Mercurial > repos > devteam > fastqc

annotate rgFastQC.xml @ 13:7d8c56e1a3aa 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-iuc/tree/master/tools/fastqc commit 35d722c0cafe2a2f2e4e2f73c265ae56ae237997
author iuc
date Fri, 24 Nov 2017 08:18:18 -0500
parents f5a25a56ab9d
children da652f6f84cc
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
13
7d8c56e1a3aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 35d722c0cafe2a2f2e4e2f73c265ae56ae237997
iuc
parents: 11
diff changeset
1 <tool id="fastqc" name="FastQC" version="0.70">
3
36980a78cc83 Uploaded
devteam
parents: 2
diff changeset
2 <description>Read Quality reports</description>
36980a78cc83 Uploaded
devteam
parents: 2
diff changeset
3 <requirements>
6
e8c90ad3cbf9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqc commit df4c0b0c6372e2984966e220fa42ecd8a3d370e8
devteam
parents: 5
diff changeset
4 <requirement type="package" version="0.11.5">fastqc</requirement>
3
36980a78cc83 Uploaded
devteam
parents: 2
diff changeset
5 </requirements>
11
f5a25a56ab9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 8991687e2ec5f75d3841c613ea5d8ffda0389654
iuc
parents: 10
diff changeset
6 <command detect_errors="exit_code"><![CDATA[
f5a25a56ab9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 8991687e2ec5f75d3841c613ea5d8ffda0389654
iuc
parents: 10
diff changeset
7 #import re
f5a25a56ab9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 8991687e2ec5f75d3841c613ea5d8ffda0389654
iuc
parents: 10
diff changeset
8 #set input_name = re.sub('[^\w\-\s]', '_', str($input_file.element_identifier))
13
7d8c56e1a3aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 35d722c0cafe2a2f2e4e2f73c265ae56ae237997
iuc
parents: 11
diff changeset
9
7d8c56e1a3aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 35d722c0cafe2a2f2e4e2f73c265ae56ae237997
iuc
parents: 11
diff changeset
10 #if $input_file.ext.endswith('.gz'):
7d8c56e1a3aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 35d722c0cafe2a2f2e4e2f73c265ae56ae237997
iuc
parents: 11
diff changeset
11 #set input_file_sl = $input_name + '.gz'
7d8c56e1a3aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 35d722c0cafe2a2f2e4e2f73c265ae56ae237997
iuc
parents: 11
diff changeset
12 #elif $input_file.ext.endswith('.bz2'):
7d8c56e1a3aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 35d722c0cafe2a2f2e4e2f73c265ae56ae237997
iuc
parents: 11
diff changeset
13 #set input_file_sl = $input_name + '.bz2'
7d8c56e1a3aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 35d722c0cafe2a2f2e4e2f73c265ae56ae237997
iuc
parents: 11
diff changeset
14 #else
7d8c56e1a3aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 35d722c0cafe2a2f2e4e2f73c265ae56ae237997
iuc
parents: 11
diff changeset
15 #set input_file_sl = $input_name
7d8c56e1a3aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 35d722c0cafe2a2f2e4e2f73c265ae56ae237997
iuc
parents: 11
diff changeset
16 #end if
7d8c56e1a3aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 35d722c0cafe2a2f2e4e2f73c265ae56ae237997
iuc
parents: 11
diff changeset
17
7d8c56e1a3aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 35d722c0cafe2a2f2e4e2f73c265ae56ae237997
iuc
parents: 11
diff changeset
18 #if 'bam' in $input_file.ext:
7d8c56e1a3aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 35d722c0cafe2a2f2e4e2f73c265ae56ae237997
iuc
parents: 11
diff changeset
19 #set format = 'bam'
7d8c56e1a3aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 35d722c0cafe2a2f2e4e2f73c265ae56ae237997
iuc
parents: 11
diff changeset
20 #elif 'sam' in $input_file.ext:
7d8c56e1a3aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 35d722c0cafe2a2f2e4e2f73c265ae56ae237997
iuc
parents: 11
diff changeset
21 #set format = 'sam'
7d8c56e1a3aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 35d722c0cafe2a2f2e4e2f73c265ae56ae237997
iuc
parents: 11
diff changeset
22 #else
