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comparison fastq_quality_boxplot.xml @ 2:3987db70a4b0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
author iuc
date Tue, 08 May 2018 13:26:13 -0400
parents f95284aa2946
children 7cf5b1d072b5
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1:f95284aa2946 2:3987db70a4b0
1 <tool id="cshl_fastq_quality_boxplot" name="Draw quality score boxplot" version="1.0.0"> 1 <tool id="cshl_fastq_quality_boxplot" name="Draw quality score boxplot" version="1.0.1">
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>fastq_quality_boxplot_graph.sh -t '$input.name' -i $input -o $output</command> 6 <expand macro="requirements" />
7 7 <command detect_errors="exit_code"><![CDATA[
8 <inputs> 8 #import re
9 <param format="txt" name="input" type="data" label="Statistics report file" help="output of 'FASTQ Statistics' tool" /> 9 #set escaped_element_identifier = re.sub('[^\w\-\s]', '_', str($input.element_identifier))
10 </inputs> 10 fastq_quality_boxplot_graph.sh
11 -t '$escaped_element_identifier'
12 -i '$input'
13 -o '$output'
14 ]]></command>
11 15
12 <outputs> 16 <inputs>
13 <data format="png" name="output" metadata_source="input" /> 17 <param name="input" type="data" format="txt" label="Statistics report file" help="output of 'FASTQ Statistics' tool" />
14 </outputs> 18 </inputs>
15 <help>
16 19
20 <outputs>
21 <data name="output" format="png" metadata_source="input" />
22 </outputs>
23 <tests>
24 <test>
25 <param name="input" value="fastq_quality_boxplot-in1.fastq" />
26 <output name="output" file="fastq_quality_boxplot-out1.png" compare="sim_size" delta="768" />
27 </test>
28 </tests>
29 <help><![CDATA[
17 **What it does** 30 **What it does**
18 31
19 Creates a boxplot graph for the quality scores in the library. 32 Creates a boxplot graph for the quality scores in the library.
20 33
21 .. class:: infomark 34 .. class:: infomark
47 ------ 60 ------
48 61
49 This tool is based on `FASTX-toolkit`__ by Assaf Gordon. 62 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
50 63
51 .. __: http://hannonlab.cshl.edu/fastx_toolkit/ 64 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
52 65 ]]></help>
53 66 <expand macro="citations" />
54
55 </help>
56 <!-- FASTQ-Quality-Boxplot is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) --> 67 <!-- FASTQ-Quality-Boxplot is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
57 </tool> 68 </tool>