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comparison fastx_nucleotides_distribution.xml @ 3:3b6c41fc2d21 draft

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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
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2:05f35740cd79 3:3b6c41fc2d21
1 <tool id="cshl_fastx_nucleotides_distribution" version="1.0.0" name="Draw nucleotides distribution chart"> 1 <tool id="cshl_fastx_nucleotides_distribution" version="1.0.1" name="Draw nucleotides distribution chart">
2 <description></description> 2 <description></description>
3 <requirements> 3 <macros>
4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement> 4 <import>macros.xml</import>
5 </requirements> 5 </macros>
6 <command>fastx_nucleotide_distribution_graph.sh -t '$input.name' -i $input -o $output</command> 6 <expand macro="requirements" />
7 7 <command detect_errors="exit_code"><![CDATA[
8 <inputs> 8 fastx_nucleotide_distribution_graph.sh
9 <param format="txt" name="input" type="data" label="Statistics Text File" help="output of 'FASTX Statistics' tool" /> 9 -t '$input.name'
10 </inputs> 10 -i '$input'
11 11 -o '$output'
12 <outputs> 12 ]]></command>
13 <data format="png" name="output" metadata_source="input" /> 13 <inputs>
14 </outputs> 14 <param name="input" type="data" format="txt" label="Statistics text file" help="Output of 'FASTX Statistics' tool" />
15 <help> 15 </inputs>
16 16 <outputs>
17 <data name="output" format="png" metadata_source="input" />
18 </outputs>
19 <tests>
20 <test>
21 <param name="input" value="fastx_nucleotides_distribution-in1.txt" />
22 <output name="output" file="fastx_nucleotides_distribution-out1.png" compare="sim_size" delta="512" />
23 </test>
24 </tests>
25 <help><![CDATA[
17 **What it does** 26 **What it does**
18 27
19 Creates a stacked-histogram graph for the nucleotide distribution in the Solexa library. 28 Creates a stacked-histogram graph for the nucleotide distribution in the Solexa library.
20 29
21 .. class:: infomark 30 .. class:: infomark
27 **Output Examples** 36 **Output Examples**
28 37
29 The following chart clearly shows the barcode used at the 5'-end of the library: **GATCT** 38 The following chart clearly shows the barcode used at the 5'-end of the library: **GATCT**
30 39
31 .. image:: fastq_nucleotides_distribution_1.png 40 .. image:: fastq_nucleotides_distribution_1.png
32 41
33 In the following chart, one can almost 'read' the most abundant sequence by looking at the dominant values: **TGATA TCGTA TTGAT GACTG AA...** 42 In the following chart, one can almost 'read' the most abundant sequence by looking at the dominant values: **TGATA TCGTA TTGAT GACTG AA...**
34 43
35 .. image:: fastq_nucleotides_distribution_2.png 44 .. image:: fastq_nucleotides_distribution_2.png
36 45
37 The following chart shows a growing number of unknown (N) nucleotides towards later cycles (which might indicate a sequencing problem): 46 The following chart shows a growing number of unknown (N) nucleotides towards later cycles (which might indicate a sequencing problem):
45 ------ 54 ------
46 55
47 This tool is based on `FASTX-toolkit`__ by Assaf Gordon. 56 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
48 57
49 .. __: http://hannonlab.cshl.edu/fastx_toolkit/ 58 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
50 59 ]]></help>
51 </help> 60 <expand macro="citations" />
52 <!-- FASTQ-Nucleotides-Distribution is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) --> 61 <!-- FASTQ-Nucleotides-Distribution is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
53 </tool> 62 </tool>