7d8c56e1a3aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 35d722c0cafe2a2f2e4e2f73c265ae56ae237997
iuc
parents: 11
diff changeset
23 #set format = 'fastq'
7d8c56e1a3aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 35d722c0cafe2a2f2e4e2f73c265ae56ae237997
iuc
parents: 11
diff changeset
24 #end if
7d8c56e1a3aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 35d722c0cafe2a2f2e4e2f73c265ae56ae237997
iuc
parents: 11
diff changeset
25
7d8c56e1a3aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 35d722c0cafe2a2f2e4e2f73c265ae56ae237997
iuc
parents: 11
diff changeset
26
7d8c56e1a3aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 35d722c0cafe2a2f2e4e2f73c265ae56ae237997
iuc
parents: 11
diff changeset
27 ln -s '${input_file}' '${input_file_sl}' &&
7d8c56e1a3aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 35d722c0cafe2a2f2e4e2f73c265ae56ae237997
iuc
parents: 11
diff changeset
28 mkdir -p '${html_file.files_path}' &&
7d8c56e1a3aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 35d722c0cafe2a2f2e4e2f73c265ae56ae237997
iuc
parents: 11
diff changeset
29 fastqc
7d8c56e1a3aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 35d722c0cafe2a2f2e4e2f73c265ae56ae237997
iuc
parents: 11
diff changeset
30 --outdir '${html_file.files_path}'
7d8c56e1a3aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 35d722c0cafe2a2f2e4e2f73c265ae56ae237997
iuc
parents: 11
diff changeset
31
8
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702
iuc
parents: 7
diff changeset
32 #if $contaminants.dataset and str($contaminants) > ''
13
7d8c56e1a3aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 35d722c0cafe2a2f2e4e2f73c265ae56ae237997
iuc
parents: 11
diff changeset
33 --contaminants '${contaminants}'
8
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702
iuc
parents: 7
diff changeset
34 #end if
13
7d8c56e1a3aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 35d722c0cafe2a2f2e4e2f73c265ae56ae237997
iuc
parents: 11
diff changeset
35
8
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702
iuc
parents: 7
diff changeset
36 #if $limits.dataset and str($limits) > ''
13
7d8c56e1a3aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 35d722c0cafe2a2f2e4e2f73c265ae56ae237997
iuc
parents: 11
diff changeset
37 --limits '${limits}'
8
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702
iuc
parents: 7
diff changeset
38 #end if
13
7d8c56e1a3aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 35d722c0cafe2a2f2e4e2f73c265ae56ae237997
iuc
parents: 11
diff changeset
39
7d8c56e1a3aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 35d722c0cafe2a2f2e4e2f73c265ae56ae237997
iuc
parents: 11
diff changeset
40 --quiet
7d8c56e1a3aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 35d722c0cafe2a2f2e4e2f73c265ae56ae237997
iuc
parents: 11
diff changeset
41 --extract
7d8c56e1a3aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 35d722c0cafe2a2f2e4e2f73c265ae56ae237997
iuc
parents: 11
diff changeset
42 -f '${format}'
7d8c56e1a3aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 35d722c0cafe2a2f2e4e2f73c265ae56ae237997
iuc
parents: 11
diff changeset
43 '${input_file_sl}'
7d8c56e1a3aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 35d722c0cafe2a2f2e4e2f73c265ae56ae237997
iuc
parents: 11
diff changeset
44
7d8c56e1a3aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 35d722c0cafe2a2f2e4e2f73c265ae56ae237997
iuc
parents: 11
diff changeset
45 && cp '${html_file.files_path}'/*/fastqc_data.txt output.txt
7d8c56e1a3aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 35d722c0cafe2a2f2e4e2f73c265ae56ae237997
iuc
parents: 11
diff changeset
46 && cp '${html_file.files_path}'/*\.html output.html
7d8c56e1a3aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 35d722c0cafe2a2f2e4e2f73c265ae56ae237997
iuc
parents: 11
diff changeset
47
6
e8c90ad3cbf9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqc commit df4c0b0c6372e2984966e220fa42ecd8a3d370e8
