Mercurial > repos > iuc > fastqe

annotate fastqe.xml @ 1:8d3aff8ba8ad draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit acc3e75aff3a12ee82d03fbfe676ec81d5451c6e"
author iuc
date Mon, 20 Jul 2020 08:04:02 -0400
parents ece21607a21d
children a252d8415583
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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8d3aff8ba8ad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit acc3e75aff3a12ee82d03fbfe676ec81d5451c6e"
iuc
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1 <tool id="fastqe" name="FASTQE" version="0.2.6">
0
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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2 <description>visualize fastq files with emoji's 🧬😎</description>
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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3 <requirements>
1
8d3aff8ba8ad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit acc3e75aff3a12ee82d03fbfe676ec81d5451c6e"
iuc
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4 <requirement type="package" version="0.2.6">fastqe</requirement>
0
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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5 </requirements>
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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6 <command detect_errors="exit_code">
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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7 <![CDATA[
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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8
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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9 #for i in $input:
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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10 ln -s '$i' '$i.element_identifier' &&
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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11 #end for
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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12
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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13 echo "<html><head><title>FASTQE Report 🤔</title></head><body><h1>FASTQE Report 🤔</h1>" > '$output' &&
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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15 fastqe
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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16 --mean
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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17 $bin
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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18 --min
1
8d3aff8ba8ad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit acc3e75aff3a12ee82d03fbfe676ec81d5451c6e"
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19 --long $long
0
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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20 --max
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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21 #for i in $input:
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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22 '$i.element_identifier'
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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23 #end for
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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24 | sed 's/$/<br>/;s/^\([^\t]*\)\t\([^\t]*\)\t/<h2>\1: \2<\/h2>\n/' >> '$output' &&
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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26 echo "</body></html>" >> '$output'
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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27 ]]></command>
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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28 <inputs>
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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29 <param label="FastQ data" name="input" type="data" format="fastq" multiple="true"/>
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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30 <param label="Bin scores" name="bin" type="boolean" truevalue="--bin" falsevalue="" />
1
8d3aff8ba8ad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit acc3e75aff3a12ee82d03fbfe676ec81d5451c6e"
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31 <param label="Maximum read length" name="long" type="integer" help="Enable long reads up to this many bp long." min="1" value="500"/>
0
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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32 </inputs>
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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33 <outputs>
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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34 <data format="html" name="output"/>
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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35 </outputs>
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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36 <tests>
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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37 <test>
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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38 <param name="input" value="test.fq,test2.fq" />
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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39 <output name="output" file="out.html" />
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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40 </test>
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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41 </tests>
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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42 <help><![CDATA[
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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43 FASTQ + Emoji = FASTQE 🤔
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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44 =========================
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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45
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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46 Compute quality stats for FASTQ files and print those stats as emoji... for some reason.
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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47
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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48 Scores can also be binned:
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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49
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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50 +-------+-------+
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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51 | Bin | Emoji |
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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52 +=======+=======+
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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53 | N | 🚫 |
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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54 +-------+-------+
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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55 | N | 🚫 |
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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56 +-------+-------+
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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57 | 2-9 | 💀 |
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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58 +-------+-------+
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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59 | 10–19 | 💩 |
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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60 +-------+-------+
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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61 | 20–24 | ⚠️ |
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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62 +-------+-------+
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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63 | 25–29 | 😄 |
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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64 +-------+-------+
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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65 | 30–34 | 😆 |
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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66 +-------+-------+
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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67 | 35–39 | 😎 |
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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68 +-------+-------+
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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69 | ≥ 40 | 😍 |
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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70 +-------+-------+
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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71
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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72
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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73 ]]></help>
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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74 <citations>
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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75 </citations>
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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76 </tool>