Mercurial > repos > qfabrepo > metadegalaxy_reheader

annotate reheader.xml @ 0:331fd79a9341 draft

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"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
author qfabrepo
date Thu, 03 Sep 2020 01:32:31 +0000
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children 9cb93e3df272
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0
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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1 <tool id="rename" name="reheader" version="1.0.0" force_history_refresh="True">
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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2 <description>Rename sequence header in FASTQ file</description>
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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3 <requirements>
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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4 <requirement type="package" version="1.74">biopython</requirement>
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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5 </requirements>
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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6 <version_command>
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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7 python ${__tool_directory__}/reheader.py --version
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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8 </version_command>
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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9 <command detect_errors="aggressive">
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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10 python ${__tool_directory__}/reheader.py -n $inputfile.display_name -i $inputfile -o $output -d $log.files_path -l $log
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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11 </command>
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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12
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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13 <inputs>
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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14 <param format="fastq,fastq.gz,fastq.bz2" name="inputfile" type="data" label="Short read data from your current history"/>
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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15 </inputs>
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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16 <outputs>
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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17 <data name="output" format="fastq" label="${tool.name}.${inputfile.display_name}"/>
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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18 <data name="log" format="txt" label="${tool.name}.${inputfile.display_name}.log"/>
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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19 </outputs>
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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20 <tests>
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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21 <test>
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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22 <param name="inputfile" value="F3D0_R1.fastq"/>
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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23 <output name="outout" file="test_output.txt"/>
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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24 </test>
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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25 </tests>
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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26
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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27 <help>
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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28 **what it does**
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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29
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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30 Renames sequence header in FASTQ file by appending SAMPLEFILENAME/1 to the end of the sequence header for the forward read or SAMPLEFILENAME_2 to the end of the sequence header for the reverse read using python_ and Biopython_
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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31
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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32 .. _python : https://www.python.org/downloads/release/python-370/
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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33 .. _Biopython : https://biopython.org/
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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34
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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35 -----
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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36
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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37 Forward Read
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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38 ------------
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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39 **Input**
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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40
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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41 - **sequence header** : @M03033:102:000000000-ATN0P:1:1101:9793:1042
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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42
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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43 **Output**
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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44
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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45 - **sequence header** : @M03033:102:000000000-ATN0P:1:1101:9793:1042_Sample1/1
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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46
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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47 Reverse Read
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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48 ------------
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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49
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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50 **Input**
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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51
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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52 - **sequence header** : @M03033:102:000000000-ATN0P:1:1101:9793:1042
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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53
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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54 **Output**
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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55
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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56 - **sequence header** : @M03033:102:000000000-ATN0P:1:1101:9793:1042_Sample1/2
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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57
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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58 -----
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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59
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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60 =========
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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61 Resources
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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62 =========
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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63
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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64 **Wrapper Authors**
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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65
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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66 QFAB Bioinformatics (support@qfab.org)
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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67 </help>
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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68
331fd79a9341 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/reheader commit 6783cd68521863b34f8e77cbb7ba404700c72313-dirty"
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69 </tool>