xml	Wed Sep 25 21:00:05 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,51 +0,0 @@
-<tool id="sra_pileup" name="Generate pileup format" version="1.1.1">
-  <description> from NCBI sra.</description>
-  <command>sra-pileup --log-level fatal 
-    #if str( $region ) != "":
-      --aligned-region $region
-    #end if
-    #if str( $minMapq ) != "":
-      --minmapq $minMapq
-    #end if
-    #if $input.input_select == "file":
-      $input.file
-    #elif $input.input_select == "accession_number":
-      $input.accession 
-    #elif $input.input_select == "text":
-      `cat $input.text`
-    #end if
-    > $output</command>
-  <version_string>sra-pileup --version</version_string>
-  <inputs>
-    <conditional name="input">
-      <param name="input_select" type="select" label="select input type">
-        <option value="accession_number">SRR accession</option>
-        <option value="file">SRA archive in current history</option>
-        <option value="text">text file containing SRR accession</option>
-      </param>
-      <when value="file">
-        <param format="sra" name="file" type="data" label="sra archive"/>
-      </when>
-      <when value="accession_number">
-        <param format="text" name="accession" type="text" label="accession"/>
-      </when>
-      <when value="text">
-        <param format="txt" name="text" type="data" label="text file"/>
-      </when>
-    </conditional>
-    <param format="text" name="region" type="text" label="aligned region"/>
-    <param format="text" name="minMapq" type="text" label="minimum mapping quality"/>
-  </inputs>
-  <outputs>
-    <data format="pileup" name="output"/>
-  </outputs>
-  <requirements>
-    <requirement type="package" version="2.3.3-3">sra_toolkit</requirement>
-  </requirements>
-  <help>
-    This tool produces pileup format from sra archives using sra-pileup. 
-    Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies. 
-    The sra-pileup program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software.
-    Contact Matt Shirley at mdshw5@gmail.com for support and bug reports.
-  </help>
-</tool>
--- a/sra_tools-04cc8176e86f/tool_dependencies.xml	Wed Sep 25 21:00:05 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,37 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-  <package name="sra_toolkit" version="2.3.3-3">
-    <install version="1.0">
-      <actions>
-        <action type="download_by_url">http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.3.3-3/sra_sdk-2.3.3-3.tar.gz</action>
-        <action type="shell_command">make release</action>
-        <action type="shell_command">make static</action>
-        <action type="shell_command">make</action>
-        <action type="make_directory">$INSTALL_DIR/bin</action>	
-        <action type="make_directory">$INSTALL_DIR/ncbi</action>	
-        <action type="make_directory">$INSTALL_DIR/ncbi/public</action>	
-        <action type="shell_command">sed -i -e "s|\$(HOME)|$INSTALL_DIR|g" -e "s|cache-enabled = \"true\"|cache-enabled = \"false\"|" bin64/ncbi/default.kfg</action>
-        <action type="shell_command">cp --recursive --dereference bin64/* $INSTALL_DIR/bin</action>
-        <action type="set_environment"><environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable></action>
-      </actions>
-    </install>
-    <readme>Tools from NCBI SRA Toolkit for extracting FASTQ and SAM format reads from SRA format archives. 
-This software release was designed to run under Linux, MacOSX operating systems on Intel x86-compatible 64 bit architectures. 
-When running on Amazon EC2, be sure to keep in mind the size limitation of EBS storage devices when requesting a 
-download of a large SRA data set.
-
-Build Requirements:
-  ar 
-  bash
-  make
-  gcc, g++
-  libxml2
-  libcurl4
-  zlib
-  
-On a debian based Linux OS use:
-
-  apt-get install build-essential libxml2-dev libcurl4-openssl-dev zlib-dev
-    </readme>
-  </package>
-</tool_dependency>