Mercurial > repos > devteam > fastx_quality_statistics
changeset 0:24597260bef8
Uploaded tool tarball.
| author | devteam |
|---|---|
| date | Tue, 20 Aug 2013 10:49:34 -0400 |
| parents | |
| children | 8c60fa8ae153 |
| files | fastx_quality_statistics.xml test-data/fastq_stats1.fastq test-data/fastq_stats1.out tool_dependencies.xml |
| diffstat | 4 files changed, 151 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fastx_quality_statistics.xml Tue Aug 20 10:49:34 2013 -0400 @@ -0,0 +1,72 @@ +<tool id="cshl_fastx_quality_statistics" version="1.0.0" name="Compute quality statistics"> + <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" version="1.0.0" name="input" type="data" label="Library to analyse" /> + </inputs> + + <tests> + <test> + <param version="1.0.0" name="input" value="fastq_stats1.fastq" ftype="fastqsanger"/> + <output version="1.0.0" name="output" file="fastq_stats1.out" /> + </test> + </tests> + + <outputs> + <data format="txt" version="1.0.0" name="output" metadata_source="input" /> + </outputs> + +<help> + +**What it does** + +Creates quality statistics report for the given Solexa/FASTQ library. + +.. class:: infomark + +**TIP:** This statistics report can be used as input for **Quality Score** and **Nucleotides Distribution** tools. + +----- + +**The output file will contain the following fields:** + +* 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. + + +For example:: + + 1 6362991 -4 40 250734117 39.41 40 40 40 0 40 40 1396976 1329101 678730 2958184 0 + 2 6362991 -5 40 250531036 39.37 40 40 40 0 40 40 1786786 1055766 1738025 1782414 0 + 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> +<!-- FASTQ-Statistics is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) --> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastq_stats1.fastq Tue Aug 20 10:49:34 2013 -0400 @@ -0,0 +1,36 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GTACGCATGACCGAACCCCCCNCCCCCCAATTGGTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +BBC?7?B6>ABB?B;BBBCC9&;BCBBBBBBBB>>A +@CSHL_3_FC042AGLLWW:1:2:7:33 +CAATGCCTCCAATTGGTTAATCCCCCTATATATACT ++CSHL_3_FC042AGLLWW:1:2:7:33 +8BBB?B;BB8?6@9B8BB=8.&1?,&;931&&&(BB +@CSHL_3_FC042AGLLWW:1:2:7:169 +GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC ++CSHL_3_FC042AGLLWW:1:2:7:169 +B@.?B=6BBB@.@BBBBBBBBBBBBBBB7=;6(663 +@CSHL_3_FC042AGLLWW:1:2:7:1436 +AATTATTTATTAAATTTTAATAATATGGGAGACACT ++CSHL_3_FC042AGLLWW:1:2:7:1436 +B?BBBBBBBBBBBBBBB@6ABBBBB@4@BBBBB77< +@CSHL_3_FC042AGLLWW:1:2:7:292 +GGAGAAATACACACAATTGGTTAATCCCCCTATATA ++CSHL_3_FC042AGLLWW:1:2:7:292 +CBCBBBBBBB6.BBBBBBBBBBB=9&66&1@>6&3& +@CSHL_3_FC042AGLLWW:1:2:7:1819 +AATTCAAACCACCCCAACCCACACACAGAGATACAA ++CSHL_3_FC042AGLLWW:1:2:7:1819 +B==2777-BB-0&96866&,66-&.6&66,6-*2.6 +@CSHL_3_FC042AGLLWW:1:2:7:1875 +GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC ++CSHL_3_FC042AGLLWW:1:2:7:1875 +BBBBBBBBB9699&9BBBBBA@;BBBBBBBBB9&96 +@CSHL_3_FC042AGLLWW:1:2:8:624 +ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG ++CSHL_3_FC042AGLLWW:1:2:8:624 +BB<4?A9ABB@>>009.6?