devteam
parents: 5
diff changeset
48 ]]></command>
3
36980a78cc83 Uploaded
devteam
parents: 2
diff changeset
49 <inputs>
10
1f6fd7a898bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 4b383d48868d7f3f6d35f242a0ee35953adcb037
iuc
parents: 9
diff changeset
50 <param format="fastq,fastq.gz,fastq.bz2,bam,sam" name="input_file" type="data"
1f6fd7a898bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 4b383d48868d7f3f6d35f242a0ee35953adcb037
iuc
parents: 9
diff changeset
51 label="Short read data from your current history" />
6
e8c90ad3cbf9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqc commit df4c0b0c6372e2984966e220fa42ecd8a3d370e8
devteam
parents: 5
diff changeset
52 <param name="contaminants" type="data" format="tabular" optional="true" label="Contaminant list"
8
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702
iuc
parents: 7
diff changeset
53 help="tab delimited file with 2 columns: name and sequence. For example: Illumina Small RNA RT Primer CAAGCAGAAGACGGCATACGA" />
3
36980a78cc83 Uploaded
devteam
parents: 2
diff changeset
54 <param name="limits" type="data" format="txt" optional="true" label="Submodule and Limit specifing file"
8
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702
iuc
parents: 7
diff changeset
55 help="a file that specifies which submodules are to be executed (default=all) and also specifies the thresholds for the each submodules warning parameter" />
3
36980a78cc83 Uploaded
devteam
parents: 2
diff changeset
56 </inputs>
36980a78cc83 Uploaded
devteam
parents: 2
diff changeset
57 <outputs>
13
7d8c56e1a3aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 35d722c0cafe2a2f2e4e2f73c265ae56ae237997
iuc
parents: 11
diff changeset
58 <data format="html" name="html_file" from_work_dir="output.html" label="${tool.name} on ${on_string}: Webpage" />
7d8c56e1a3aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 35d722c0cafe2a2f2e4e2f73c265ae56ae237997
iuc
parents: 11
diff changeset
59 <data format="txt" name="text_file" from_work_dir="output.txt" label="${tool.name} on ${on_string}: RawData" />
3
36980a78cc83 Uploaded
devteam
parents: 2
diff changeset
60 </outputs>
36980a78cc83 Uploaded
devteam
parents: 2
diff changeset
61 <tests>
36980a78cc83 Uploaded
devteam
parents: 2
diff changeset
62 <test>
36980a78cc83 Uploaded
devteam
parents: 2
diff changeset
63 <param name="input_file" value="1000gsample.fastq" />
36980a78cc83 Uploaded
devteam
parents: 2
diff changeset
64 <param name="contaminants" value="fastqc_contaminants.txt" ftype="tabular" />
36980a78cc83 Uploaded
devteam
parents: 2
diff changeset
65 <output name="html_file" file="fastqc_report.html" ftype="html" lines_diff="100"/>
13
7d8c56e1a3aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 35d722c0cafe2a2f2e4e2f73c265ae56ae237997
iuc
parents: 11
diff changeset
66 <output name="text_file" file="fastqc_data.txt" ftype="txt" lines_diff="2"/>
3
36980a78cc83 Uploaded
devteam
parents: 2
diff changeset
67 </test>
36980a78cc83 Uploaded
devteam
parents: 2
diff changeset
68 <test>
36980a78cc83 Uploaded
devteam
parents: 2
diff changeset
69 <param name="input_file" value="1000gsample.fastq" />
36980a78cc83 Uploaded
devteam
parents: 2
diff changeset
70 <param name="limits" value="fastqc_customlimits.txt" ftype="txt" />
6
e8c90ad3cbf9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqc commit df4c0b0c6372e2984966e220fa42ecd8a3d370e8
devteam
parents: 5
diff changeset
71 <output name="html_file" file="fastqc_report2.html" ftype="html" compare="sim_size" delta="4096"/>
13
7d8c56e1a3aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 35d722c0cafe2a2f2e4e2f73c265ae56ae237997
iuc
parents: 11
diff changeset
72 <output name="text_file" file="fastqc_data2.txt" ftype="txt" lines_diff="2"/>
3
36980a78cc83 Uploaded
devteam
parents: 2
diff changeset
73 </test>
7
ec73b7c83b2c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqc commit 8918618a5ef7bdca55a31cd919efa593044a376e
devteam
parents: 6
diff changeset
74 <test>
8
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702
iuc
parents: 7
diff changeset
75 <param name="input_file" value="1000gsample.fastq.gz" ftype="fastq.gz" />
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702
iuc
parents: 7
diff changeset
76 <param name="contaminants" value="fastqc_contaminants.txt" ftype="tabular" />
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702
iuc
parents: 7
diff changeset
77 <output name="html_file" file="fastqc_report.html" ftype="html" lines_diff="100"/>
13
7d8c56e1a3aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 35d722c0cafe2a2f2e4e2f73c265ae56ae237997
iuc
parents: 11
diff changeset
78 <output name="text_file" file="fastqc_data.txt" ftype="txt" lines_diff="2"/>
8
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702
iuc
parents: 7
diff changeset
79 </test>
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702
iuc
parents: 7
diff changeset
80 <test>
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702
iuc
parents: 7
diff changeset
81 <param name="input_file" value="1000gsample.fastq.bz2" ftype="fastq.bz2" />
7
ec73b7c83b2c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqc commit 8918618a5ef7bdca55a31cd919efa593044a376e
devteam
parents: 6
diff changeset
82 <param name="contaminants" value="fastqc_contaminants.txt" ftype="tabular" />
ec73b7c83b2c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqc commit 8918618a5ef7bdca55a31cd919efa593044a376e
devteam
parents: 6
diff changeset
83 <output name="html_file" file="fastqc_report.html" ftype="html" lines_diff="100"/>
13
7d8c56e1a3aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 35d722c0cafe2a2f2e4e2f73c265ae56ae237997
iuc
parents: 11
diff changeset
84 <output name="text_file" file="fastqc_data.txt" ftype="txt" lines_diff="2"/>
7d8c56e1a3aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 35d722c0cafe2a2f2e4e2f73c265ae56ae237997
iuc
parents: 11
diff changeset
85 </test>
7d8c56e1a3aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 35d722c0cafe2a2f2e4e2f73c265ae56ae237997
iuc
parents: 11
diff changeset
86 <test>
7d8c56e1a3aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 35d722c0cafe2a2f2e4e2f73c265ae56ae237997
iuc
parents: 11
diff changeset
87 <param name="input_file" value="hisat_output_1.bam" ftype="bam" />
7d8c56e1a3aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 35d722c0cafe2a2f2e4e2f73c265ae56ae237997
iuc
parents: 11
diff changeset
88 <output name="html_file" file="fastqc_report_hisat.html" ftype="html" lines_diff="100"/>
7d8c56e1a3aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 35d722c0cafe2a2f2e4e2f73c265ae56ae237997
iuc
parents: 11
diff changeset
89 <output name="text_file" file="fastqc_data_hisat.txt" ftype="txt" lines_diff="2"/>
7
ec73b7c83b2c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqc commit 8918618a5ef7bdca55a31cd919efa593044a376e
devteam
parents: 6
diff changeset
90 </test>
3
36980a78cc83 Uploaded
devteam
parents: 2
diff changeset
91 </tests>
36980a78cc83 Uploaded
devteam
parents: 2
diff changeset
92 <help>
0
d5e4121e45ed Imported from capsule None
devteam
parents:
diff changeset
93 .. class:: infomark
d5e4121e45ed Imported from capsule None
devteam
parents:
diff changeset
94
d5e4121e45ed Imported from capsule None
devteam
parents:
diff changeset
95 **Purpose**
d5e4121e45ed Imported from capsule None
devteam
parents:
diff changeset
96
d5e4121e45ed Imported from capsule None
devteam
parents:
diff changeset
97 FastQC aims to provide a simple way to do some quality control checks on raw
6
e8c90ad3cbf9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqc commit df4c0b0c6372e2984966e220fa42ecd8a3d370e8
devteam
parents: 5
diff changeset
98 sequence data coming from high throughput sequencing pipelines.
