Mercurial > repos > iuc > pimento_auto
comparison auto.xml @ 0:f41d29b1a43e draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
| author | iuc |
|---|---|
| date | Tue, 05 Aug 2025 09:20:38 +0000 |
| parents | |
| children |
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| -1:000000000000 | 0:f41d29b1a43e |
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| 1 <tool id="pimento_auto" name="PIMENTO Primer cutoff prediction" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="@LICENSE@"> | |
| 2 <description>Infers primers by predicting optimal cutoff points from read conservation patterns</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="creators"/> | |
| 7 <expand macro="requirements"/> | |
| 8 <command detect_errors="aggressive"><![CDATA[ | |
| 9 pimento auto -i '$input' -st '$strand' -o sample | |
| 10 ]]></command> | |
| 11 <inputs> | |
| 12 <param name="input" type="data" label="Input reads" format="fastqsanger.gz"/> | |
| 13 <param name="strand" type="select" label="Strand" format="fastqsanger.gz"> | |
| 14 <option value="F">Forward</option> | |
| 15 <option value="R">Reverse</option> | |
| 16 <option value="FR">Both, forward and reverse</option> | |
| 17 </param> | |
| 18 </inputs> | |
| 19 <outputs> | |
| 20 <data name="output" label="${tool.name} on ${on_string}: Automatically inferred primers" format="fasta" from_work_dir="sample_auto_primers.fasta"/> | |
| 21 </outputs> | |
| 22 <tests> | |
| 23 <test expect_num_outputs="1"> | |
| 24 <param name="input" value="test.fastq.gz"/> | |
| 25 <param name="strand" value="FR"/> | |
| 26 <output name="output"> | |
| 27 <assert_contents> | |
| 28 <has_line line=">F_auto"/> | |
| 29 <has_line line="CCTACGGGDGGCWGCAGT"/> | |
| 30 <has_n_lines n="4"/> | |
| 31 </assert_contents> | |
| 32 </output> | |
| 33 </test> | |
| 34 </tests> | |
| 35 <help><![CDATA[ | |
| 36 Runs the primer cutoff strategy for primer inference. Using patterns of | |
| 37 base-conservation values for input reads, this strategy identifies potential | |
| 38 cutoff points where a primer sequence could end. An optimal choice of cutoff | |
| 39 based on the change in base-conservation before and after a cutoff is then | |
| 40 made. Finally a consensus sequence is generated using this cutoff point and | |
| 41 the input reads, which are saved to an output FASTA file. | |
| 42 ]]></help> | |
| 43 <expand macro="citations"/> | |
| 44 </tool> |