Mercurial > repos > matt-shirley > sra_tools
changeset 26:5f57967aac3e draft
implement prefetch caching and accession input for fastq_dump
| author | Matt Shirley <mdshw5@gmail.com> |
|---|---|
| date | Sat, 29 Jun 2013 11:14:03 -0400 |
| parents | 7e033744cb20 |
| children | 2295c666e6ce |
| files | fastq_dump.xml tool_dependencies.xml |
| diffstat | 2 files changed, 22 insertions(+), 4 deletions(-) [+] |
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--- a/fastq_dump.xml Wed Jun 19 16:48:18 2013 -0400 +++ b/fastq_dump.xml Sat Jun 29 11:14:03 2013 -0400 @@ -1,9 +1,26 @@ -<tool id="fastq_dump" name="Extract fastq" version="1.0.2"> +<tool id="fastq_dump" name="Extract fastq" version="1.0.3"> <description> format reads from NCBI sra.</description> - <command>fastq-dump --log-level fatal --accession '${input.name}' --stdout $split $aligned '$input' > $output </command> + <command> + #if $input.input_select=="file" + fastq-dump --log-level fatal --accession '${input.sra.name}' --stdout $split $aligned $input.sra > $output + #else + fastq-dump --log-level fatal --accession $input.accession --stdout $split $aligned $input.accession > $output + #end if + </command> <version_string>fastq-dump --version</version_string> <inputs> - <param format="sra" name="input" type="data" label="sra archive"/> + <conditional name="input"> + <param name="input_select" type="select" label="Select input type"> + <option value="accession">SRR accession</option> + <option value="sra">SRA archive in current history</option> + </param> + <when value="file"> + <param format="sra" name="input" type="data" label="sra archive"/> + </when> + <when value="accession_number"> + <param format="text" name="input" type="text" label="accession"/> + </when> + </conditional> <param format="text" name="split" type="select" value=""> <label>Split read pairs</label> <option value="">No</option>
--- a/tool_dependencies.xml Wed Jun 19 16:48:18 2013 -0400 +++ b/tool_dependencies.xml Sat Jun 29 11:14:03 2013 -0400 @@ -7,7 +7,8 @@ <action type="shell_command">make release</action> <action type="shell_command">make static</action> <action type="shell_command">make</action> - <action type="make_directory">$INSTALL_DIR/bin</action> + <action type="make_directory">$INSTALL_DIR/bin</action> + <action type="shell_command">sed -i -e 's/HOME/INSTALL_DIR/g' 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>