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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta commit 49709e680f90372edd2b8a2715d95e5949641afa
author bgruening
date Tue, 14 Jan 2025 21:52:36 +0000
parents 733ca84b21ee
children
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7521d865e770 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta commit 49709e680f90372edd2b8a2715d95e5949641afa
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1 <tool id="rbc_splitfasta" name="Split Fasta" version="0.5.0" profile="23.0">
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2 <description>files into a collection</description>
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3 <requirements>
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4 <requirement type="package" version="1.76">biopython</requirement>
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5 </requirements>
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6 <command detect_errors="aggressive">
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7 <![CDATA[
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8 #if $splitmode.splitmode_select == "each":
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9 python $__tool_directory__/split_fasta.py --records '$inputFile.metadata.sequences' --limit "\${GALAXY_FILE_LIMIT:-0}" '$inputFile'
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10 #else if $splitmode.splitmode_select == "chunks":
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11 python $__tool_directory__/split_fasta.py --records '$inputFile.metadata.sequences' --limit "\${GALAXY_FILE_LIMIT:-0}" --num-chunks '$splitmode.num_chunks' '$inputFile'
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12 #end if
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13 ]]></command>
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14 <inputs>
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15 <param name="inputFile" type="data" format="fasta" label="Fasta file to split"/>
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16 <conditional name="splitmode">
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17 <param name="splitmode_select" type="select" label="Split mode">
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18 <option value="each">Each sequence in its own dataset</option>
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19 <option value="chunks">Split into a number of chunks</option>
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20 </param>
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21 <when value="chunks">
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22 <param name="num_chunks" type="integer" value="10" label="Number of chunks to split into" />
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23 </when>
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24 <when value="each"/>
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25 </conditional>
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26 </inputs>
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27 <outputs>
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28 <collection name="splitted_fasta" type="list" label="${tool.name} on ${on_string}">
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29 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="splits" ext="fasta" visible="false"/>
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30 </collection>
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31 </outputs>
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32 <tests>
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33 <test>
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34 <param name="inputFile" value="sample1.fasta" />
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35 <param name="splitmode|splitmode_select" value="each" />
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36 <output_collection name="splitted_fasta" count="3">
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37 <element name="ID1" file="ID1.fasta" ftype="fasta" />
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38 <element name="ID2" file="ID2.fasta" ftype="fasta" />
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39 <element name="ID3" file="ID3.fasta" ftype="fasta" />
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40 </output_collection>
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41 </test>
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42 <test>
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43 <param name="inputFile" value="sample2.fasta" />
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44 <param name="splitmode|splitmode_select" value="chunks" />
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45 <param name="num_chunks" value="4" />
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46 <output_collection name="splitted_fasta" count="4">
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47 <element name="part1" file="part1.fasta" ftype="fasta" />
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48 <element name="part2" file="part2.fasta" ftype="fasta" />
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49 <element name="part3" file="part3.fasta" ftype="fasta" />
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50 <element name="part4" file="part4.fasta" ftype="fasta" />
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51 </output_collection>
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52 </test>
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53 </tests>
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54 <help><![CDATA[
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55 Takes an input FASTA file and writes entries (i.e. sequences) to separate datasets, which are organized in a dataset collection.
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56 There are two modes: 1) each sequence is written to its own data set which is named by the ID of the sequence or 2) The file is split into a given number of chunks which are numbered.
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57 ]]></help>
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58 <citations>
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59 <citation type="bibtex">
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60 @ARTICLE{bgruening_galaxytools,
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61 Author = {Björn Grüning, Cameron Smith, Torsten Houwaart, Nicola Soranzo, Eric Rasche},
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62 keywords = {bioinformatics, ngs, galaxy, cheminformatics, rna},
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63 title = {{Galaxy Tools - A collection of bioinformatics and cheminformatics tools for the Galaxy environment}},
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64 url = {https://github.com/bgruening/galaxytools}
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65 }
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66 </citation>
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67 </citations>
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68 </tool>