Mercurial > repos > devteam > fastx_nucleotides_distribution

annotate fastx_nucleotides_distribution.xml @ 3:3b6c41fc2d21 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/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
author iuc
date Tue, 08 May 2018 12:51:52 -0400
parents 05f35740cd79
children 67e441bc4265
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
3b6c41fc2d21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
1 <tool id="cshl_fastx_nucleotides_distribution" version="1.0.1" name="Draw nucleotides distribution chart">
3b6c41fc2d21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
2 <description></description>
3b6c41fc2d21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
3 <macros>
3b6c41fc2d21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
4 <import>macros.xml</import>
3b6c41fc2d21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
5 </macros>
3b6c41fc2d21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
6 <expand macro="requirements" />
3b6c41fc2d21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
7 <command detect_errors="exit_code"><![CDATA[
3b6c41fc2d21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
8 fastx_nucleotide_distribution_graph.sh
3b6c41fc2d21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
9 -t '$input.name'
3b6c41fc2d21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
10 -i '$input'
3b6c41fc2d21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
11 -o '$output'
3b6c41fc2d21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
12 ]]></command>
3b6c41fc2d21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
13 <inputs>
3b6c41fc2d21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
14 <param name="input" type="data" format="txt" label="Statistics text file" help="Output of 'FASTX Statistics' tool" />
3b6c41fc2d21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
15 </inputs>
3b6c41fc2d21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
16 <outputs>
3b6c41fc2d21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
17 <data name="output" format="png" metadata_source="input" />
3b6c41fc2d21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
18 </outputs>
3b6c41fc2d21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
19 <tests>
3b6c41fc2d21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
20 <test>
3b6c41fc2d21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
21 <param name="input" value="fastx_nucleotides_distribution-in1.txt" />
3b6c41fc2d21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
22 <output name="output" file="fastx_nucleotides_distribution-out1.png" compare="sim_size" delta="512" />
3b6c41fc2d21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
23 </test>
3b6c41fc2d21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
24 </tests>
3b6c41fc2d21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
25 <help><![CDATA[
0
cef4256a0b26 Uploaded
devteam
parents:
diff changeset
26 **What it does**
cef4256a0b26 Uploaded
devteam
parents:
diff changeset
27
cef4256a0b26 Uploaded
devteam
parents:
diff changeset
28 Creates a stacked-histogram graph for the nucleotide distribution in the Solexa library.
cef4256a0b26 Uploaded
devteam
parents:
diff changeset
29
cef4256a0b26 Uploaded
devteam
parents:
diff changeset
30 .. class:: infomark
cef4256a0b26 Uploaded
devteam
parents:
diff changeset
31
cef4256a0b26 Uploaded
devteam
parents:
diff changeset
32 **TIP:** Use the **FASTQ Statistics** tool to generate the report file needed for this tool.
cef4256a0b26 Uploaded
devteam
parents:
diff changeset
33
cef4256a0b26 Uploaded
devteam
parents:
diff changeset
34 -----
cef4256a0b26 Uploaded
devteam
parents:
diff changeset
35
cef4256a0b26 Uploaded
devteam
parents:
diff changeset
36 **Output Examples**
cef4256a0b26 Uploaded
devteam
parents:
diff changeset
37
cef4256a0b26 Uploaded
devteam
parents:
diff changeset
38 The following chart clearly shows the barcode used at the 5'-end of the library: **GATCT**
cef4256a0b26 Uploaded
devteam
parents:
diff changeset
39
2
05f35740cd79 Uploaded tool help images.
devteam
parents: 1
diff changeset
40 .. image:: fastq_nucleotides_distribution_1.png
3
3b6c41fc2d21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
41
0
cef4256a0b26 Uploaded
devteam
parents:
diff changeset
42 In the following chart, one can almost 'read' the most abundant sequence by looking at the dominant values: **TGATA TCGTA TTGAT GACTG AA...**
cef4256a0b26 Uploaded
devteam
parents:
diff changeset
43
2
05f35740cd79 Uploaded tool help images.
devteam
parents: 1
diff changeset
44 .. image:: fastq_nucleotides_distribution_2.png
0
cef4256a0b26 Uploaded
devteam
parents:
diff changeset
45
cef4256a0b26 Uploaded
devteam
parents:
diff changeset
46 The following chart shows a growing number of unknown (N) nucleotides towards later cycles (which might indicate a sequencing problem):
cef4256a0b26 Uploaded
devteam
parents:
diff changeset
47
2
05f35740cd79 Uploaded tool help images.
devteam
parents: 1
diff changeset
48 .. image:: fastq_nucleotides_distribution_3.png
0
cef4256a0b26 Uploaded
devteam
parents:
diff changeset
49
cef4256a0b26 Uploaded
devteam
parents:
diff changeset
50 But most of the time, the chart will look rather random:
cef4256a0b26 Uploaded
devteam
parents:
diff changeset
51
2
05f35740cd79 Uploaded tool help images.
devteam
parents: 1
diff changeset
52 .. image:: fastq_nucleotides_distribution_4.png
0
cef4256a0b26 Uploaded
devteam
parents:
diff changeset
53
cef4256a0b26 Uploaded
devteam
parents:
diff changeset
54 ------
cef4256a0b26 Uploaded
devteam
parents:
diff changeset
55
cef4256a0b26 Uploaded
devteam
parents:
diff changeset
56 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
cef4256a0b26 Uploaded
devteam
parents:
diff changeset
57
cef4256a0b26 Uploaded
devteam
parents:
diff changeset
58 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
3
3b6c41fc2d21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
59 ]]></help>
3b6c41fc2d21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
60 <expand macro="citations" />
3b6c41fc2d21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
61 <!-- FASTQ-Nucleotides-Distribution is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
0
cef4256a0b26 Uploaded
devteam
parents:
diff changeset
62 </tool>