0
d5e4121e45ed Imported from capsule None
devteam
parents:
diff changeset
99 It provides a modular set of analyses which you can use to give a quick
6
e8c90ad3cbf9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqc commit df4c0b0c6372e2984966e220fa42ecd8a3d370e8
devteam
parents: 5
diff changeset
100 impression of whether your data has any problems of
0
d5e4121e45ed Imported from capsule None
devteam
parents:
diff changeset
101 which you should be aware before doing any further analysis.
d5e4121e45ed Imported from capsule None
devteam
parents:
diff changeset
102
d5e4121e45ed Imported from capsule None
devteam
parents:
diff changeset
103 The main functions of FastQC are:
d5e4121e45ed Imported from capsule None
devteam
parents:
diff changeset
104
8
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702
iuc
parents: 7
diff changeset
105 - Import of data from BAM, SAM or FastQ/FastQ.gz files (any variant),
0
d5e4121e45ed Imported from capsule None
devteam
parents:
diff changeset
106 - Providing a quick overview to tell you in which areas there may be problems
d5e4121e45ed Imported from capsule None
devteam
parents:
diff changeset
107 - Summary graphs and tables to quickly assess your data
d5e4121e45ed Imported from capsule None
devteam
parents:
diff changeset
108 - Export of results to an HTML based permanent report
d5e4121e45ed Imported from capsule None
devteam
parents:
diff changeset
109 - Offline operation to allow automated generation of reports without running the interactive application
d5e4121e45ed Imported from capsule None
devteam
parents:
diff changeset
110
d5e4121e45ed Imported from capsule None
devteam
parents:
diff changeset
111 -----
d5e4121e45ed Imported from capsule None
devteam
parents:
diff changeset
112
d5e4121e45ed Imported from capsule None
devteam
parents:
diff changeset
113 .. class:: infomark
d5e4121e45ed Imported from capsule None
devteam
parents:
diff changeset
114
d5e4121e45ed Imported from capsule None
devteam
parents:
diff changeset
115 **FastQC**
d5e4121e45ed Imported from capsule None
devteam
parents:
diff changeset
116
d5e4121e45ed Imported from capsule None
devteam
parents:
diff changeset
117 This is a Galaxy wrapper. It merely exposes the external package FastQC_ which is documented at FastQC_
d5e4121e45ed Imported from capsule None
devteam
parents:
diff changeset
118 Kindly acknowledge it as well as this tool if you use it.
10
1f6fd7a898bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 4b383d48868d7f3f6d35f242a0ee35953adcb037
iuc
parents: 9
diff changeset
119 FastQC incorporates the Picard-tools_ libraries for SAM/BAM processing.
0
d5e4121e45ed Imported from capsule None
devteam
parents:
diff changeset
120
d5e4121e45ed Imported from capsule None
devteam
parents:
diff changeset
121 The contaminants file parameter was borrowed from the independently developed
d5e4121e45ed Imported from capsule None
devteam
parents:
diff changeset
122 fastqcwrapper contributed to the Galaxy Community Tool Shed by J. Johnson.
1
67355741fbc3 Uploaded from GH
devteam
parents: 0
diff changeset
123 Adaption to version 0.11.2 by T. McGowan.
0
d5e4121e45ed Imported from capsule None
devteam
parents:
diff changeset
124
d5e4121e45ed Imported from capsule None
devteam
parents:
diff changeset
125 -----
d5e4121e45ed Imported from capsule None
devteam
parents:
diff changeset
126
d5e4121e45ed Imported from capsule None
devteam
parents:
diff changeset
127 .. class:: infomark
d5e4121e45ed Imported from capsule None
devteam
parents:
diff changeset
128
d5e4121e45ed Imported from capsule None
devteam
parents:
diff changeset
129 **Inputs and outputs**
d5e4121e45ed Imported from capsule None
devteam
parents:
diff changeset
130
6
e8c90ad3cbf9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqc commit df4c0b0c6372e2984966e220fa42ecd8a3d370e8
devteam
parents: 5
diff changeset
131 FastQC_ is the best place to look for documentation - it's very good.
0
d5e4121e45ed Imported from capsule None
devteam
parents:
diff changeset
132 A summary follows below for those in a tearing hurry.
d5e4121e45ed Imported from capsule None
devteam
parents:
diff changeset
133
7
ec73b7c83b2c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqc commit 8918618a5ef7bdca55a31cd919efa593044a376e
devteam
parents: 6
diff changeset
134 This wrapper will accept a Galaxy fastq, fastq.gz, sam or bam as the input read file to check.
0
d5e4121e45ed Imported from capsule None
devteam
parents:
diff changeset
135 It will also take an optional file containing a list of contaminants information, in the form of
1
67355741fbc3 Uploaded from GH
devteam
parents: 0
diff changeset
136 a tab-delimited file with 2 columns, name and sequence. As another option the tool takes a custom
67355741fbc3 Uploaded from GH
devteam
parents: 0
diff changeset
137 limits.txt file that allows setting the warning thresholds for the different modules and also specifies
67355741fbc3 Uploaded from GH
devteam
parents: 0
diff changeset
138 which modules to include in the output.
