Mercurial > repos > devteam > fastq_quality_converter
changeset 1:253c7f4976e3 draft
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
| author | devteam |
|---|---|
| date | Tue, 13 Oct 2015 12:39:43 -0400 |
| parents | ee975578075f |
| children | 0b7eccecaa34 |
| files | fastq_quality_converter.xml tool_dependencies.xml |
| diffstat | 2 files changed, 51 insertions(+), 52 deletions(-) [+] |
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--- a/fastq_quality_converter.xml Tue Aug 20 10:37:12 2013 -0400 +++ b/fastq_quality_converter.xml Tue Oct 13 12:39:43 2015 -0400 @@ -1,68 +1,68 @@ <tool id="cshl_fastq_quality_converter" name="Quality format converter" version="1.0.0"> - <description>(ASCII-Numeric)</description> + <description>(ASCII-Numeric)</description> <requirements> <requirement type="package" version="0.0.13">fastx_toolkit</requirement> </requirements> - <command>zcat -f $input | fastq_quality_converter $QUAL_FORMAT -o $output -Q $offset</command> - <inputs> - <param format="fastq" name="input" type="data" label="Library to convert" /> + <command> +<![CDATA[ +zcat -f < '$input' | fastq_quality_converter $QUAL_FORMAT -o '$output' -Q $offset +]]> + </command> + <inputs> + <param format="fastq" name="input" type="data" label="Library to convert" /> - <param name="QUAL_FORMAT" type="select" label="Desired output format"> - <option value="-a">ASCII (letters) quality scores</option> - <option value="-n">Numeric quality scores</option> - </param> - + <param name="QUAL_FORMAT" type="select" label="Desired output format"> + <option value="-a">ASCII (letters) quality scores</option> + <option value="-n">Numeric quality scores</option> + </param> + <param name="offset" type="select" label="FASTQ ASCII offset"> <option value="33">33</option> <option selected="true" value="64">64</option> - </param> + </param> </inputs> - - <tests> - <test> - <!-- ASCII to NUMERIC --> - <param name="input" value="fastq_qual_conv1.fastq" /> - <param name="QUAL_FORMAT" value="Numeric quality scores" /> - <param name="offset" value="64" /> - <output name="output" file="fastq_qual_conv1.out" /> - </test> - <test> - <!-- ASCII to ASCII (basically, a no-op, but it should still produce a valid output --> - <param name="input" value="fastq_qual_conv1.fastq" /> - <param name="QUAL_FORMAT" value="ASCII (letters) quality scores" /> - <param name="offset" value="64" /> - <output name="output" file="fastq_qual_conv1a.out" /> - </test> - <test> - <!-- NUMERIC to ASCII --> - <param name="input" value="fastq_qual_conv2.fastq" /> - <param name="QUAL_FORMAT" value="ASCII (letters) quality scores" /> - <param name="offset" value="64" /> - <output name="output" file="fastq_qual_conv2.out" /> - </test> - <test> - <!-- NUMERIC to NUMERIC (basically, a no-op, but it should still produce a valid output --> - <param name="input" value="fastq_qual_conv2.fastq" /> - <param name="QUAL_FORMAT" value="Numeric quality scores" /> - <param name="offset" value="64" /> - <output name="output" file="fastq_qual_conv2n.out" /> - </test> - </tests> - - <outputs> - <data format="fastq" name="output" metadata_source="input" /> - </outputs> -<help> - + <outputs> + <data format="fastq" name="output" metadata_source="input" /> + </outputs> + <tests> + <test> + <!-- ASCII to NUMERIC --> + <param name="input" value="fastq_qual_conv1.fastq" /> + <param name="QUAL_FORMAT" value="Numeric quality scores" /> + <param name="offset" value="64" /> + <output name="output" file="fastq_qual_conv1.out" /> + </test> + <test> + <!-- ASCII to ASCII (basically, a no-op, but it should still produce a valid output --> + <param name="input" value="fastq_qual_conv1.fastq" /> + <param name="QUAL_FORMAT" value="ASCII (letters) quality scores" /> + <param name="offset" value="64" /> + <output name="output" file="fastq_qual_conv1a.out" /> + </test> + <test> + <!-- NUMERIC to ASCII --> + <param name="input" value="fastq_qual_conv2.fastq" /> + <param name="QUAL_FORMAT" value="ASCII (letters) quality scores" /> + <param name="offset" value="64" /> + <output name="output" file="fastq_qual_conv2.out" /> + </test> + <test> + <!-- NUMERIC to NUMERIC (basically, a no-op, but it should still produce a valid output --> + <param name="input" value="fastq_qual_conv2.fastq" /> + <param name="QUAL_FORMAT" value="Numeric quality scores" /> + <param name="offset" value="64" /> + <output name="output" file="fastq_qual_conv2n.out" /> + </test> + </tests> + <help> **What it does** Converts a Solexa FASTQ file to/from numeric or ASCII quality format. -.. class:: warningmark +.. class:: warningmark Re-scaling is **not** performed. (e.g. conversion from Phred scale to Solexa scale). - ----- FASTQ with Numeric quality scores:: @@ -93,7 +93,6 @@ This tool is based on `FASTX-toolkit`__ by Assaf Gordon. .. __: http://hannonlab.cshl.edu/fastx_toolkit/ - -</help> + </help> <!-- FASTQ-Quality-Converter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) --> </tool>
--- a/tool_dependencies.xml Tue Aug 20 10:37:12 2013 -0400 +++ b/tool_dependencies.xml Tue Oct 13 12:39:43 2015 -0400 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> <package name="fastx_toolkit" version="0.0.13"> - <repository changeset_revision="1cd326991d32" name="package_fastx_toolkit_0_0_13" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="e76e81b3eccf" name="package_fastx_toolkit_0_0_13" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency>