Mercurial > repos > devteam > fastq_quality_boxplot

annotate fastq_quality_boxplot.xml @ 7:485db772db61 draft default tip

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/tool_collections/fastx_toolkit/fastq_quality_boxplot commit 17bcf78f445b2e515122330caccb591d8de2a5b4
author iuc
date Wed, 23 Apr 2025 05:17:36 +0000
parents 101dc4d70c89
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
101dc4d70c89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot commit fd099d17eceaa319fbfe429f4725328d88b18c9f
iuc
parents: 5
diff changeset
1 <tool id="cshl_fastq_quality_boxplot" name="Draw quality score boxplot" version="1.0.1+galaxy@VERSION_SUFFIX@" profile="22.05">
4
439eed933bf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 3
diff changeset
2 <description></description>
439eed933bf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 3
diff changeset
3 <macros>
439eed933bf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 3
diff changeset
4 <import>macros.xml</import>
439eed933bf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 3
diff changeset
5 </macros>
439eed933bf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 3
diff changeset
6 <expand macro="requirements" />
439eed933bf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 3
diff changeset
7 <command detect_errors="exit_code"><![CDATA[
439eed933bf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 3
diff changeset
8 #import re
439eed933bf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 3
diff changeset
9 #set escaped_element_identifier = re.sub('[^\w\-\s]', '_', str($input.element_identifier))
439eed933bf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 3
diff changeset
10 fastq_quality_boxplot_graph.sh
439eed933bf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 3
diff changeset
11 -t '$escaped_element_identifier'
439eed933bf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 3
diff changeset
12 -i '$input'
439eed933bf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 3
diff changeset
13 -o '$output'
439eed933bf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 3
diff changeset
14 ]]></command>
0
9f71775d0fe2 Uploaded
devteam
parents:
diff changeset
15
4
439eed933bf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 3
diff changeset
16 <inputs>
439eed933bf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 3
diff changeset
17 <param name="input" type="data" format="txt" label="Statistics report file" help="output of 'FASTQ Statistics' tool" />
439eed933bf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 3
diff changeset
18 </inputs>
0
9f71775d0fe2 Uploaded
devteam
parents:
diff changeset
19
4
439eed933bf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 3
diff changeset
20 <outputs>
439eed933bf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 3
diff changeset
21 <data name="output" format="png" metadata_source="input" />
439eed933bf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 3
diff changeset
22 </outputs>
439eed933bf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 3
diff changeset
23 <tests>
439eed933bf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 3
diff changeset
24 <test>
439eed933bf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 3
diff changeset
25 <param name="input" value="fastq_quality_boxplot-in1.fastq" />
5
5a28b303e432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
iuc
parents: 4
diff changeset
26 <output name="output" file="fastq_quality_boxplot-out1.png" compare="sim_size" delta="10000" />
4
439eed933bf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 3
diff changeset
27 </test>
439eed933bf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 3
diff changeset
28 </tests>
439eed933bf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 3
diff changeset
29 <help><![CDATA[
0
9f71775d0fe2 Uploaded
devteam
parents:
diff changeset
30 **What it does**
9f71775d0fe2 Uploaded
devteam
parents:
diff changeset
31
9f71775d0fe2 Uploaded
devteam
parents:
diff changeset
32 Creates a boxplot graph for the quality scores in the library.
9f71775d0fe2 Uploaded
devteam
parents:
diff changeset
33
9f71775d0fe2 Uploaded
devteam
parents:
diff changeset
34 .. class:: infomark
9f71775d0fe2 Uploaded
devteam
parents:
diff changeset
35
9f71775d0fe2 Uploaded
devteam
parents:
diff changeset
36 **TIP:** Use the **FASTQ Statistics** tool to generate the report file needed for this tool.
9f71775d0fe2 Uploaded
devteam
parents:
diff changeset
37
9f71775d0fe2 Uploaded
devteam
parents:
diff changeset
38 -----
9f71775d0fe2 Uploaded
devteam
parents:
diff changeset
39
9f71775d0fe2 Uploaded
devteam
parents:
diff changeset
40 **Output Examples**
9f71775d0fe2 Uploaded
devteam
parents:
diff changeset
41
9f71775d0fe2 Uploaded
devteam
parents:
diff changeset
42 * Black horizontal lines are medians
9f71775d0fe2 Uploaded
devteam
parents:
diff changeset
43 * Rectangular red boxes show the Inter-quartile Range (IQR) (top value is Q3, bottom value is Q1)
9f71775d0fe2 Uploaded
devteam
parents:
diff changeset
44 * Whiskers show outlier at max. 1.5*IQR
9f71775d0fe2 Uploaded
devteam
parents:
diff changeset
45
9f71775d0fe2 Uploaded
devteam
parents:
diff changeset
46
9f71775d0fe2 Uploaded
devteam
parents:
diff changeset
47 An excellent quality library (median quality is 40 for almost all 36 cycles):
9f71775d0fe2 Uploaded
devteam
parents:
diff changeset
48
3
cd82df766cab Add missing help images.
Dave Bouvier <dave@bx.psu.edu>
parents: 2
diff changeset
49 .. image:: fastq_quality_boxplot_1.png
0
9f71775d0fe2 Uploaded
devteam
parents:
diff changeset
50
9f71775d0fe2 Uploaded
devteam
parents:
diff changeset
51
9f71775d0fe2 Uploaded
devteam
parents:
diff changeset
52 A relatively good quality library (median quality degrades towards later cycles):
9f71775d0fe2 Uploaded
devteam
parents:
diff changeset
53
3
cd82df766cab Add missing help images.
Dave Bouvier <dave@bx.psu.edu>
parents: 2
diff changeset
54 .. image:: fastq_quality_boxplot_2.png
0
9f71775d0fe2 Uploaded
devteam
parents:
diff changeset
55
9f71775d0fe2 Uploaded
devteam
parents:
diff changeset
56 A low quality library (median drops quickly):
9f71775d0fe2 Uploaded
devteam
parents:
diff changeset
57
3
cd82df766cab Add missing help images.
Dave Bouvier <dave@bx.psu.edu>
parents: 2
diff changeset
58 .. image:: fastq_quality_boxplot_3.png
0
9f71775d0fe2 Uploaded
devteam
parents:
diff changeset
59
4
439eed933bf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 3
diff changeset
60 ]]></help>
439eed933bf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 3
diff changeset
61 <expand macro="citations" />
0
9f71775d0fe2 Uploaded
devteam
parents:
diff changeset
62 <!-- FASTQ-Quality-Boxplot is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
3
cd82df766cab Add missing help images.
Dave Bouvier <dave@bx.psu.edu>
parents: 2
diff changeset
63 </tool>