Mercurial > repos > bvalot > fasta_filter_0_1
comparison fasta_filter_accession.xml @ 0:bc23da9d464c draft default tip
planemo upload for repository http://172.20.124.12:3000/bvalot3/PythonScript commit 9676573ee48ce5343600ab45cd3ac1a6adddabe4
| author | bvalot |
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| date | Tue, 14 Jun 2022 08:15:55 +0000 |
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| -1:000000000000 | 0:bc23da9d464c |
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| 1 <tool id="fasta_filter_accession_wrapper" name="Filter accession" version="0.1"> | |
| 2 <description></description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="1.78">biopython</requirement> | |
| 5 </requirements> | |
| 6 <stdio> | |
| 7 <exit_code range="1:" level="fatal" /> | |
| 8 </stdio> | |
| 9 <version_command>$__tool_directory__/fasta_filter_to_accession.py -v</version_command> | |
| 10 <command> | |
| 11 $__tool_directory__/fasta_filter_to_accession.py | |
| 12 -o '$output' | |
| 13 '$fasta' | |
| 14 #for $access in $accessions.split(" ") | |
| 15 '$access' | |
| 16 #end for | |
| 17 </command> | |
| 18 <inputs> | |
| 19 <param name="fasta" type="data" format="fasta" label="Database to filter on fasta" help="FASTA format" /> | |
| 20 <param name="accessions" type="text" value="" optional="false" size="4X50" | |
| 21 label="List of accessions to conserved" | |
| 22 help="Separated each accession by a space" /> | |
| 23 </inputs> | |
| 24 <outputs> | |
| 25 <data name="output" format="fasta" label="${tool.name} on ${on_string}: fasta" /> | |
| 26 </outputs> | |
| 27 <tests> | |
| 28 <test expect_num_outputs="1"> | |
| 29 <param name="fasta" value="input.fasta" /> | |
| 30 <param name="accessions" value="NODE_236_length_305_cov_44.745614" /> | |
| 31 <output name="output" file="filter_acc.fasta" ftype="fasta" /> | |
| 32 </test> | |
| 33 </tests> | |
| 34 <help> | |
| 35 **What it does** | |
| 36 | |
| 37 Filter a fasta file based on accessions. | |
| 38 | |
| 39 **License and citation** | |
| 40 | |
| 41 This Galaxy tool is Copyright © 2018 `B. Valot` and is released under the `GPL3 license`. | |
| 42 | |
| 43 </help> | |
| 44 <citations> | |
| 45 </citations> | |
| 46 </tool> |