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diff fastqe.xml @ 0:ece21607a21d draft

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"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>