Mercurial > repos > iuc > fastqe

annotate fastqe.xml @ 2:a252d8415583 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"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
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
a252d8415583 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 7f1ac61222e3b10cd9a82c7b35ea53985c06ba9c"
iuc
parents: 1
diff changeset
1 <tool id="fastqe" name="FASTQE" version="0.2.6+galaxy0">
0
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
2 <description>visualize fastq files with emoji's 🧬😎</description>
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
3 <requirements>
1
8d3aff8ba8ad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit acc3e75aff3a12ee82d03fbfe676ec81d5451c6e"
iuc
parents: 0
diff changeset
4 <requirement type="package" version="0.2.6">fastqe</requirement>
2
a252d8415583 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 7f1ac61222e3b10cd9a82c7b35ea53985c06ba9c"
iuc
parents: 1
diff changeset
5 <requirement type="package" version="4.7">sed</requirement>
0
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
6 </requirements>
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
7 <command detect_errors="exit_code">
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
8 <![CDATA[
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
9
2
a252d8415583 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 7f1ac61222e3b10cd9a82c7b35ea53985c06ba9c"
iuc
parents: 1
diff changeset
10 #import re
a252d8415583 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 7f1ac61222e3b10cd9a82c7b35ea53985c06ba9c"
iuc
parents: 1
diff changeset
11
a252d8415583 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 7f1ac61222e3b10cd9a82c7b35ea53985c06ba9c"
iuc
parents: 1
diff changeset
12 #set $filenames = [re.sub('[^\w\-\s.]', '_', $i.element_identifier) for $i in $input]
a252d8415583 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 7f1ac61222e3b10cd9a82c7b35ea53985c06ba9c"
iuc
parents: 1
diff changeset
13 #for $i, $filename in zip($input, $filenames):
a252d8415583 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 7f1ac61222e3b10cd9a82c7b35ea53985c06ba9c"
iuc
parents: 1
diff changeset
14 ln -s '$i' '$filename' &&
0
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
15 #end for
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
16
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
17 echo "<html><head><title>FASTQE Report 🤔</title></head><body><h1>FASTQE Report 🤔</h1>" > '$output' &&
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
18
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
19 fastqe
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
20 --mean
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
21 $bin
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
22 --min
1
8d3aff8ba8ad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit acc3e75aff3a12ee82d03fbfe676ec81d5451c6e"
iuc
parents: 0
diff changeset
23 --long $long
0
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
24 --max
2
a252d8415583 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 7f1ac61222e3b10cd9a82c7b35ea53985c06ba9c"
iuc
parents: 1
diff changeset
25 #for $filename in $filenames:
a252d8415583 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 7f1ac61222e3b10cd9a82c7b35ea53985c06ba9c"
iuc
parents: 1
diff changeset
26 '$filename'
0
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
27 #end for
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
28 | sed 's/$/<br>/;s/^\([^\t]*\)\t\([^\t]*\)\t/<h2>\1: \2<\/h2>\n/' >> '$output' &&
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
29
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
30 echo "</body></html>" >> '$output'
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
31 ]]></command>
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
32 <inputs>
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
33 <param label="FastQ data" name="input" type="data" format="fastq" multiple="true"/>
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
34 <param label="Bin scores" name="bin" type="boolean" truevalue="--bin" falsevalue="" />
1
8d3aff8ba8ad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit acc3e75aff3a12ee82d03fbfe676ec81d5451c6e"
iuc
parents: 0
diff changeset
35 <param label="Maximum read length" name="long" type="integer" help="Enable long reads up to this many bp long." min="1" value="500"/>
0
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
36 </inputs>
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
37 <outputs>
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
38 <data format="html" name="output"/>
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
39 </outputs>
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
40 <tests>
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
41 <test>
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
42 <param name="input" value="test.fq,test2.fq" />
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
43 <output name="output" file="out.html" />
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
44 </test>
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
45 </tests>
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
46 <help><![CDATA[
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
47 FASTQ + Emoji = FASTQE 🤔
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
48 =========================
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
49
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
50 Compute quality stats for FASTQ files and print those stats as emoji... for some reason.
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
51
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
52 Scores can also be binned:
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
53
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
54 +-------+-------+
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
55 | Bin | Emoji |
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
56 +=======+=======+
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
57 | N | 🚫 |
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
58 +-------+-------+
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
59 | 2-9 | 💀 |
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
60 +-------+-------+
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
61 | 10–19 | 💩 |
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
62 +-------+-------+
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
63 | 20–24 | ⚠️ |
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
64 +-------+-------+
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
65 | 25–29 | 😄 |
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
66 +-------+-------+
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
67 | 30–34 | 😆 |
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
68 +-------+-------+
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
69 | 35–39 | 😎 |
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
70 +-------+-------+
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
71 | ≥ 40 | 😍 |
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
72 +-------+-------+
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
73
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
74
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
75 ]]></help>
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
76 <citations>
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
77 </citations>
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
parents:
diff changeset
78 </tool>