Mercurial > repos > iuc > fastqe
diff fastqe.xml @ 0:ece21607a21d draft
"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 |
| parents | |
| children | 8d3aff8ba8ad |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fastqe.xml Mon Jul 13 15:14:11 2020 -0400 @@ -0,0 +1,74 @@ +<tool id="fastqe" name="FASTQE" version="0.1.1"> + <description>visualize fastq files with emoji's 🧬😎</description> + <requirements> + <requirement type="package" version="0.1.1">fastqe</requirement> + </requirements> + <command detect_errors="exit_code"> + <![CDATA[ + + #for i in $input: + ln -s '$i' '$i.element_identifier' && + #end for + + echo "<html><head><title>FASTQE Report 🤔</title></head><body><h1>FASTQE Report 🤔</h1>" > '$output' && + + fastqe + --mean + $bin + --min + --max + #for i in $input: + '$i.element_identifier' + #end for + | sed 's/$/<br>/;s/^\([^\t]*\)\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" multiple="true"/> + <param label="Bin scores" name="bin" type="boolean" truevalue="--bin" falsevalue="" /> + </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> + </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 | 🚫 | ++-------+-------+ +| N | 🚫 | ++-------+-------+ +| 2-9 | 💀 | ++-------+-------+ +| 10–19 | 💩 | ++-------+-------+ +| 20–24 | ⚠️ | ++-------+-------+ +| 25–29 | 😄 | ++-------+-------+ +| 30–34 | 😆 | ++-------+-------+ +| 35–39 | 😎 | ++-------+-------+ +| ≥ 40 | 😍 | ++-------+-------+ + + +]]></help> + <citations> + </citations> +</tool>