Mercurial > repos > iuc > fastqe

<tool id="fastqe" name="FASTQE" version="0.3.1+galaxy0">
    <description>visualize fastq files with emoji's 🧬😎</description>
    <requirements>
        <requirement type="package" version="0.3.1">fastqe</requirement>
        <requirement type="package" version="4.7">sed</requirement>
    </requirements>
    <command detect_errors="exit_code">
    <![CDATA[
    #import re

    mkdir inputs &&
    #for $i in $input
        #set identifier = re.sub('[^\w\-\s.]', '_', $i.element_identifier)
        #if $i.ext.endswith(".gz") and not $identifier.endswith(".gz")
            #set identifier+=".gz"
        #end if
        ln -s $i 'inputs/$identifier' &&
    #end for

    echo "<html><head><meta http-equiv=\"content-type\" content=\"text/html; charset=utf-8\"><title>FASTQE Report 🤔</title></head><body><h1>FASTQE Report 🤔</h1>" > '$output' &&

    fastqe
        $bin
        ${" ".join(str($tpe).split(","))}
        --long $long
        ./inputs/*
        | sed 's/$/<br>/;s/^\.\/inputs\/\([^\t]*\)\t\([^\t]*\)\t/<h2>\1: \2<\/h2>\n/;' >> '$output' &&

    echo "</body></html>" >> '$output'
    ]]></command>
    <inputs>
        <param label="FastQ data" name="input" type="data" format="fastq,fastq.gz" multiple="true"/>
        <param label="Bin scores" name="bin" type="boolean" truevalue="--bin" falsevalue="" />
        <param label="Score types to show" name="tpe" type="select" multiple="true">
            <option value="--min" selected="true">Minimum</option>
            <option value="--mean" selected="true">Mean</option>
            <option value="--max" selected="true">Maximum</option>
        </param>
        <param label="Maximum read length" name="long" type="integer" help="Enable long reads up to this many bp long." min="1" value="500"/>
    </inputs>
    <outputs>
        <data format="html" name="output"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="test.fq,test2.fq" />
            <output name="output" file="out.html" />
        </test>
        <test>
            <param name="input" value="test.fq.gz,test2.fq.gz" />
            <output name="output" file="out2.html"/>
        </test>
    </tests>
    <help><![CDATA[
FASTQ + Emoji = FASTQE 🤔
=========================

Compute quality stats for FASTQ files and print those stats as emoji... for some reason.

Scores can also be binned:

+-------+-------+
| Bin   | Emoji |
+=======+=======+
| N     | 🚫    |
+-------+-------+
| 2-9   | 💀    |
+-------+-------+
| 10–19 | 💩    |
+-------+-------+
| 20–24 | ⚠️    |
+-------+-------+
| 25–29 | 😄    |
+-------+-------+
| 30–34 | 😆    |
+-------+-------+
| 35–39 | 😎    |
+-------+-------+
| ≥ 40  | 😍    |
+-------+-------+


]]></help>
    <citations>
        <citation type="bibtex">
            @misc{githubFASTQE,
            author = {A Lonsdale},
            year = {2017},
            title = {FASTQE},
            publisher = {GitHub},
            journal = {GitHub repository},
            url = {https://github.com/fastqe/fastqe}
            }
        </citation>
    </citations>
</tool>
author	iuc
date	Sat, 13 Jan 2024 23:55:53 +0000
parents	89d299153577
children	c1a33f603da2