Mercurial > repos > iuc > fastqe

annotate fastqe.xml @ 2:cbedff6218a3 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 4edf8f17bc1a8aaf25622afc9c0c048ff7fa2f0f"
author iuc
date Fri, 24 Jul 2020 19:13:07 +0000
parents 01902d7aa584
children 82a8161b6a19
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
cbedff6218a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 4edf8f17bc1a8aaf25622afc9c0c048ff7fa2f0f"
iuc
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diff changeset
1 <tool id="fastqe" name="FASTQE" version="0.2.6+galaxy0">
0
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"
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3 <requirements>
1
01902d7aa584 "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>
2
cbedff6218a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 4edf8f17bc1a8aaf25622afc9c0c048ff7fa2f0f"
iuc
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5 <requirement type="package" version="4.7">sed</requirement>
0
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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6 </requirements>
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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7 <command detect_errors="exit_code">
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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8 <![CDATA[
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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9
2
cbedff6218a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 4edf8f17bc1a8aaf25622afc9c0c048ff7fa2f0f"
iuc
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10 #import re
cbedff6218a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 4edf8f17bc1a8aaf25622afc9c0c048ff7fa2f0f"
iuc
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11
cbedff6218a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 4edf8f17bc1a8aaf25622afc9c0c048ff7fa2f0f"
iuc
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12 #set $filenames = [re.sub('[^\w\-\s.]', '_', $i.element_identifier) for $i in $input]
cbedff6218a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 4edf8f17bc1a8aaf25622afc9c0c048ff7fa2f0f"
iuc
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13 #for $i, $filename in zip($input, $filenames):
cbedff6218a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 4edf8f17bc1a8aaf25622afc9c0c048ff7fa2f0f"
iuc
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14 ln -s '$i' '$filename' &&
0
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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15 #end for
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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16
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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17 echo "<html><head><title>FASTQE Report 🤔</title></head><body><h1>FASTQE Report 🤔</h1>" > '$output' &&
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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18
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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19 fastqe
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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20 --mean
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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21 $bin
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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22 --min
1
01902d7aa584 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit acc3e75aff3a12ee82d03fbfe676ec81d5451c6e"
iuc
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23 --long $long
0
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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24 --max
2
cbedff6218a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 4edf8f17bc1a8aaf25622afc9c0c048ff7fa2f0f"
iuc
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25 #for $filename in $filenames:
cbedff6218a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 4edf8f17bc1a8aaf25622afc9c0c048ff7fa2f0f"
iuc
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26 '$filename'
0
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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27 #end for
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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28 | sed 's/$/<br>/;s/^\([^\t]*\)\t\([^\t]*\)\t/<h2>\1: \2<\/h2>\n/' >> '$output' &&
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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29
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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30 echo "</body></html>" >> '$output'
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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31 ]]></command>
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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32 <inputs>
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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33 <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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34 <param label="Bin scores" name="bin" type="boolean" truevalue="--bin" falsevalue="" />
1
01902d7aa584 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit acc3e75aff3a12ee82d03fbfe676ec81d5451c6e"
iuc
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35 <param label="Maximum read length" name="long" type="integer" help="Enable long reads up to this many bp long." min="1" value="500"/>
0
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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36 </inputs>
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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37 <outputs>
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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38 <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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39 </outputs>
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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40 <tests>
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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41 <test>
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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42 <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"
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43 <output name="output" file="out.html" />
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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44 </test>
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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45 </tests>
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
iuc
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46 <help><![CDATA[
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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47 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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48 =========================
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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49
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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50 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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51
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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52 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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53
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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54 +-------+-------+
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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55 | Bin | Emoji |
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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56 +=======+=======+
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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57 | N | 🚫 |
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 | 2-9 | 💀 |
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 | 10–19 | 💩 |
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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62 +-------+-------+
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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63 | 20–24 | ⚠️ |
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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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 | 25–29 | 😄 |
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 | 30–34 | 😆 |
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 | 35–39 | 😎 |
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 | ≥ 40 | 😍 |
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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72 +-------+-------+
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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73
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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74
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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75 ]]></help>
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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76 <citations>
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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77 </citations>
688b66fcf6fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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78 </tool>