| Previous changeset 1:57adb07cccfc (2013-12-03) Next changeset 3:43a7370aa010 (2018-05-08) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7 |
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modified:
fastq_quality_filter.xml tool_dependencies.xml |
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| diff -r 57adb07cccfc -r e41385662e5e fastq_quality_filter.xml --- a/fastq_quality_filter.xml Tue Dec 03 12:36:13 2013 -0500 +++ b/fastq_quality_filter.xml Wed Nov 11 12:37:55 2015 -0500 |
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| @@ -1,48 +1,48 @@ <tool id="cshl_fastq_quality_filter" version="1.0.0" name="Filter by quality"> - <description></description> + <description></description> <requirements> <requirement type="package" version="0.0.13">fastx_toolkit</requirement> </requirements> - <command>zcat -f '$input' | fastq_quality_filter -q $quality -p $percent -v -o $output + <command> +<![CDATA[ +zcat -f < '$input' | fastq_quality_filter -q $quality -p $percent -v -o '$output' #if $input.ext == "fastqsanger": --Q 33 + -Q 33 #end if - </command> - - <inputs> - <param format="fastqsolexa,fastqsanger" name="input" type="data" label="Library to filter" /> +]]> + </command> - <param name="quality" size="4" type="integer" value="20"> - <label>Quality cut-off value</label> - </param> + <inputs> + <param format="fastqsolexa,fastqsanger" name="input" type="data" label="Library to filter" /> - <param name="percent" size="4" type="integer" value="90"> - <label>Percent of bases in sequence that must have quality equal to / higher than cut-off value</label> - </param> - </inputs> + <param name="quality" type="integer" value="20"> + <label>Quality cut-off value</label> + </param> - <tests> - <test> - <!-- Test1: 100% of bases with quality 33 or higher (pretty steep requirement...) --> - <param name="input" value="fastq_qual_filter1.fastq" ftype="fastqsolexa" /> - <param name="quality" value="33"/> - <param name="percent" value="100"/> - <param name="output" file="fastq_qual_filter1a.out" /> - </test> - <test> - <!-- Test2: 80% of bases with quality 20 or higher --> - <param name="input" value="fastq_qual_filter1.fastq" ftype="fastqsolexa"/> - <param name="quality" value="20"/> - <param name="percent" value="80"/> - <param name="output" file="fastq_qual_filter1b.out" /> - </test> - </tests> - - <outputs> - <data format="input" name="output" metadata_source="input" /> - </outputs> - - <help> + <param name="percent" type="integer" value="90"> + <label>Percent of bases in sequence that must have quality equal to / higher than cut-off value</label> + </param> + </inputs> + <outputs> + <data format_source="input" name="output" metadata_source="input" /> + </outputs> + <tests> + <test> + <!-- Test1: 100% of bases with quality 33 or higher (pretty steep requirement...) --> + <param name="input" value="fastq_qual_filter1.fastq" ftype="fastqsolexa" /> + <param name="quality" value="33"/> + <param name="percent" value="100"/> + <output name="output" ftype="fastqsolexa" file="fastq_qual_filter1a.out" /> + </test> + <test> + <!-- Test2: 80% of bases with quality 20 or higher --> + <param name="input" value="fastq_qual_filter1.fastq" ftype="fastqsolexa"/> + <param name="quality" value="20"/> + <param name="percent" value="80"/> + <output name="output" ftype="fastqsolexa" file="fastq_qual_filter1b.out" /> + </test> + </tests> + <help> **What it does** This tool filters reads based on quality scores. @@ -77,7 +77,7 @@ This tool is based on `FASTX-toolkit`__ by Assaf Gordon. - .. __: http://hannonlab.cshl.edu/fastx_toolkit/ - </help> + .. __: http://hannonlab.cshl.edu/fastx_toolkit/ + </help> <!-- FASTQ-Quality-Filter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) --> </tool> |
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| diff -r 57adb07cccfc -r e41385662e5e tool_dependencies.xml --- a/tool_dependencies.xml Tue Dec 03 12:36:13 2013 -0500 +++ b/tool_dependencies.xml Wed Nov 11 12:37:55 2015 -0500 |
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| @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> <package name="fastx_toolkit" version="0.0.13"> - <repository changeset_revision="ec66ae4c269b" name="package_fastx_toolkit_0_0_13" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="ec66ae4c269b" name="package_fastx_toolkit_0_0_13" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> |