Mercurial > repos > devteam > fastq_stats
annotate fastq_stats.xml @ 4:f0e7deab6518 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
author | iuc |
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date | Wed, 19 Feb 2020 12:34:52 -0500 |
parents | b1cea1b2fcd0 |
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f0e7deab6518
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
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1 <tool id="fastq_stats" name="FASTQ Summary Statistics" version="@TOOL_VERSION@"> |
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e2cf940128d5
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit f2582539542b33240234e8ea6093e25d0aee9b6a
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2 <description>by column</description> |
4
f0e7deab6518
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
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3 <macros> |
f0e7deab6518
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
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4 <import>macros.xml</import> |
f0e7deab6518
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
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5 </macros> |
f0e7deab6518
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
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6 <expand macro="requirements"/> |
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b1cea1b2fcd0
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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7 <edam_topics> |
b1cea1b2fcd0
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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8 <edam_topic>topic_0622</edam_topic> |
b1cea1b2fcd0
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit 31edb920789fbd080260f853bc856be72fa7cfa8"
devteam
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9 </edam_topics> |
b1cea1b2fcd0
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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10 <edam_operations> |
b1cea1b2fcd0
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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11 <edam_operation>operation_3180</edam_operation> |
b1cea1b2fcd0
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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12 </edam_operations> |
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e2cf940128d5
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit f2582539542b33240234e8ea6093e25d0aee9b6a
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13 <command><![CDATA[ |
e2cf940128d5
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit f2582539542b33240234e8ea6093e25d0aee9b6a
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14 gx-fastq-stats '$input_file' '$output_file' '${input_file.extension[len('fastq'):]}' |
e2cf940128d5
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit f2582539542b33240234e8ea6093e25d0aee9b6a
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15 ]]></command> |
e2cf940128d5
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit f2582539542b33240234e8ea6093e25d0aee9b6a
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16 <inputs> |
e2cf940128d5
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit f2582539542b33240234e8ea6093e25d0aee9b6a
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17 <param name="input_file" type="data" format="fastqsanger,fastqillumina,fastqsolexa,fastqcssanger,fastqsanger.gz,fastqillumina.gz,fastqsolexa.gz,fastqcssanger.gz,fastqsanger.bz2,fastqillumina.bz2,fastqsolexa.bz2,fastqcssanger.bz2" label="FASTQ File"/> |
e2cf940128d5
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit f2582539542b33240234e8ea6093e25d0aee9b6a
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18 </inputs> |
e2cf940128d5
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
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19 <outputs> |
e2cf940128d5
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
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20 <data name="output_file" format="tabular" /> |
e2cf940128d5
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
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21 </outputs> |
e2cf940128d5
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit f2582539542b33240234e8ea6093e25d0aee9b6a
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22 <tests> |
e2cf940128d5
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit f2582539542b33240234e8ea6093e25d0aee9b6a
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23 <test> |
e2cf940128d5
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
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24 <param name="input_file" value="fastq_stats1.fastq" ftype="fastqsanger" /> |
e2cf940128d5
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
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25 <output name="output_file" file="fastq_stats_1_out.tabular" /> |
e2cf940128d5
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit f2582539542b33240234e8ea6093e25d0aee9b6a
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26 </test> |
e2cf940128d5
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
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27 </tests> |
e2cf940128d5
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit f2582539542b33240234e8ea6093e25d0aee9b6a
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28 <help><![CDATA[ |
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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29 **What is does** |
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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30 |
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e2cf940128d5
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit f2582539542b33240234e8ea6093e25d0aee9b6a
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31 This tool creates summary statistics on a FASTQ file. |
0 | 32 |
33 .. class:: infomark | |
34 | |
35 **TIP:** This statistics report can be used as input for the **Boxplot** tools. | |
36 | |
37 ----- | |
38 | |
39 **The output file will contain the following fields:** | |
40 | |
41 * column = column number (1 to 36 for a 36-cycles read Solexa file) | |
42 * count = number of bases found in this column. | |
43 * min = Lowest quality score value found in this column. | |
44 * max = Highest quality score value found in this column. | |
45 * sum = Sum of quality score values for this column. | |
46 * mean = Mean quality score value for this column. | |
47 * Q1 = 1st quartile quality score. | |
48 * med = Median quality score. | |
49 * Q3 = 3rd quartile quality score. | |
50 * IQR = Inter-Quartile range (Q3-Q1). | |
51 * lW = 'Left-Whisker' value (for boxplotting). | |
52 * rW = 'Right-Whisker' value (for boxplotting). | |
53 * outliers = Scores falling beyond the left and right whiskers (comma separated list). | |
54 * A_Count = Count of 'A' nucleotides found in this column. | |
55 * C_Count = Count of 'C' nucleotides found in this column. | |
56 * G_Count = Count of 'G' nucleotides found in this column. | |
57 * T_Count = Count of 'T' nucleotides found in this column. | |
58 * N_Count = Count of 'N' nucleotides found in this column. | |
59 * Other_Nucs = Comma separated list of other nucleotides found in this column. | |
60 * Other_Count = Comma separated count of other nucleotides found in this column. | |
61 | |
62 For example:: | |
63 | |
64 #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 | |
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e2cf940128d5
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit f2582539542b33240234e8ea6093e25d0aee9b6a
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65 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 |
e2cf940128d5
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit f2582539542b33240234e8ea6093e25d0aee9b6a
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66 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 |
e2cf940128d5
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit f2582539542b33240234e8ea6093e25d0aee9b6a
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67 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 |
e2cf940128d5
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit f2582539542b33240234e8ea6093e25d0aee9b6a
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68 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 |
e2cf940128d5
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit f2582539542b33240234e8ea6093e25d0aee9b6a
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69 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 |
0 | 70 |
71 ----- | |
72 | |
73 .. class:: warningmark | |
74 | |
75 Adapter bases in color space reads are excluded from statistics. | |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit f2582539542b33240234e8ea6093e25d0aee9b6a
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76 ]]></help> |
e2cf940128d5
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit f2582539542b33240234e8ea6093e25d0aee9b6a
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77 <citations> |
e2cf940128d5
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit f2582539542b33240234e8ea6093e25d0aee9b6a
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78 <citation type="doi">10.1093/bioinformatics/btq281</citation> |
e2cf940128d5
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit f2582539542b33240234e8ea6093e25d0aee9b6a
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79 </citations> |
0 | 80 </tool> |