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comparison 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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-1:000000000000 0:331fd79a9341
1 <tool id="rename" name="reheader" version="1.0.0" force_history_refresh="True">
2 <description>Rename sequence header in FASTQ file</description>
3 <requirements>
4 <requirement type="package" version="1.74">biopython</requirement>
5 </requirements>
6 <version_command>
7 python ${__tool_directory__}/reheader.py --version
8 </version_command>
9 <command detect_errors="aggressive">
10 python ${__tool_directory__}/reheader.py -n $inputfile.display_name -i $inputfile -o $output -d $log.files_path -l $log
11 </command>
12
13 <inputs>
14 <param format="fastq,fastq.gz,fastq.bz2" name="inputfile" type="data" label="Short read data from your current history"/>
15 </inputs>
16 <outputs>
17 <data name="output" format="fastq" label="${tool.name}.${inputfile.display_name}"/>
18 <data name="log" format="txt" label="${tool.name}.${inputfile.display_name}.log"/>
19 </outputs>
20 <tests>
21 <test>
22 <param name="inputfile" value="F3D0_R1.fastq"/>
23 <output name="outout" file="test_output.txt"/>
24 </test>
25 </tests>
26
27 <help>
28 **what it does**
29
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_
31
32 .. _python : https://www.python.org/downloads/release/python-370/
33 .. _Biopython : https://biopython.org/
34
35 -----
36
37 Forward Read
38 ------------
39 **Input**
40
41 - **sequence header** : @M03033:102:000000000-ATN0P:1:1101:9793:1042
42
43 **Output**
44
45 - **sequence header** : @M03033:102:000000000-ATN0P:1:1101:9793:1042_Sample1/1
46
47 Reverse Read
48 ------------
49
50 **Input**
51
52 - **sequence header** : @M03033:102:000000000-ATN0P:1:1101:9793:1042
53
54 **Output**
55
56 - **sequence header** : @M03033:102:000000000-ATN0P:1:1101:9793:1042_Sample1/2
57
58 -----
59
60 =========
61 Resources
62 =========
63
64 **Wrapper Authors**
65
66 QFAB Bioinformatics (support@qfab.org)
67 </help>
68
69 </tool>