Mercurial > repos > devteam > fastq_stats

annotate fastq_stats.xml @ 2:e2cf940128d5 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit f2582539542b33240234e8ea6093e25d0aee9b6a
author devteam
date Sat, 30 Sep 2017 13:55:30 -0400
parents daaf552153fe
children b1cea1b2fcd0
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
e2cf940128d5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
1 <tool id="fastq_stats" name="FASTQ Summary Statistics" version="1.1.1">
e2cf940128d5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
2 <description>by column</description>
e2cf940128d5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
3 <requirements>
e2cf940128d5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
4 <requirement type="package" version="1.1.1">galaxy_sequence_utils</requirement>
e2cf940128d5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
5 </requirements>
e2cf940128d5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
6 <command><![CDATA[
e2cf940128d5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
7 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
devteam
parents: 1
diff changeset
8 ]]></command>
e2cf940128d5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
9 <inputs>
e2cf940128d5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
10 <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
devteam
parents: 1
diff changeset
11 </inputs>
e2cf940128d5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
12 <outputs>
e2cf940128d5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
13 <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
parents: 1
diff changeset
14 </outputs>
e2cf940128d5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
15 <tests>
e2cf940128d5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
16 <test>
e2cf940128d5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
17 <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
parents: 1
diff changeset
18 <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
devteam
parents: 1
diff changeset
19 </test>
e2cf940128d5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
20 </tests>
e2cf940128d5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
21 <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
devteam
parents: 0
diff changeset
22 **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
devteam
parents: 0
diff changeset
23
2
e2cf940128d5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
24 This tool creates summary statistics on a FASTQ file.
0
9b7b4e0ca9db Imported from capsule None
devteam
parents:
diff changeset
25
9b7b4e0ca9db Imported from capsule None
devteam
parents:
diff changeset
26 .. class:: infomark
9b7b4e0ca9db Imported from capsule None
devteam
parents:
diff changeset
27
9b7b4e0ca9db Imported from capsule None
devteam
parents:
diff changeset
28 **TIP:** This statistics report can be used as input for the **Boxplot** tools.
9b7b4e0ca9db Imported from capsule None
devteam
parents:
diff changeset
29
9b7b4e0ca9db Imported from capsule None
devteam
parents:
diff changeset
30 -----
9b7b4e0ca9db Imported from capsule None
devteam
parents:
diff changeset
31
9b7b4e0ca9db Imported from capsule None
devteam
parents:
diff changeset
32 **The output file will contain the following fields:**
9b7b4e0ca9db Imported from capsule None
devteam
parents:
diff changeset
33
9b7b4e0ca9db Imported from capsule None
devteam
parents:
diff changeset
34 * column = column number (1 to 36 for a 36-cycles read Solexa file)
9b7b4e0ca9db Imported from capsule None
devteam
parents:
diff changeset
35 * count = number of bases found in this column.
9b7b4e0ca9db Imported from capsule None
devteam
parents:
diff changeset
36 * min = Lowest quality score value found in this column.
9b7b4e0ca9db Imported from capsule None
devteam
parents:
diff changeset
37 * max = Highest quality score value found in this column.
9b7b4e0ca9db Imported from capsule None
devteam
parents:
diff changeset
38 * sum = Sum of quality score values for this column.
9b7b4e0ca9db Imported from capsule None
devteam
parents:
diff changeset
39 * mean = Mean quality score value for this column.
9b7b4e0ca9db Imported from capsule None
devteam
parents:
diff changeset
40 * Q1 = 1st quartile quality score.
9b7b4e0ca9db Imported from capsule None
devteam
parents:
diff changeset
41 * med = Median quality score.
9b7b4e0ca9db Imported from capsule None
devteam
parents:
diff changeset
42 * Q3 = 3rd quartile quality score.
9b7b4e0ca9db Imported from capsule None
devteam
parents:
diff changeset
43 * IQR = Inter-Quartile range (Q3-Q1).
9b7b4e0ca9db Imported from capsule None
devteam
parents:
diff changeset
44 * lW = 'Left-Whisker' value (for boxplotting).
9b7b4e0ca9db Imported from capsule None
devteam
parents:
diff changeset
45 * rW = 'Right-Whisker' value (for boxplotting).
9b7b4e0ca9db Imported from capsule None
devteam
parents:
diff changeset
46 * outliers = Scores falling beyond the left and right whiskers (comma separated list).
9b7b4e0ca9db Imported from capsule None
devteam
parents:
diff changeset
47 * A_Count = Count of 'A' nucleotides found in this column.
9b7b4e0ca9db Imported from capsule None
devteam
parents:
diff changeset
48 * C_Count = Count of 'C' nucleotides found in this column.
9b7b4e0ca9db Imported from capsule None
devteam
parents:
diff changeset
49 * G_Count = Count of 'G' nucleotides found in this column.
9b7b4e0ca9db Imported from capsule None
devteam
parents:
diff changeset
50 * T_Count = Count of 'T' nucleotides found in this column.
9b7b4e0ca9db Imported from capsule None
devteam
parents:
diff changeset
51 * N_Count = Count of 'N' nucleotides found in this column.
9b7b4e0ca9db Imported from capsule None
devteam
parents:
diff changeset
52 * Other_Nucs = Comma separated list of other nucleotides found in this column.
9b7b4e0ca9db Imported from capsule None
devteam
parents:
diff changeset
53 * Other_Count = Comma separated count of other nucleotides found in this column.
9b7b4e0ca9db Imported from capsule None
devteam
parents:
diff changeset
54
9b7b4e0ca9db Imported from capsule None
devteam
parents:
diff changeset
55 For example::
9b7b4e0ca9db Imported from capsule None
devteam
parents:
diff changeset
56
9b7b4e0ca9db Imported from capsule None
devteam
parents:
diff changeset
57 #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
2
e2cf940128d5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
58 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
devteam
parents: 1
diff changeset
59 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
devteam
parents: 1
diff changeset
60 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
devteam
parents: 1
diff changeset
61 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
devteam
parents: 1
diff changeset
62 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
9b7b4e0ca9db Imported from capsule None
devteam
parents:
diff changeset
63
9b7b4e0ca9db Imported from capsule None
devteam
parents:
diff changeset
64 -----
9b7b4e0ca9db Imported from capsule None
devteam
parents:
diff changeset
65
9b7b4e0ca9db Imported from capsule None
devteam
parents:
diff changeset
66 .. class:: warningmark
9b7b4e0ca9db Imported from capsule None
devteam
parents:
diff changeset
67
9b7b4e0ca9db Imported from capsule None
devteam
parents:
diff changeset
68 Adapter bases in color space reads are excluded from statistics.
2
e2cf940128d5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
69 ]]></help>
e2cf940128d5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
70 <citations>
e2cf940128d5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
71 <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
devteam
parents: 1
diff changeset
72 </citations>
0
9b7b4e0ca9db Imported from capsule None
devteam
parents:
diff changeset
73 </tool>