Mercurial > repos > devteam > fastx_quality_statistics
changeset 2:76cefe061c3d draft
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
| author | devteam |
|---|---|
| date | Tue, 13 Oct 2015 12:41:32 -0400 |
| parents | 8c60fa8ae153 |
| children | 29924496aeb0 |
| files | fastx_quality_statistics.xml tool_dependencies.xml |
| diffstat | 2 files changed, 34 insertions(+), 35 deletions(-) [+] |
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--- a/fastx_quality_statistics.xml Tue Nov 26 12:49:06 2013 -0500 +++ b/fastx_quality_statistics.xml Tue Oct 13 12:41:32 2015 -0400 @@ -1,27 +1,27 @@ <tool id="cshl_fastx_quality_statistics" version="1.0.0" name="Compute quality statistics"> - <description></description> + <description></description> <requirements> <requirement type="package" version="0.0.13">fastx_toolkit</requirement> </requirements> - <command>zcat -f $input | fastx_quality_stats -o $output -Q 33</command> - - <inputs> - <param format="fastqsanger" name="input" type="data" label="Library to analyse" /> - </inputs> + <command> +<![CDATA[ +zcat -f < '$input' | fastx_quality_stats -o '$output' -Q 33 +]]> + </command> - <tests> - <test> - <param name="input" value="fastq_stats1.fastq" ftype="fastqsanger"/> - <output name="output" file="fastq_stats1.out" /> - </test> - </tests> - - <outputs> - <data format="txt" name="output" metadata_source="input" /> - </outputs> - -<help> - + <inputs> + <param format="fastqsanger" name="input" type="data" label="Library to analyse" /> + </inputs> + <outputs> + <data format="txt" name="output" metadata_source="input" /> + </outputs> + <tests> + <test> + <param name="input" value="fastq_stats1.fastq" ftype="fastqsanger"/> + <output name="output" file="fastq_stats1.out" /> + </test> + </tests> + <help> **What it does** Creates quality statistics report for the given Solexa/FASTQ library. @@ -34,23 +34,23 @@ **The output file will contain the following fields:** -* column = column number (1 to 36 for a 36-cycles read Solexa file) +* column = column number (1 to 36 for a 36-cycles read Solexa file) * count = number of bases found in this column. * min = Lowest quality score value found in this column. * max = Highest quality score value found in this column. * sum = Sum of quality score values for this column. * mean = Mean quality score value for this column. -* Q1 = 1st quartile quality score. -* med = Median quality score. -* Q3 = 3rd quartile quality score. -* IQR = Inter-Quartile range (Q3-Q1). -* lW = 'Left-Whisker' value (for boxplotting). -* rW = 'Right-Whisker' value (for boxplotting). -* A_Count = Count of 'A' nucleotides found in this column. -* C_Count = Count of 'C' nucleotides found in this column. -* G_Count = Count of 'G' nucleotides found in this column. -* T_Count = Count of 'T' nucleotides found in this column. -* N_Count = Count of 'N' nucleotides found in this column. +* Q1 = 1st quartile quality score. +* med = Median quality score. +* Q3 = 3rd quartile quality score. +* IQR = Inter-Quartile range (Q3-Q1). +* lW = 'Left-Whisker' value (for boxplotting). +* rW = 'Right-Whisker' value (for boxplotting). +* A_Count = Count of 'A' nucleotides found in this column. +* C_Count = Count of 'C' nucleotides found in this column. +* G_Count = Count of 'G' nucleotides found in this column. +* T_Count = Count of 'T' nucleotides found in this column. +* N_Count = Count of 'N' nucleotides found in this column. For example:: @@ -60,13 +60,12 @@ 3 6362991 -5 40 248722469 39.09 40 40 40 0 40 40 2296384 984875 1443989 1637743 0 4 6362991 -4 40 248214827 39.01 40 40 40 0 40 40 2536861 1167423 1248968 1409739 0 36 6362991 -5 40 117158566 18.41 7 15 30 23 -5 40 4074444 1402980 63287 822035 245 - + ------ This tool is based on `FASTX-toolkit`__ by Assaf Gordon. .. __: http://hannonlab.cshl.edu/fastx_toolkit/ - -</help> + </help> <!-- FASTQ-Statistics is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) --> </tool>
--- a/tool_dependencies.xml Tue Nov 26 12:49:06 2013 -0500 +++ b/tool_dependencies.xml Tue Oct 13 12:41:32 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>