Mercurial > repos > devteam > fastq_stats
annotate fastq_stats.xml @ 1:daaf552153fe draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit a1517c9d22029095120643bbe2c8fa53754dd2b7
| author | devteam |
|---|---|
| date | Wed, 11 Nov 2015 12:42:31 -0500 |
| parents | 9b7b4e0ca9db |
| children | e2cf940128d5 |
| rev | line source |
|---|---|
| 0 | 1 <tool id="fastq_stats" name="FASTQ Summary Statistics" version="1.0.0"> |
| 2 <description>by column</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="1.0.0">galaxy_sequence_utils</requirement> | |
| 5 </requirements> | |
| 6 <command interpreter="python">fastq_stats.py '$input_file' '$output_file' '${input_file.extension[len( 'fastq' ):]}'</command> | |
| 7 <inputs> | |
| 8 <param name="input_file" type="data" format="fastqsanger,fastqillumina,fastqsolexa,fastqcssanger" label="FASTQ File"/> | |
| 9 </inputs> | |
| 10 <outputs> | |
| 11 <data name="output_file" format="tabular" /> | |
| 12 </outputs> | |
| 13 <tests> | |
| 14 <test> | |
| 15 <param name="input_file" value="fastq_stats1.fastq" ftype="fastqsanger" /> | |
| 16 <output name="output_file" file="fastq_stats_1_out.tabular" /> | |
| 17 </test> | |
| 18 </tests> | |
| 19 <help> | |
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daaf552153fe
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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20 **What is does** |
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daaf552153fe
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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21 |
| 0 | 22 This tool creates summary statistics on a FASTQ file. |
| 23 | |
| 24 .. class:: infomark | |
| 25 | |
| 26 **TIP:** This statistics report can be used as input for the **Boxplot** tools. | |
| 27 | |
| 28 ----- | |
| 29 | |
| 30 **The output file will contain the following fields:** | |
| 31 | |
| 32 * column = column number (1 to 36 for a 36-cycles read Solexa file) | |
| 33 * count = number of bases found in this column. | |
| 34 * min = Lowest quality score value found in this column. | |
| 35 * max = Highest quality score value found in this column. | |
| 36 * sum = Sum of quality score values for this column. | |
| 37 * mean = Mean quality score value for this column. | |
| 38 * Q1 = 1st quartile quality score. | |
| 39 * med = Median quality score. | |
| 40 * Q3 = 3rd quartile quality score. | |
| 41 * IQR = Inter-Quartile range (Q3-Q1). | |
| 42 * lW = 'Left-Whisker' value (for boxplotting). | |
| 43 * rW = 'Right-Whisker' value (for boxplotting). | |
| 44 * outliers = Scores falling beyond the left and right whiskers (comma separated list). | |
| 45 * A_Count = Count of 'A' nucleotides found in this column. | |
| 46 * C_Count = Count of 'C' nucleotides found in this column. | |
| 47 * G_Count = Count of 'G' nucleotides found in this column. | |
| 48 * T_Count = Count of 'T' nucleotides found in this column. | |
| 49 * N_Count = Count of 'N' nucleotides found in this column. | |
| 50 * Other_Nucs = Comma separated list of other nucleotides found in this column. | |
| 51 * Other_Count = Comma separated count of other nucleotides found in this column. | |
| 52 | |
| 53 For example:: | |
| 54 | |
| 55 #column count min max sum mean Q1 med Q3 IQR lW rW outliers A_Count C_Count G_Count T_Count N_Count other_bases other_base_count | |
| 56 1 14336356 2 33 450600675 31.4306281875 32.0 33.0 33.0 1.0 31 33 2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30 4482314 2199633 4425957 3208745 19707 | |
| 57 2 14336356 2 34 441135033 30.7703737965 30.0 33.0 33.0 3.0 26 34 2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25 4419184 2170537 4627987 3118567 81 | |
| 58 3 14336356 2 34 433659182 30.2489127642 29.0 32.0 33.0 4.0 23 34 2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22 4310988 2941988 3437467 3645784 129 | |
| 59 4 14336356 2 34 433635331 30.2472490917 29.0 32.0 33.0 4.0 23 34 2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22 4110637 3007028 3671749 3546839 103 | |
| 60 5 14336356 2 34 432498583 30.167957813 29.0 32.0 33.0 4.0 23 34 2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22 4348275 2935903 3293025 3759029 124 | |
| 61 | |
| 62 ----- | |
| 63 | |
| 64 .. class:: warningmark | |
| 65 | |
| 66 Adapter bases in color space reads are excluded from statistics. | |
| 67 | |
| 68 ------ | |
| 69 | |
| 70 </help> | |
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1
daaf552153fe
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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71 |
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daaf552153fe
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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72 <citations> |
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daaf552153fe
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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73 <citation type="doi">10.1093/bioinformatics/btq281</citation> |
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daaf552153fe
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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74 </citations> |
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daaf552153fe
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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75 |
| 0 | 76 </tool> |