Mercurial > repos > matt-shirley > sra_tools
changeset 37:4da2d7f0128e draft
Exposed more options for fastq_dump and sam_dump
author | Matt Shirley <mdshw5@gmail.com> |
---|---|
date | Thu, 01 Aug 2013 13:57:27 -0400 |
parents | b5274b0e61bc |
children | a0925f507352 |
files | fastq_dump.xml sam_dump.xml sra_fetch.xml |
diffstat | 3 files changed, 128 insertions(+), 50 deletions(-) [+] |
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--- a/fastq_dump.xml Sun Jun 30 19:50:44 2013 -0400 +++ b/fastq_dump.xml Thu Aug 01 13:57:27 2013 -0400 @@ -1,5 +1,5 @@ -<tool id="fastq_dump" name="Extract fastq" version="1.0.3"> - <description> format reads from NCBI sra.</description> +<tool id="fastq_dump" name="Extract reads" version="1.1.0"> + <description> from NCBI SRA.</description> <command> fastq-dump --log-level fatal #if $input.input_select == "file": @@ -7,24 +7,44 @@ #else: --accession $input.accession #end if + --defline-seq '@\$sn[_\$rn]/\$ri' --stdout - $split - $aligned + #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 + --minSpotId $minID #end if #if str( $maxID ) != "": - --minSpotId $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 #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: @@ -35,52 +55,67 @@ <version_string>fastq-dump --version</version_string> <inputs> <conditional name="input"> - <param name="input_select" type="select" label="Select input type"> + <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"/> + <param format="sra" name="file" type="data" label="sra archive"/> </when> <when value="accession_number"> - <param format="text" name="accession" type="text" label="accession"/> + <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=""> - <label>Split read pairs</label> - <option value="">No</option> - <option value="--split-spot">Yes</option> + <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="aligned" type="select" value=""> - <label>Specify alignment</label> - <option value="">All</option> - <option value="--aligned">Only aligned</option> - <option value="--unaligned">Only unaligned</option> + <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="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> + <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="fastqsanger" name="output"/> + <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="Cannot find fastq-dump binary"/> + <exit_code range="127" level="fatal" description="Could not locate fastq-dump binary"/> </stdio> <requirements> <requirement type="package" version="2.3.2-4">sra_toolkit</requirement> </requirements> <help> - This tool extracts fastq format reads from sra archives using fastq-dump. + 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. Contact Matt Shirley at mdshw5@gmail.com for support and bug reports. </help>
--- a/sam_dump.xml Sun Jun 30 19:50:44 2013 -0400 +++ b/sam_dump.xml Thu Aug 01 13:57:27 2013 -0400 @@ -1,24 +1,67 @@ -<tool id="sam_dump" name="Extract SAM" version="1.0.2"> - <description> format reads from NCBI sra.</description> - <command>sam-dump $header $aligned $primary '$input' > $output</command> +<tool id="sam_dump" name="Extract reads" version="1.1.0"> + <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 $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 $input.input_select == "file": + $input.file + #else: + $input.accession + #end if + > $output + </command> <version_string>sam-dump --version</version_string> <inputs> - <param format="SRA" name="input" type="data" label="sra archive"/> - <param format="text" name="header" type="select" value=""> - <label>Output SAM header</label> - <option value="--header">Yes</option> - <option value="--no-header">No</option> + <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="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="aligned" type="select" value=""> - <label>Output unaligned reads as well as aligned reads</label> - <option value="">No</option> - <option value="--unaligned">Yes</option> + <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=""> - <label>Output only primary aligments</label> - <option value="">No</option> - <option value="--primary">Yes</option> + <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"/> </inputs> <outputs> <data format="sam" name="output"/> @@ -27,8 +70,8 @@ <requirement type="package" version="2.3.2-4">sra_toolkit</requirement> </requirements> <help> - This tool extracts sam format reads from sra archives using sam-dump. + 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. Contact Matt Shirley at mdshw5@gmail.com for support and bug reports. </help> -</tool> +</tool> \ No newline at end of file
--- a/sra_fetch.xml Sun Jun 30 19:50:44 2013 -0400 +++ b/sra_fetch.xml Thu Aug 01 13:57:27 2013 -0400 @@ -1,13 +1,13 @@ -<tool id="sra_fetch" name="Fetch sra run" version="1.0.3"> - <description> by accession from NCBI sra.</description> +<tool id="sra_fetch" name="Fetch SRA archive" version="1.0.3"> + <description> by accession from NCBI SRA.</description> <command interpreter="python">sra_fetch.py --accession '$accession' --out '$output'</command> <inputs> <param name="accession" size="13" type="text" value="SRR000001" label="sra run accession"/> </inputs> <outputs> - <data format="sra" name="output" label="Fetch sra ${accession.value}"/> + <data format="sra" name="output" label="${accession.value}"/> </outputs> <help> - This tool fetches sra archives by accession from NCBI over ftp. + This tool fetches sra archives by accession from NCBI over FTP. </help> </tool>