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comparison fasta_clipping_histogram.xml @ 4:40ec4170291e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_clipping_histogram commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
author iuc
date Tue, 08 May 2018 10:45:30 -0400
parents d0969fa24eb1
children cf0a5c96c7f8
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3:d0969fa24eb1 4:40ec4170291e
1 <tool id="cshl_fasta_clipping_histogram" name="Length Distribution" version="1.0.0"> 1 <tool id="cshl_fasta_clipping_histogram" name="Length Distribution" version="1.0.1">
2 <description>chart</description> 2 <description>chart</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>fasta_clipping_histogram.pl $input $outfile</command> 6 <expand macro="requirements">
7 <requirement type="package" version="1.49">perl-gdgraph</requirement>
8 </expand>
9 <command detect_errors="exit_code"><![CDATA[
10 fasta_clipping_histogram.pl
11 '$input'
12 '$outfile'
13 ]]></command>
7 14
8 <inputs> 15 <inputs>
9 <param format="fasta" name="input" type="data" label="Library to analyze" /> 16 <expand macro="fasta_input" />
10 </inputs> 17 </inputs>
11 18
12 <outputs> 19 <outputs>
13 <data format="png" name="outfile" metadata_source="input" /> 20 <data name="outfile" format="png" metadata_source="input" />
14 </outputs> 21 </outputs>
15 <tests> 22 <tests>
23 <test>
24 <param name="input" value="fasta_clipping_histogram-in1.fa" />
25 <output name="outfile" file="fasta_clipping_histogram-out1.png" compare="sim_size" delta="512" />
26 </test>
27 <test>
28 <param name="input" value="fasta_clipping_histogram-in2.fa" />
29 <output name="outfile" file="fasta_clipping_histogram-out2.png" compare="sim_size" delta="512" />
30 </test>
16 </tests> 31 </tests>
17 <help> 32 <help><![CDATA[
18 **What it does** 33 **What it does**
19 34
20 This tool creates a histogram image of sequence lengths distribution in a given fasta dataset file. 35 This tool creates a histogram image of sequence lengths distribution in a given fasta dataset file.
21 36
22 **TIP:** Use this tool after clipping your library (with **FASTX Clipper tool**), to visualize the clipping results. 37 **TIP:** Use this tool after clipping your library (with **FASTX Clipper tool**), to visualize the clipping results.
39 54
40 **Input Formats** 55 **Input Formats**
41 56
42 This tool accepts short-reads FASTA files. The reads don't have to be short, but they do have to be on a single line, like so:: 57 This tool accepts short-reads FASTA files. The reads don't have to be short, but they do have to be on a single line, like so::
43 58
44 >sequence1 59 >sequence1
45 AGTAGTAGGTGATGTAGAGAGAGAGAGAGTAG 60 AGTAGTAGGTGATGTAGAGAGAGAGAGAGTAG
46 >sequence2 61 >sequence2
47 GTGTGTGTGGGAAGTTGACACAGTA 62 GTGTGTGTGGGAAGTTGACACAGTA
48 >sequence3 63 >sequence3
49 CCTTGAGATTAACGCTAATCAAGTAAAC 64 CCTTGAGATTAACGCTAATCAAGTAAAC
50 65
51 If the sequences span over multiple lines:: 66 If the sequences span over multiple lines::
52 67
53 >sequence1 68 >sequence1
54 CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAG 69 CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAG
55 TCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAG 70 TCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAG
56 aactggtctttacctTTAAGTTG 71 aactggtctttacctTTAAGTTG
57 72
58 Use the **FASTA Width Formatter** tool to re-format the FASTA into a single-lined sequences:: 73 Use the **FASTA Width Formatter** tool to re-format the FASTA into a single-lined sequences::
59 74
60 >sequence1 75 >sequence1
61 CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAGaactggtctttacctTTAAGTTG 76 CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAGaactggtctttacctTTAAGTTG
96 111
97 ------ 112 ------
98 113
99 This tool is based on `FASTX-toolkit`__ by Assaf Gordon. 114 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
100 115
101 .. __: http://hannonlab.cshl.edu/fastx_toolkit/ 116 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
102 </help> 117 ]]></help>
118 <expand macro="citations" />
103 </tool> 119 </tool>