Mercurial > repos > iuc > tracy_basecall
comparison tracy_basecall.xml @ 0:d24b41831175 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
| author | iuc |
|---|---|
| date | Tue, 12 Oct 2021 14:18:49 +0000 |
| parents | |
| children | 5c4c8c4104b2 |
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| -1:000000000000 | 0:d24b41831175 |
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| 1 <tool id="tracy_basecall" name="tracy Basecall" version="@TOOL_VERSION@+galaxy0" profile="20.09"> | |
| 2 <description>from Sanger chromatogram tracefile</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <expand macro="version_command" /> | |
| 8 <command detect_errors="exit_code"><![CDATA[ | |
| 9 tracy basecall --pratio $pratio --format $format --output '$output' '$tracefile' | |
| 10 ]]></command> | |
| 11 <inputs> | |
| 12 <param name="tracefile" type="data" format="ab1,scf" label="Chromatogram tracefile" /> | |
| 13 <param argument="--pratio" type="float" label="Peak ratio to call a base" value="0.33" min="0" /> | |
| 14 <param argument="--format" type="select" label="Output format"> | |
| 15 <option value="fasta" selected="true">FASTA</option> | |
| 16 <option value="fastq">FASTQ</option> | |
| 17 <option value="tsv">TSV (tabular)</option> | |
| 18 <option value="json">JSON</option> | |
| 19 </param> | |
| 20 </inputs> | |
| 21 <outputs> | |
| 22 <data name="output" format="fasta" label="tracy basecall on ${on_string}"> | |
| 23 <change_format> | |
| 24 <when input="format" value="fasta" format="fasta"/> | |
| 25 <when input="format" value="fastq" format="fastq"/> | |
| 26 <when input="format" value="tsv" format="tabular"/> | |
| 27 <when input="format" value="json" format="json" /> | |
| 28 </change_format> | |
| 29 </data> | |
| 30 </outputs> | |
| 31 <tests> | |
| 32 <test> | |
| 33 <param name="tracefile" value="input1.ab1" ftype="ab1" /> | |
| 34 <output name="output" file="output1.fasta" ftype="fasta" /> | |
| 35 </test> | |
| 36 <test> | |
| 37 <param name="tracefile" value="input1.ab1" ftype="ab1" /> | |
| 38 <param name="format" value="json" /> | |
| 39 <output name="output" file="output1.json" ftype="json" /> | |
| 40 </test> | |
| 41 <test> | |
| 42 <param name="tracefile" value="input1.ab1" ftype="ab1" /> | |
| 43 <param name="pratio" value="0.2" /> | |
| 44 <output name="output" file="output2.fasta" ftype="fasta" /> | |
| 45 </test> | |
| 46 <test> | |
| 47 <param name="tracefile" value="input2.scf" ftype="scf" /> | |
| 48 <param name="format" value="fasta" /> | |
| 49 <output name="output" file="output3.fasta" ftype="fasta" /> | |
| 50 </test> | |
| 51 </tests> | |
| 52 <help><![CDATA[ | |
| 53 **What it does** | |
| 54 | |
| 55 Basecall a chromatogram trace file (using tracy_) and output the primary sequence (highest peak) in FASTQ or FASTA format. If FASTQ | |
| 56 format is used, the quality scores are Sanger quality scores. | |
| 57 | |
| 58 @pratio@ | |
| 59 | |
| 60 Read more here_ | |
| 61 | |
| 62 .. _tracy: https://github.com/gear-genomics/tracy | |
| 63 .. _here: https://www.gear-genomics.com/docs/tracy/cli/#basecalling-a-chromatogram-trace-file | |
| 64 | |
| 65 ]]></help> | |
| 66 <expand macro="citations" /> | |
| 67 </tool> |