Mercurial > repos > ecology > ab1_fastq_converter
comparison ab1fastq.xml @ 0:307518fb51af draft default tip
"planemo upload for repository https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq commit dbecaa89a5afa0cc73ae00a716c98ae46fa97b58"
author | ecology |
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date | Wed, 12 Jan 2022 15:12:58 +0000 |
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-1:000000000000 | 0:307518fb51af |
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1 <tool id="ab1_fastq_converter" name="ab1 to FASTQ converter" version="@VERSION@"> | |
2 <description></description> | |
3 <macros> | |
4 <import>ab1fastq_macros.xml</import> | |
5 </macros> | |
6 <requirements> | |
7 <requirement type="package" version="1.28.0">bioconductor-sangerseqr</requirement> | |
8 <requirement type="package" version="@VERSION@">bioconductor-crisprvariants</requirement> | |
9 </requirements> | |
10 <version_command><![CDATA[ | |
11 echo $(R --version | grep version | grep -v GNU)", sangerseqR version" $(R --vanilla --slave -e "library(sangerseqR); cat(sessionInfo()\\$otherPkgs\$sangerseqR\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", CrispRVariants version" $(R --vanilla --slave -e "library(CrispRVariants); cat(sessionInfo()\\$otherPkgs\$CrispRVariants\$Version)" 2> /dev/null | grep -v -i "WARNING: ") | |
12 ]]></version_command> | |
13 <command detect_errors="exit_code"><![CDATA[ | |
14 Rscript | |
15 '$__tool_directory__/ab1_fastq.R' | |
16 '$input' | |
17 '${input.display_name}' | |
18 #if $tr.trim=='true' | |
19 'TRUE' | |
20 '$tr.cutoff' | |
21 '$tr.minseq' | |
22 '$tr.offset' | |
23 #else | |
24 'FALSE' | |
25 '0.05' | |
26 '20' | |
27 '33' | |
28 #end if | |
29 '$output' | |
30 ]]> | |
31 </command> | |
32 <inputs> | |
33 <param name="input" type="data" format="ab1" label="Input ab1 file"/> | |
34 <conditional name="tr"> | |
35 <param name="trim" type="select" label="Do you want trim ends according to quality scores ?"> | |
36 <option value="false" selected="true">No, use full sequences.</option> | |
37 <option value="true">Yes, trim low-quality ends.</option> | |
38 </param> | |
39 <when value="false"> | |
40 </when> | |
41 <when value="true"> | |
42 <param name="cutoff" type="float" value="0.05" min="0" max="1" label="Probability cutoff you want to use to trim"/> | |
43 <param name="minseq" type="integer" value="20" min="0" label="Minimum sequence length to allow the trim"/> | |
44 <param name="offset" type="float" value="33" min="0" label="Phred offset for quality scores"/> | |
45 </when> | |
46 </conditional> | |
47 </inputs> | |
48 <outputs> | |
49 <data name="output" from_work_dir="output.fastq" format="fastq" label="${input.display_name}.fastq"/> | |
50 </outputs> | |
51 <tests> | |
52 <test> | |
53 <param name="input" value="test_file.AB1"/> | |
54 <param name="trim" value="false"/> | |
55 <output name="output" value="out_file.fastq"/> | |
56 </test> | |
57 </tests> | |
58 <help><![CDATA[ | |
59 ============================ | |
60 Convert ab1 files into FASTQ | |
61 ============================ | |
62 | |
63 .ab1, .AB1 or .abi files are common sanger sequencing outputs, this tool permits you to convert it into fastq so it can be used into many galaxy tools. | |
64 | |
65 This tool can also trim ends of your sequence based on the quality statistics. | |
66 ]]></help> | |
67 <citations> | |
68 <citation type="doi">10.1038/nbt.3628</citation> | |
69 <citation type="doi">10.5061/dryad.b331s</citation> | |
70 </citations> | |
71 </tool> |