Mercurial > repos > iuc > tracy_basecall

annotate tracy_basecall.xml @ 0:f2e0d83186c7 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
author iuc
date Tue, 12 Oct 2021 14:21:34 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
1 <tool id="tracy_basecall" name="tracy Basecall" version="@TOOL_VERSION@+galaxy0" profile="20.09">
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
2 <description>from Sanger chromatogram tracefile</description>
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
3 <macros>
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
4 <import>macros.xml</import>
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
5 </macros>
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
6 <expand macro="requirements" />
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
7 <expand macro="version_command" />
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
8 <command detect_errors="exit_code"><![CDATA[
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
9 tracy basecall --pratio $pratio --format $format --output '$output' '$tracefile'
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
10 ]]></command>
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
11 <inputs>
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
12 <param name="tracefile" type="data" format="ab1,scf" label="Chromatogram tracefile" />
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
13 <param argument="--pratio" type="float" label="Peak ratio to call a base" value="0.33" min="0" />
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
14 <param argument="--format" type="select" label="Output format">
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
15 <option value="fasta" selected="true">FASTA</option>
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
16 <option value="fastq">FASTQ</option>
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
17 <option value="tsv">TSV (tabular)</option>
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
18 <option value="json">JSON</option>
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
19 </param>
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
20 </inputs>
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
21 <outputs>
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
22 <data name="output" format="fasta" label="tracy basecall on ${on_string}">
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
23 <change_format>
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
24 <when input="format" value="fasta" format="fasta"/>
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
25 <when input="format" value="fastq" format="fastq"/>
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
26 <when input="format" value="tsv" format="tabular"/>
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
27 <when input="format" value="json" format="json" />
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
28 </change_format>
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
29 </data>
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
30 </outputs>
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
31 <tests>
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
32 <test>
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
33 <param name="tracefile" value="input1.ab1" ftype="ab1" />
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
34 <output name="output" file="output1.fasta" ftype="fasta" />
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
35 </test>
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
36 <test>
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
37 <param name="tracefile" value="input1.ab1" ftype="ab1" />
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
38 <param name="format" value="json" />
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
39 <output name="output" file="output1.json" ftype="json" />
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
40 </test>
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
41 <test>
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
42 <param name="tracefile" value="input1.ab1" ftype="ab1" />
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
43 <param name="pratio" value="0.2" />
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
44 <output name="output" file="output2.fasta" ftype="fasta" />
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
45 </test>
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
46 <test>
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
47 <param name="tracefile" value="input2.scf" ftype="scf" />
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
48 <param name="format" value="fasta" />
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
49 <output name="output" file="output3.fasta" ftype="fasta" />
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
50 </test>
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
51 </tests>
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
52 <help><![CDATA[
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
53 **What it does**
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
54
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
55 Basecall a chromatogram trace file (using tracy_) and output the primary sequence (highest peak) in FASTQ or FASTA format. If FASTQ
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
56 format is used, the quality scores are Sanger quality scores.
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
57
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
58 @pratio@
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
59
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
60 Read more here_
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
61
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
62 .. _tracy: https://github.com/gear-genomics/tracy
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
63 .. _here: https://www.gear-genomics.com/docs/tracy/cli/#basecalling-a-chromatogram-trace-file
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
64
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
65 ]]></help>
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
66 <expand macro="citations" />
f2e0d83186c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
parents:
diff changeset
67 </tool>