Mercurial > repos > rplanel > sequence_splitter
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"planemo upload for repository https://github.com/rplanel/galaxy-tools/tree/master/tools/sequence-splitter commit 98f957247a46eabf7e561bd94328b6a03a4d73b9"
author | rplanel |
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date | Sat, 21 Nov 2020 08:50:21 +0000 |
parents | 7b509a1801e4 |
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<tool id="sequence-splitter" name="Sequence Splitter" version="@WRAPPER_VERSION@"> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <edam_operations> <edam_operation>operation_2409</edam_operation> <edam_operation>operation_3359</edam_operation> </edam_operations> <edam_topics> <edam_topic>topic_3307</edam_topic> <edam_topic>topic_0080</edam_topic> </edam_topics> <command detect_errors="exit_code"> <![CDATA[ ln -s '$sequences' ./sequences.${sequences.ext} && python '$__tool_directory__/sequence-splitter.py' -s ./sequences.$sequences.ext #if $sequences.is_of_type("fasta") -f fasta #else -f fastq #end if #if $split_mode.selector == 'chunk_size' -c $split_mode.chunk_size #else -n $split_mode.nb_chunk #end if -o 'outputs' ]]> </command> <inputs> <param type="data" name="sequences" format="fasta,fastq" /> <conditional name="split_mode"> <param name="selector" type="select" label="Split by:"> <option value="chunk_size">Number of sequence(s) by chunk</option> <option value="nb_chunk">Number of chunk(s)</option> </param> <when value="chunk_size"> <param name="chunk_size" label="Chunk size" type="integer" min="1" value="100" help="How many sequences by chunk ?" /> </when> <when value="nb_chunk"> <param name="nb_chunk" label="Number of chunks" type="integer" min="1" value="10" help="How many chunks ?" /> </when> </conditional> </inputs> <outputs> <collection name="split_output" type="list" label="splitted sequences"> <discover_datasets pattern="(?P<designation>\w+-chunk-\d+)\.(?P<ext>.+)" directory="outputs" /> </collection> <data format="txt" name="logfile" from_work_dir="sequence-splitter.log" label="${tool.name} logfile on ${on_string}" /> </outputs> <tests> <!-- CHUNK SIZE --> <test> <param name="sequences" value="sample.fastq" /> <conditional name="split_mode"> <param name="selector" value="chunk_size" /> <param name="chunk_size" value="2" /> </conditional> <output_collection name="split_output" type="list" count="5"> <element name="sequences-chunk-1" file="sample-chunk-1.fastq" ftype="fastqsanger" compare="diff" /> <element name="sequences-chunk-2" file="sample-chunk-2.fastq" ftype="fastqsanger" compare="diff" /> <element name="sequences-chunk-3" file="sample-chunk-3.fastq" ftype="fastqsanger" compare="diff" /> <element name="sequences-chunk-4" file="sample-chunk-4.fastq" ftype="fastqsanger" compare="diff" /> <element name="sequences-chunk-5" file="sample-chunk-5.fastq" ftype="fastqsanger" compare="diff" /> </output_collection> </test> <test> <param name="sequences" value="sample.fasta" /> <conditional name="split_mode"> <param name="selector" value="chunk_size" /> <param name="chunk_size" value="5" /> </conditional> <output_collection name="split_output" type="list" count="1"> <element name="sequences-chunk-1" file="sample-5-chunk-1.fasta" ftype="fasta" compare="diff" /> </output_collection> </test> <!-- NUMBER CHUNK --> <test> <param name="sequences" value="sample.fastq" /> <conditional name="split_mode"> <param name="selector" value="nb_chunk" /> <param name="nb_chunk" value="2" /> </conditional> <output_collection name="split_output" type="list" count="2"> <element name="sequences-chunk-1" file="sample-3-chunk-1.fastq" ftype="fastqsanger" compare="diff" /> <element name="sequences-chunk-2" file="sample-3-chunk-2.fastq" ftype="fastqsanger" compare="diff" /> </output_collection> </test> <test> <param name="sequences" value="sample.fastq" /> <conditional name="split_mode"> <param name="selector" value="nb_chunk" /> <param name="nb_chunk" value="4" /> </conditional> <output_collection name="split_output" type="list" count="4"> <element name="sequences-chunk-1" file="sample-4-chunk-1.fastq" ftype="fastqsanger" compare="diff" /> <element name="sequences-chunk-2" file="sample-4-chunk-2.fastq" ftype="fastqsanger" compare="diff" /> <element name="sequences-chunk-3" file="sample-4-chunk-3.fastq" ftype="fastqsanger" compare="diff" /> <element name="sequences-chunk-4" file="sample-4-chunk-4.fastq" ftype="fastqsanger" compare="diff" /> </output_collection> </test> <test> <param name="sequences" value="sample.fasta" /> <conditional name="split_mode"> <param name="selector" value="nb_chunk" /> <param name="nb_chunk" value="10" /> </conditional> <output_collection name="split_output" type="list" count="4"> <element name="sequences-chunk-1" file="sample-2-chunk-1.fasta" ftype="fasta" compare="diff" /> <element name="sequences-chunk-2" file="sample-2-chunk-2.fasta" ftype="fasta" compare="diff" /> <element name="sequences-chunk-3" file="sample-2-chunk-3.fasta" ftype="fasta" compare="diff" /> <element name="sequences-chunk-4" file="sample-2-chunk-4.fasta" ftype="fasta" compare="diff" /> </output_collection> </test> </tests> <help> <![CDATA[ Usage: sequence-splitter.py [-h] [-s SEQUENCES] [-f FORMAT] (-c CHUNK_SIZE | -n NB_CHUNK) [-o OUTPUT] Split fasta/fastq files optional arguments: -h, --help show this help message and exit -s SEQUENCES, --sequences SEQUENCES File that contains the sequences -f FORMAT, --format FORMAT File format (fastq, fasta) -c CHUNK_SIZE, --chunk-size CHUNK_SIZE The number of sequences by chunks -n NB_CHUNK, --nb-chunk NB_CHUNK Number of chunks -o OUTPUT, --output OUTPUT The output directory where the chunks will be saved ]]> </help> <expand macro="citations" /> </tool>