Mercurial > repos > matt-shirley > sra_tools
changeset 34:7803126704c6 draft
exposed many more options for fastq-dump
| author | Matt Shirley <mdshw5@gmail.com> |
|---|---|
| date | Sun, 30 Jun 2013 19:20:38 -0400 |
| parents | 9ad900168ded |
| children | a93bb9eb93c5 |
| files | fastq_dump.xml tool_dependencies.xml |
| diffstat | 2 files changed, 37 insertions(+), 5 deletions(-) [+] |
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--- a/fastq_dump.xml Sun Jun 30 16:18:09 2013 -0400 +++ b/fastq_dump.xml Sun Jun 30 19:20:38 2013 -0400 @@ -1,11 +1,31 @@ <tool id="fastq_dump" name="Extract fastq" version="1.0.3"> <description> format reads from NCBI sra.</description> <command> - #if $input.input_select=="file" - fastq-dump --log-level fatal --accession '${input.file.name}' --stdout $split $aligned $input.file > $output - #else - fastq-dump --log-level fatal $input.accession > $output + fastq-dump --log-level fatal + #if $input.input_select == "file": + --accession '${input.file.name}' + #else: + --accession $input.accession #end if + --stdout + $split + $aligned + #if str( $param_type.minID ) != "": + --minSpotId $minID + #if str( $param_type.maxID ) != "": + --minSpotId $maxID + #if str( $param_type.minlen ) != "": + --minReadLen $minlen + #if str( $param_type.readfilter ) != "": + --read-filter $readfilter + #if str( $param_type.region ) != "": + --aligned-region $region + #if $input.input_select=="file": + $input.file + #else: + $input.accession + #end if + > $output </command> <version_string>fastq-dump --version</version_string> <inputs> @@ -21,6 +41,9 @@ <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> @@ -32,6 +55,15 @@ <option value="--aligned">Only aligned</option> <option value="--unaligned">Only unaligned</option> </param> + <param format="text" name="region" type="text" label="Aligned region"/> + <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> </inputs> <outputs> <data format="fastqsanger" name="output"/>