Mercurial > repos > jdv > krakentools

comparison extract_kraken_reads.xml @ 2:5b17dec256d6 draft

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"planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit 5a46334c82e70f4cd7e65e0269dc7efbe756f0c5-dirty"
author jdv
date Thu, 01 Apr 2021 16:49:28 +0000
parents 92b1c7935d72
children b302dc008a4e
comparison
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1:92b1c7935d72 2:5b17dec256d6
62 <when value="paired_collection"> 62 <when value="paired_collection">
63 <param name="input_1" format="fastq,fastqsanger,fasta" type="data_collection" collection_type="paired" label="Paired Collection" help="FASTQ or FASTA read pair collection" /> 63 <param name="input_1" format="fastq,fastqsanger,fasta" type="data_collection" collection_type="paired" label="Paired Collection" help="FASTQ or FASTA read pair collection" />
64 </when> 64 </when>
65 65
66 </conditional> 66 </conditional>
67 <param argument="results" format="tabular" type="data" label="Results" help="Results (classification) file from Kraken/KrakenUniq/Kraken2" /> 67 <param name="results" argument="-k" format="tabular" type="data" label="Results" help="Results (classification) file from Kraken/KrakenUniq/Kraken2" />
68 <param argument="report" format="tabular" type="data" label="Report" optional="True" help="Report file from Kraken/KrakenUniq/Kraken2" /> 68 <param name="report" argument="--report" format="tabular" type="data" label="Report" optional="True" help="Report file from Kraken/KrakenUniq/Kraken2" />
69 69
70 <param argument="--taxid" type="text" value="" label="Taxonomic ID(s) to match" help="Space-delimited list of taxonomic IDs for which to extract matching reads"> 70 <param name="taxid" argument="--taxid" type="text" value="" label="Taxonomic ID(s) to match" help="Space-delimited list of taxonomic IDs for which to extract matching reads">
71 <validator type="regex" message="Enter a space-separated list of numeric tax IDs">^\d+[\d ]*$</validator> 71 <validator type="regex" message="Enter a space-separated list of numeric tax IDs">^\d+[\d ]*$</validator>
72 </param> 72 </param>
73 <param argument="--max" type="integer" value="100000000" min="1" label="Maximum reads to save" help="Maximum number of reads to save for each ID" /> 73 <param name="max" argument="--max" type="integer" value="100000000" min="1" label="Maximum reads to save" help="Maximum number of reads to save for each ID" />
74 <param argument="--exclude" type="boolean" value="False" truevalue="--exclude" falsevalue="" label="Invert output" help="Instead of finding reads that match given taxonomic IDs, find all reads that DO NOT match given IDs" /> 74 <param name="exclude" argument="--exclude" type="boolean" value="False" truevalue="--exclude" falsevalue="" label="Invert output" help="Instead of finding reads that match given taxonomic IDs, find all reads that DO NOT match given IDs" />
75 <param argument="--fastq-output" type="boolean" value="False" truevalue="--fastq-output" falsevalue="" label="Output as FASTQ" help="Write output as FASTQ instead of the default FASTA" /> 75 <param name="fastq_output" argument="--fastq-output" type="boolean" value="False" truevalue="--fastq-output" falsevalue="" label="Output as FASTQ" help="Write output as FASTQ instead of the default FASTA" />
76 <param argument="--include-parents" type="boolean" value="False" truevalue="--include-parents" falsevalue="" label="Include parents" help="Include reads classified at parent levels of the specified tax IDs" /> 76 <param name="include_parents" argument="--include-parents" type="boolean" value="False" truevalue="--include-parents" falsevalue="" label="Include parents" help="Include reads classified at parent levels of the specified tax IDs" />
77 <param argument="--include-children" type="boolean" value="False" truevalue="--include-children" falsevalue="" label="Include children" help="Include reads classified more specifically than the specified tax IDs" /> 77 <param name="include_children" argument="--include-children" type="boolean" value="False" truevalue="--include-children" falsevalue="" label="Include children" help="Include reads classified more specifically than the specified tax IDs" />
78 78
79 </inputs> 79 </inputs>
80 80
81 <outputs> 81 <outputs>
82 <data name="output_1" format="fasta" metadata_source="input_1" label="${tool.name} on ${on_string}: forward reads"> 82 <data name="output_1" format="fasta" metadata_source="input_1" label="${tool.name} on ${on_string}: forward reads">