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comparison fastqe.xml @ 2:a252d8415583 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 7f1ac61222e3b10cd9a82c7b35ea53985c06ba9c"
author iuc
date Fri, 24 Jul 2020 14:30:21 -0400
parents 8d3aff8ba8ad
children 819b8c1657d5
comparison
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1:8d3aff8ba8ad 2:a252d8415583
1 <tool id="fastqe" name="FASTQE" version="0.2.6"> 1 <tool id="fastqe" name="FASTQE" version="0.2.6+galaxy0">
2 <description>visualize fastq files with emoji's 🧬😎</description> 2 <description>visualize fastq files with emoji's 🧬😎</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.2.6">fastqe</requirement> 4 <requirement type="package" version="0.2.6">fastqe</requirement>
5 <requirement type="package" version="4.7">sed</requirement>
5 </requirements> 6 </requirements>
6 <command detect_errors="exit_code"> 7 <command detect_errors="exit_code">
7 <![CDATA[ 8 <![CDATA[
8 9
9 #for i in $input: 10 #import re
10 ln -s '$i' '$i.element_identifier' && 11
12 #set $filenames = [re.sub('[^\w\-\s.]', '_', $i.element_identifier) for $i in $input]
13 #for $i, $filename in zip($input, $filenames):
14 ln -s '$i' '$filename' &&
11 #end for 15 #end for
12 16
13 echo "<html><head><title>FASTQE Report 🤔</title></head><body><h1>FASTQE Report 🤔</h1>" > '$output' && 17 echo "<html><head><title>FASTQE Report 🤔</title></head><body><h1>FASTQE Report 🤔</h1>" > '$output' &&
14 18
15 fastqe 19 fastqe
16 --mean 20 --mean
17 $bin 21 $bin
18 --min 22 --min
19 --long $long 23 --long $long
20 --max 24 --max
21 #for i in $input: 25 #for $filename in $filenames:
22 '$i.element_identifier' 26 '$filename'
23 #end for 27 #end for
24 | sed 's/$/<br>/;s/^\([^\t]*\)\t\([^\t]*\)\t/<h2>\1: \2<\/h2>\n/' >> '$output' && 28 | sed 's/$/<br>/;s/^\([^\t]*\)\t\([^\t]*\)\t/<h2>\1: \2<\/h2>\n/' >> '$output' &&
25 29
26 echo "</body></html>" >> '$output' 30 echo "</body></html>" >> '$output'
27 ]]></command> 31 ]]></command>
50 +-------+-------+ 54 +-------+-------+
51 | Bin | Emoji | 55 | Bin | Emoji |
52 +=======+=======+ 56 +=======+=======+
53 | N | 🚫 | 57 | N | 🚫 |
54 +-------+-------+ 58 +-------+-------+
55 | N | 🚫 |
56 +-------+-------+
57 | 2-9 | 💀 | 59 | 2-9 | 💀 |
58 +-------+-------+ 60 +-------+-------+
59 | 10–19 | 💩 | 61 | 10–19 | 💩 |
60 +-------+-------+ 62 +-------+-------+
61 | 20–24 | ⚠️ | 63 | 20–24 | ⚠️ |