Mercurial > repos > matt-shirley > ncbi_sra_toolkit

changeset 8:558a88cd49e4

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bump toolkit versions, old registration path
author Matt Shirley <mdshw5@gmail.com>
date Thu, 13 Mar 2014 16:11:04 -0400
parents e724bff23fb6
children eb55ff614fed
files datatypes_conf.xml fastq_dump.xml sam_dump.xml sra.py
diffstat 4 files changed, 23 insertions(+), 25 deletions(-) [+]
line wrap: on
line diff
--- a/datatypes_conf.xml	Thu Mar 13 16:08:12 2014 -0400
+++ b/datatypes_conf.xml	Thu Mar 13 16:11:04 2014 -0400
@@ -4,9 +4,9 @@
     <datatype_file name="sra.py"/>
   </datatype_files>
   <registration>
-    <datatype extension="sra" type="galaxy.datatypes.binary:Sra" mimetype="application/octet-stream" display_in_upload="true"/>
+    <datatype extension="sra" type="galaxy.datatypes.sra:Sra" mimetype="application/octet-stream" display_in_upload="true"/>
   </registration>
   <sniffers>
-    <sniffer type="galaxy.datatypes.binary:Sra"/>
+    <sniffer type="galaxy.datatypes.sra:Sra"/>
   </sniffers>
 </datatypes>
--- a/fastq_dump.xml	Thu Mar 13 16:08:12 2014 -0400
+++ b/fastq_dump.xml	Thu Mar 13 16:11:04 2014 -0400
@@ -1,14 +1,14 @@
 <tool id="fastq_dump" name="Extract reads" version="1.1.1">
   <description> from NCBI SRA.</description>
   <command>
-    fastq-dump --log-level fatal 
+    fastq-dump --log-level fatal
     #if $input.input_select == "file":
-      --accession '${input.file.name}' 
+      --accession '${input.file.name}'
     #else:
-      --accession $input.accession 
+      --accession $input.accession
     #end if
-    --defline-seq '@\$sn[_\$rn]/\$ri' 
-    --stdout 
+    --defline-seq '@\$sn[_\$rn]/\$ri'
+    --stdout
     #if $split == "yes":
       --split-spot
     #end if
@@ -19,16 +19,16 @@
       --unaligned
     #end if
     #if str( $minID ) != "":
-      --minSpotId $minID 
+      --minSpotId $minID
     #end if
     #if str( $maxID ) != "":
-      --maxSpotId $maxID 
+      --maxSpotId $maxID
     #end if
     #if str( $minlen ) != "":
-      --minReadLen $minlen 
+      --minReadLen $minlen
     #end if
     #if str( $readfilter ) != "":
-      --read-filter $readfilter 
+      --read-filter $readfilter
     #end if
     #if str( $region ) != "":
       --aligned-region $region
@@ -48,7 +48,7 @@
     #if $input.input_select=="file":
       $input.file
     #else:
-        $input.accession 
+        $input.accession
     #end if
     > $output
   </command>
@@ -112,11 +112,11 @@
     <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>
+    <requirement type="package" version="2.3.4-2">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. 
+    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>
--- a/sam_dump.xml	Thu Mar 13 16:08:12 2014 -0400
+++ b/sam_dump.xml	Thu Mar 13 16:11:04 2014 -0400
@@ -1,7 +1,7 @@
 <tool id="sam_dump" name="Extract reads" version="1.1.2">
   <description> in SAM format from NCBI SRA.</description>
   <command>
-    sam-dump --log-level fatal 
+    sam-dump --log-level fatal
     #if str( $region ) != "":
       --aligned-region $region
     #end if
@@ -14,7 +14,7 @@
     #if $header == "yes":
       --header
     #else:
-      --no-header 
+      --no-header
     #end if
     #if str( $alignments ) == "both":
       --unaligned
@@ -31,12 +31,12 @@
     #if $input.input_select == "file":
       $input.file
     #elif $input.input_select == "accession_number":
-      $input.accession 
+      $input.accession
     #elif $input.input_select == "text":
       `cat $input.text`
     #end if
     > $output
-  </command>  
+  </command>
   <version_string>sam-dump --version</version_string>
   <inputs>
     <conditional name="input">
@@ -88,12 +88,12 @@
     </data>
   </outputs>
   <requirements>
-    <requirement type="package" version="2.3.3-3">sra_toolkit</requirement>
+    <requirement type="package" version="2.3.4-2">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. 
+    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
+</tool>
--- a/sra.py	Thu Mar 13 16:08:12 2014 -0400
+++ b/sra.py	Thu Mar 13 16:11:04 2014 -0400
@@ -41,5 +41,3 @@
             return dataset.peek
         except:
             return 'Binary sra file (%s)' % (nice_size(dataset.get_size()))
-
-Binary.register_sniffable_binary_format('sra', 'sra', 'Sra')