Mercurial > repos > iuc > fastqe

annotate fastqe.xml @ 3:819b8c1657d5 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
author iuc
date Fri, 19 Mar 2021 21:37:48 +0000
parents a252d8415583
children ecb38e2798cd
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rev   line source
3
819b8c1657d5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
iuc
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1 <tool id="fastqe" name="FASTQE" version="0.2.6+galaxy1">
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
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4 <requirement type="package" version="0.2.6">fastqe</requirement>
2
a252d8415583 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 7f1ac61222e3b10cd9a82c7b35ea53985c06ba9c"
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5 <requirement type="package" version="4.7">sed</requirement>
0
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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6 </requirements>
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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7 <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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8 <![CDATA[
2
a252d8415583 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 7f1ac61222e3b10cd9a82c7b35ea53985c06ba9c"
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9 #import re
a252d8415583 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 7f1ac61222e3b10cd9a82c7b35ea53985c06ba9c"
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10
3
819b8c1657d5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
iuc
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11 mkdir inputs &&
819b8c1657d5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
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12 #for $i in $input
819b8c1657d5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
iuc
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13 #set identifier = re.sub('[^\w\-\s.]', '_', $i.element_identifier)
819b8c1657d5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
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14 #if $i.ext.endswith(".gz") and not $identifier.endswith(".gz")
819b8c1657d5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
iuc
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15 #set identifier+=".gz"
819b8c1657d5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
iuc
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16 #end if
819b8c1657d5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
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17 ln -s $i inputs/$identifier &&
0
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18 #end for
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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19
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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20 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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22 fastqe
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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23 $bin
3
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24 ${" ".join(str($tpe).split(","))}
1
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25 --long $long
3
819b8c1657d5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
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26 ./inputs/*
819b8c1657d5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
iuc
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27 | sed 's/$/<br>/;s/^\.\/inputs\/\([^\t]*\)\t\([^\t]*\)\t/<h2>\1: \2<\/h2>\n/;' >> '$output' &&
0
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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28
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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29 echo "</body></html>" >> '$output'
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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30 ]]></command>
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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31 <inputs>
3
819b8c1657d5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
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32 <param label="FastQ data" name="input" type="data" format="fastq,fastq.gz" multiple="true"/>
0
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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33 <param label="Bin scores" name="bin" type="boolean" truevalue="--bin" falsevalue="" />
3
819b8c1657d5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
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34 <param label="Score types to show" name="tpe" type="select" multiple="true">
819b8c1657d5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
iuc
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35 <option value="--min" selected="true">Minimum</option>
819b8c1657d5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
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36 <option value="--mean" selected="true">Minimum</option>
819b8c1657d5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
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37 <option value="--max" selected="true">Minimum</option>
819b8c1657d5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
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38 </param>
1
8d3aff8ba8ad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit acc3e75aff3a12ee82d03fbfe676ec81d5451c6e"
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39 <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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40 </inputs>
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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41 <outputs>
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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42 <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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43 </outputs>
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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44 <tests>
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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45 <test>
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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46 <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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47 <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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48 </test>
3
819b8c1657d5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
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49 <test>
819b8c1657d5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
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50 <param name="input" value="test.fq.gz,test2.fq.gz" />
819b8c1657d5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
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51 <output name="output" file="out.html" lines_diff="12"/>
819b8c1657d5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
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52 </test>
0
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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53 </tests>
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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54 <help><![CDATA[
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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55 FASTQ + Emoji = FASTQE 🤔
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
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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58 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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59
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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60 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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61
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 | Bin | Emoji |
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 | N | 🚫 |
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 | 2-9 | 💀 |
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 | 10–19 | 💩 |
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 | 20–24 | ⚠️ |
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 | 25–29 | 😄 |
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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74 +-------+-------+
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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75 | 30–34 | 😆 |
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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76 +-------+-------+
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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77 | 35–39 | 😎 |
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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78 +-------+-------+
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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79 | ≥ 40 | 😍 |
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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80 +-------+-------+
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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81
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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82
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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83 ]]></help>
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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84 <citations>
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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85 </citations>
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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86 </tool>