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comparison fastqe.xml @ 3:819b8c1657d5 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
author iuc
date Fri, 19 Mar 2021 21:37:48 +0000
parents a252d8415583
children ecb38e2798cd
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2:a252d8415583 3:819b8c1657d5
1 <tool id="fastqe" name="FASTQE" version="0.2.6+galaxy0"> 1 <tool id="fastqe" name="FASTQE" version="0.2.6+galaxy1">
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 <requirement type="package" version="4.7">sed</requirement>
6 </requirements> 6 </requirements>
7 <command detect_errors="exit_code"> 7 <command detect_errors="exit_code">
8 <![CDATA[ 8 <![CDATA[
9
10 #import re 9 #import re
11 10
12 #set $filenames = [re.sub('[^\w\-\s.]', '_', $i.element_identifier) for $i in $input] 11 mkdir inputs &&
13 #for $i, $filename in zip($input, $filenames): 12 #for $i in $input
14 ln -s '$i' '$filename' && 13 #set identifier = re.sub('[^\w\-\s.]', '_', $i.element_identifier)
14 #if $i.ext.endswith(".gz") and not $identifier.endswith(".gz")
15 #set identifier+=".gz"
16 #end if
17 ln -s $i inputs/$identifier &&
15 #end for 18 #end for
16 19
17 echo "<html><head><title>FASTQE Report 🤔</title></head><body><h1>FASTQE Report 🤔</h1>" > '$output' && 20 echo "<html><head><title>FASTQE Report 🤔</title></head><body><h1>FASTQE Report 🤔</h1>" > '$output' &&
18 21
19 fastqe 22 fastqe
20 --mean
21 $bin 23 $bin
22 --min 24 ${" ".join(str($tpe).split(","))}
23 --long $long 25 --long $long
24 --max 26 ./inputs/*
25 #for $filename in $filenames: 27 | sed 's/$/<br>/;s/^\.\/inputs\/\([^\t]*\)\t\([^\t]*\)\t/<h2>\1: \2<\/h2>\n/;' >> '$output' &&
26 '$filename'
27 #end for
28 | sed 's/$/<br>/;s/^\([^\t]*\)\t\([^\t]*\)\t/<h2>\1: \2<\/h2>\n/' >> '$output' &&
29 28
30 echo "</body></html>" >> '$output' 29 echo "</body></html>" >> '$output'
31 ]]></command> 30 ]]></command>
32 <inputs> 31 <inputs>
33 <param label="FastQ data" name="input" type="data" format="fastq" multiple="true"/> 32 <param label="FastQ data" name="input" type="data" format="fastq,fastq.gz" multiple="true"/>
34 <param label="Bin scores" name="bin" type="boolean" truevalue="--bin" falsevalue="" /> 33 <param label="Bin scores" name="bin" type="boolean" truevalue="--bin" falsevalue="" />
34 <param label="Score types to show" name="tpe" type="select" multiple="true">
35 <option value="--min" selected="true">Minimum</option>
36 <option value="--mean" selected="true">Minimum</option>
37 <option value="--max" selected="true">Minimum</option>
38 </param>
35 <param label="Maximum read length" name="long" type="integer" help="Enable long reads up to this many bp long." min="1" value="500"/> 39 <param label="Maximum read length" name="long" type="integer" help="Enable long reads up to this many bp long." min="1" value="500"/>
36 </inputs> 40 </inputs>
37 <outputs> 41 <outputs>
38 <data format="html" name="output"/> 42 <data format="html" name="output"/>
39 </outputs> 43 </outputs>
40 <tests> 44 <tests>
41 <test> 45 <test>
42 <param name="input" value="test.fq,test2.fq" /> 46 <param name="input" value="test.fq,test2.fq" />
43 <output name="output" file="out.html" /> 47 <output name="output" file="out.html" />
48 </test>
49 <test>
50 <param name="input" value="test.fq.gz,test2.fq.gz" />
51 <output name="output" file="out.html" lines_diff="12"/>
44 </test> 52 </test>
45 </tests> 53 </tests>
46 <help><![CDATA[ 54 <help><![CDATA[
47 FASTQ + Emoji = FASTQE 🤔 55 FASTQ + Emoji = FASTQE 🤔
48 ========================= 56 =========================