@<.6@BBBBBBBBBBBB +@CSHL_3_FC042AGLLWW:1:2:8:250 +TGCCGCGCACACTGATGCAATTGGTTAATCCCCCTA ++CSHL_3_FC042AGLLWW:1:2:8:250 +BBBBBBBB?BBBBBBCCC<,91&6<39;?+6,3,9&
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastq_stats1.out Tue Aug 20 10:49:34 2013 -0400 @@ -0,0 +1,37 @@ +column count min max sum mean Q1 med Q3 IQR lW rW A_Count C_Count G_Count T_Count N_Count Max_count +1 9 23 34 288 32.00 33 33 33 0 33 33 3 1 4 1 0 9 +2 9 28 33 287 31.89 31 33 33 2 28 33 3 3 2 1 0 9 +3 9 13 34 268 29.78 28 33 33 5 21 34 5 1 0 3 0 9 +4 9 17 33 261 29.00 30 33 33 3 26 33 1 2 3 3 0 9 +5 9 22 33 269 29.89 30 33 33 3 26 33 3 3 3 0 0 9 +6 9 22 33 277 30.78 30 33 33 3 26 33 5 3 0 1 0 9 +7 9 21 33 258 28.67 24 33 33 9 21 33 4 1 3 1 0 9 +8 9 12 33 263 29.22 32 33 33 1 31 33 2 1 1 5 0 9 +9 9 29 33 290 32.22 33 33 33 0 33 33 3 3 2 1 0 9 +10 9 23 33 277 30.78 32 33 33 1 31 33 1 4 2 2 0 9 +11 9 12 33 245 27.22 21 31 33 12 12 33 5 2 1 1 0 9 +12 9 13 33 214 23.78 15 24 33 18 13 33 2 4 2 1 0 9 +13 9 5 33 249 27.67 29 31 33 4 23 33 2 1 1 5 0 9 +14 9 5 33 233 25.89 24 33 33 9 11 33 3 3 2 1 0 9 +15 9 15 33 251 27.89 24 33 33 9 15 33 5 1 1 2 0 9 +16 9 23 34 269 29.89 24 33 33 9 23 34 3 1 2 3 0 9 +17 9 13 34 266 29.56 33 33 33 0 33 33 2 3 1 3 0 9 +18 9 21 34 272 30.22 31 33 33 2 28 34 0 5 1 3 0 9 +19 9 5 34 244 27.11 27 30 33 6 18 34 4 4 1 0 0 9 +20 9 11 34 241 26.78 23 32 33 10 11 34 3 4 2 0 0 9 +21 9 13 33 240 26.67 24 27 33 9 13 33 1 4 0 4 0 9 +22 9 5 33 190 21.11 13 21 33 20 5 33 1 4 0 3 1 9 +23 9 5 33 205 22.78 16 26 33 17 5 33 4 4 1 0 0 9 +24 9 5 33 247 27.44 28 31 33 5 21 33 1 5 1 2 0 9 +25 9 11 34 241 26.78 24 33 33 9 11 34 3 4 0 2 0 9 +26 9 5 33 212 23.56 18 31 33 15 5 33 0 6 0 3 0 9 +27 9 5 33 227 25.22 21 26 33 12 5 33 3 4 1 1 0 9 +28 9 21 33 255 28.33 24 31 33 9 21 33 2 4 3 0 0 9 +29 9 5 33 228 25.33 21 30 33 12 5 33 2 4 1 2 0 9 +30 9 10 33 213 23.67 16 28 33 17 10 33 3 4 2 0 0 9 +31 9 5 33 236 26.22 21 31 33 12 5 33 1 4 1 3 0 9 +32 9 5 33 210 23.33 12 29 33 21 5 33 3 3 0 3 0 9 +33 9 5 33 183 20.33 9 21 33 24 5 33 1 4 2 2 0 9 +34 9 5 33 150 16.67 7 17 22 15 5 33 3 4 1 1 0 9 +35 9 13 33 217 24.11 21 24 29 8 13 33 1 4 1 3 0 9 +36 9 5 33 195 21.67 18 21 32 14 5 33 3 2 1 3 0 9
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Aug 20 10:49:34 2013 -0400 @@ -0,0 +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" /> + </package> +</tool_dependency>