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annotate fastqe.xml @ 0:688b66fcf6fe 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 19:13:47 +0000
parents
children 01902d7aa584
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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diff changeset
1 <tool id="fastqe" name="FASTQE" version="0.1.1">
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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2 <description>visualize fastq files with emoji's 🧬😎</description>
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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3 <requirements>
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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4 <requirement type="package" version="0.1.1">fastqe</requirement>
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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5 </requirements>
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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6 <command detect_errors="exit_code">
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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7 <![CDATA[
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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8
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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9 #for i in $input:
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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10 ln -s '$i' '$i.element_identifier' &&
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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11 #end for
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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12
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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13 echo "<html><head><title>FASTQE Report 🤔</title></head><body><h1>FASTQE Report 🤔</h1>" > '$output' &&
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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14
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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15 fastqe
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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16 --mean
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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17 $bin
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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18 --min
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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19 --max
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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20 #for i in $input:
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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21 '$i.element_identifier'
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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22 #end for
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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23 | sed 's/$/<br>/;s/^\([^\t]*\)\t\([^\t]*\)\t/<h2>\1: \2<\/h2>\n/' >> '$output' &&
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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24
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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25 echo "</body></html>" >> '$output'
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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26 ]]></command>
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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27 <inputs>
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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28 <param label="FastQ data" name="input" type="data" format="fastq" multiple="true"/>
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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29 <param label="Bin scores" name="bin" type="boolean" truevalue="--bin" falsevalue="" />
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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30 </inputs>
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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31 <outputs>
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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32 <data format="html" name="output"/>
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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33 </outputs>
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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34 <tests>
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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35 <test>
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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36 <param name="input" value="test.fq,test2.fq" />
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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37 <output name="output" file="out.html" />
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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38 </test>
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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39 </tests>
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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40 <help><![CDATA[
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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41 FASTQ + Emoji = FASTQE 🤔
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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42 =========================
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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43
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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diff changeset
44 Compute quality stats for FASTQ files and print those stats as emoji... for some reason.
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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45
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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46 Scores can also be binned:
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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47
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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48 +-------+-------+
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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49 | Bin | Emoji |
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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50 +=======+=======+
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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51 | N | 🚫 |
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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52 +-------+-------+
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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53 | N | 🚫 |
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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54 +-------+-------+
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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55 | 2-9 | 💀 |
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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56 +-------+-------+
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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57 | 10–19 | 💩 |
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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58 +-------+-------+
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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59 | 20–24 | ⚠️ |
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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60 +-------+-------+
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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61 | 25–29 | 😄 |
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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62 +-------+-------+
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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63 | 30–34 | 😆 |
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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64 +-------+-------+
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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65 | 35–39 | 😎 |
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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66 +-------+-------+
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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67 | ≥ 40 | 😍 |
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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68 +-------+-------+
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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69
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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70
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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71 ]]></help>
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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72 <citations>
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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73 </citations>
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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74 </tool>