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annotate fastqe.xml @ 6:d77a9c2a242d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 5646f6da410ca4155299571ddc57d0040a643158
author iuc
date Sat, 13 Jan 2024 23:55:53 +0000
parents 89d299153577
children c1a33f603da2
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
d77a9c2a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 5646f6da410ca4155299571ddc57d0040a643158
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1 <tool id="fastqe" name="FASTQE" version="0.3.1+galaxy0">
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2 <description>visualize fastq files with emoji's 🧬😎</description>
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3 <requirements>
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4 <requirement type="package" version="0.3.1">fastqe</requirement>
2
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5 <requirement type="package" version="4.7">sed</requirement>
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6 </requirements>
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7 <command detect_errors="exit_code">
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8 <![CDATA[
2
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9 #import re
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10
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11 mkdir inputs &&
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12 #for $i in $input
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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")
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15 #set identifier+=".gz"
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16 #end if
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17 ln -s $i 'inputs/$identifier' &&
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18 #end for
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19
5
89d299153577 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit c4004b4ce3c5c26e5e9e3b611af9c3ebb25928ae"
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20 echo "<html><head><meta http-equiv=\"content-type\" content=\"text/html; charset=utf-8\"><title>FASTQE Report 🤔</title></head><body><h1>FASTQE Report 🤔</h1>" > '$output' &&
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22 fastqe
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23 $bin
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24 ${" ".join(str($tpe).split(","))}
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25 --long $long
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26 ./inputs/*
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27 | sed 's/$/<br>/;s/^\.\/inputs\/\([^\t]*\)\t\([^\t]*\)\t/<h2>\1: \2<\/h2>\n/;' >> '$output' &&
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28
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29 echo "</body></html>" >> '$output'
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30 ]]></command>
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31 <inputs>
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32 <param label="FastQ data" name="input" type="data" format="fastq,fastq.gz" multiple="true"/>
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33 <param label="Bin scores" name="bin" type="boolean" truevalue="--bin" falsevalue="" />
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34 <param label="Score types to show" name="tpe" type="select" multiple="true">
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35 <option value="--min" selected="true">Minimum</option>
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36 <option value="--mean" selected="true">Mean</option>
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37 <option value="--max" selected="true">Maximum</option>
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38 </param>
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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"/>
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40 </inputs>
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41 <outputs>
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42 <data format="html" name="output"/>
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43 </outputs>
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44 <tests>
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45 <test>
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46 <param name="input" value="test.fq,test2.fq" />
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47 <output name="output" file="out.html" />
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48 </test>
3
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49 <test>
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50 <param name="input" value="test.fq.gz,test2.fq.gz" />
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d77a9c2a242d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 5646f6da410ca4155299571ddc57d0040a643158
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51 <output name="output" file="out2.html"/>
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52 </test>
0
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53 </tests>
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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 🤔
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56 =========================
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57
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58 Compute quality stats for FASTQ files and print those stats as emoji... for some reason.
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59
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60 Scores can also be binned:
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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 |
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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 | 🚫 |
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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 | 💀 |
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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 | 💩 |
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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 | ⚠️ |
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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 | 😄 |
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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 | 😆 |
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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 +-------+-------+
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81
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82
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83 ]]></help>
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84 <citations>
6
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85 <citation type="bibtex">
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86 @misc{githubFASTQE,
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87 author = {A Lonsdale},
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88 year = {2017},
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89 title = {FASTQE},
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90 publisher = {GitHub},
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91 journal = {GitHub repository},
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92 url = {https://github.com/fastqe/fastqe}
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93 }
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94 </citation>
0
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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95 </citations>
ece21607a21d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 2da1480c5e2f439a6b30a253871a86bb05c39aa0"
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96 </tool>