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comparison fastqe.xml @ 0:ece21607a21d draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
author iuc
date Mon, 13 Jul 2020 15:14:11 -0400
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-1:000000000000 0:ece21607a21d
1 <tool id="fastqe" name="FASTQE" version="0.1.1">
2 <description>visualize fastq files with emoji's 🧬😎</description>
3 <requirements>
4 <requirement type="package" version="0.1.1">fastqe</requirement>
5 </requirements>
6 <command detect_errors="exit_code">
7 <![CDATA[
8
9 #for i in $input:
10 ln -s '$i' '$i.element_identifier' &&
11 #end for
12
13 echo "<html><head><title>FASTQE Report 🤔</title></head><body><h1>FASTQE Report 🤔</h1>" > '$output' &&
14
15 fastqe
16 --mean
17 $bin
18 --min
19 --max
20 #for i in $input:
21 '$i.element_identifier'
22 #end for
23 | sed 's/$/<br>/;s/^\([^\t]*\)\t\([^\t]*\)\t/<h2>\1: \2<\/h2>\n/' >> '$output' &&
24
25 echo "</body></html>" >> '$output'
26 ]]></command>
27 <inputs>
28 <param label="FastQ data" name="input" type="data" format="fastq" multiple="true"/>
29 <param label="Bin scores" name="bin" type="boolean" truevalue="--bin" falsevalue="" />
30 </inputs>
31 <outputs>
32 <data format="html" name="output"/>
33 </outputs>
34 <tests>
35 <test>
36 <param name="input" value="test.fq,test2.fq" />
37 <output name="output" file="out.html" />
38 </test>
39 </tests>
40 <help><![CDATA[
41 FASTQ + Emoji = FASTQE 🤔
42 =========================
43
44 Compute quality stats for FASTQ files and print those stats as emoji... for some reason.
45
46 Scores can also be binned:
47
48 +-------+-------+
49 | Bin | Emoji |
50 +=======+=======+
51 | N | 🚫 |
52 +-------+-------+
53 | N | 🚫 |
54 +-------+-------+
55 | 2-9 | 💀 |
56 +-------+-------+
57 | 10–19 | 💩 |
58 +-------+-------+
59 | 20–24 | ⚠️ |
60 +-------+-------+
61 | 25–29 | 😄 |
62 +-------+-------+
63 | 30–34 | 😆 |
64 +-------+-------+
65 | 35–39 | 😎 |
66 +-------+-------+
67 | ≥ 40 | 😍 |
68 +-------+-------+
69
70
71 ]]></help>
72 <citations>
73 </citations>
74 </tool>