diff sra_tools-04cc8176e86f/fastq_dump.xml @ 0:c386fe82db82

Initial commit, moving from test tool shed.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sra_tools-04cc8176e86f/fastq_dump.xml	Wed Sep 25 21:00:05 2013 -0400
@@ -0,0 +1,123 @@
+<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 [e-mail] for support and bug reports.
+  </help>
+</tool>