0
d5e4121e45ed Imported from capsule None
devteam
parents:
diff changeset
139
1
67355741fbc3 Uploaded from GH
devteam
parents: 0
diff changeset
140 The tool produces a basic text and a HTML output file that contain all of the results, including the following:
0
d5e4121e45ed Imported from capsule None
devteam
parents:
diff changeset
141
d5e4121e45ed Imported from capsule None
devteam
parents:
diff changeset
142 - Basic Statistics
d5e4121e45ed Imported from capsule None
devteam
parents:
diff changeset
143 - Per base sequence quality
d5e4121e45ed Imported from capsule None
devteam
parents:
diff changeset
144 - Per sequence quality scores
d5e4121e45ed Imported from capsule None
devteam
parents:
diff changeset
145 - Per base sequence content
d5e4121e45ed Imported from capsule None
devteam
parents:
diff changeset
146 - Per base GC content
d5e4121e45ed Imported from capsule None
devteam
parents:
diff changeset
147 - Per sequence GC content
d5e4121e45ed Imported from capsule None
devteam
parents:
diff changeset
148 - Per base N content
d5e4121e45ed Imported from capsule None
devteam
parents:
diff changeset
149 - Sequence Length Distribution
d5e4121e45ed Imported from capsule None
devteam
parents:
diff changeset
150 - Sequence Duplication Levels
d5e4121e45ed Imported from capsule None
devteam
parents:
diff changeset
151 - Overrepresented sequences
d5e4121e45ed Imported from capsule None
devteam
parents:
diff changeset
152 - Kmer Content
d5e4121e45ed Imported from capsule None
devteam
parents:
diff changeset
153
d5e4121e45ed Imported from capsule None
devteam
parents:
diff changeset
154 All except Basic Statistics and Overrepresented sequences are plots.
9
0a7c65540937 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 168f7aeb0f9f38de6dec873f3cbf0c30014fdd72
iuc
parents: 8
diff changeset
155 .. _FastQC: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
10
1f6fd7a898bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 4b383d48868d7f3f6d35f242a0ee35953adcb037
iuc
parents: 9
diff changeset
156 .. _Picard-tools: https://broadinstitute.github.io/picard/
2
bf15645bae10 Uploaded from GH
devteam
parents: 1
diff changeset
157 </help>
bf15645bae10 Uploaded from GH
devteam
parents: 1
diff changeset
158 <citations>
bf15645bae10 Uploaded from GH
devteam
parents: 1
diff changeset
159 <citation type="bibtex">
8
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702
iuc
parents: 7
diff changeset
160 @unpublished{andrews_s,
2
bf15645bae10 Uploaded from GH
devteam
parents: 1
diff changeset
161 author = {Andrews, S.},
bf15645bae10 Uploaded from GH
devteam
parents: 1
diff changeset
162 keywords = {bioinformatics, ngs, qc},
bf15645bae10 Uploaded from GH
devteam
parents: 1
diff changeset
163 priority = {2},
bf15645bae10 Uploaded from GH
devteam
parents: 1
diff changeset
164 title = {{FastQC A Quality Control tool for High Throughput Sequence Data}},
bf15645bae10 Uploaded from GH
devteam
parents: 1
diff changeset
165 url = {http://www.bioinformatics.babraham.ac.uk/projects/fastqc/}
bf15645bae10 Uploaded from GH
devteam
parents: 1
diff changeset
166 }
bf15645bae10 Uploaded from GH
devteam
parents: 1
diff changeset
167 </citation>
bf15645bae10 Uploaded from GH
devteam
parents: 1
diff changeset
168 </citations>
0
d5e4121e45ed Imported from capsule None
devteam
parents:
diff changeset
169 </tool>