Mercurial > repos > iuc > krakentools_extract_kraken_reads
diff extract_kraken_reads.xml @ 0:519e0835abd7 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 92c58a65005708fbd56b27b86969c01a1258ddb9
| author | iuc |
|---|---|
| date | Wed, 15 Mar 2023 18:18:27 +0000 |
| parents | |
| children | f329328da134 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/extract_kraken_reads.xml Wed Mar 15 18:18:27 2023 +0000 @@ -0,0 +1,251 @@ +<tool id="krakentools_extract_kraken_reads" name="Krakentools: Extract Kraken Reads By ID" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description> + Extract reads that were classified by the Kraken family at specified taxonomic IDs + </description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"> + <requirement type="package" version="1.12">gzip</requirement> + </expand> + <command detect_errors="exit_code"> + <![CDATA[ + + ##set input + #if $library.type == 'paired': + #set input_1 = $library.input_1 + #set input_2 = $library.input_2 + #else if $library.type == 'paired_collection' + #set input_1 = $library.input_1.forward + #set input_2 = $library.input_1.reverse + #else + #set input_1 = $library.input_1 + #end if + + ## name output according to --fastq_output param + ## tests fails if file does not have correct ending + #if str($fastq_output) == '': + #set temp_output_1 = 'output_1.fasta' + #set temp_output_2 = 'output_2.fasta' + #else: + #set temp_output_1 = 'output_1.fastq' + #set temp_output_2 = 'output_2.fastq' + #end if + + ## do not quote $taxid + extract_kraken_reads.py + -k '$results' + -s '$input_1' + -o '$temp_output_1' + --taxid $taxid + --max '$max' + $include_parents + $include_children + $exclude + $fastq_output + + #if str( $library.type ) != "single": + -s2 '$input_2' + -o2 '$temp_output_2' + #end if + #if $include_parents or $include_children: + --report '$report' + #end if + + ##compress output + && gzip -cvf '$temp_output_1' > output_1.gz + + #if str( $library.type ) != "single": + && gzip -cvf '$temp_output_2' > output_2.gz + #end if + + ]]> + </command> + <inputs> + <!-- Reads --> + <conditional name="library"> + <param name="type" type="select" label="Single or paired reads?"> + <option value="single"> + Single + </option> + <option value="paired"> + Paired + </option> + <option value="paired_collection"> + Paired Collection + </option> + </param> + <when value="single"> + <param name="input_1" format="fastq,fasta" type="data" label="FASTQ/A file" help="FASTQ or FASTQ input reads (may be gzipped)" /> + </when> + <when value="paired"> + <param name="input_1" format="fastq,fasta" type="data" label="FASTQ/A forward file" help="FASTQ or FASTQ input reads (may be gzipped)" /> + <param name="input_2" format="fastq,fasta" type="data" label="FASTQ/A reverse file" help="FASTQ or FASTQ input reads (for paired reads, may be gzipped)" /> + </when> + <when value="paired_collection"> + <param name="input_1" format="fastq,fasta" type="data_collection" collection_type="paired" label="Paired Collection" help="FASTQ or FASTA read pair collection (may be gzipped)" /> + </when> + </conditional> + <param name="results" argument="-k" format="tabular" type="data" label="Results" help="Results (classification) file from Kraken/KrakenUniq/Kraken2" /> + <param argument="--report" format="tabular" type="data" label="Report" optional="true" help="Report file from Kraken/KrakenUniq/Kraken2" /> + <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"> + <validator type="regex" message="Enter a space-separated list of numeric tax IDs">^\d+[\d ]*$</validator> + </param> + <param argument="--max" type="integer" value="100000000" min="1" label="Maximum reads to save" help="Maximum number of reads to save for each ID" /> + <param argument="--exclude" type="boolean" value="False" truevalue="--exclude" falsevalue="" label="Invert output" help="Instead of finding reads that match given taxonomic IDs, find all reads that DO NOT match given IDs" /> + <param argument="--fastq_output" type="boolean" value="False" truevalue="--fastq-output" falsevalue="" label="Output as FASTQ" help="Write output as FASTQ instead of the default FASTA" /> + <param argument="--include_parents" type="boolean" value="False" truevalue="--include-parents" falsevalue="" label="Include parents" help="Include reads classified at parent levels of the specified tax IDs" /> + <param argument="--include_children" type="boolean" value="False" truevalue="--include-children" falsevalue="" label="Include children" help="Include reads classified more specifically than the specified tax IDs" /> + </inputs> + <outputs> + <data name="output_1" format="fasta.gz" from_work_dir="output_1.gz" metadata_source="input_1" label="${tool.name} on ${on_string}: forward reads"> + <filter> + (library['type'] == 'single' or library['type'] == 'paired') + </filter> + <change_format> + <when input="fastq_output" value="--fastq-output" format="fastq.gz" /> + </change_format> + </data> + <data name="output_2" format="fasta.gz" from_work_dir="output_2.gz" metadata_source="input_2" label="${tool.name} on ${on_string}: reverse reads"> + <filter> + (library['type'] == 'paired') + </filter> + <change_format> + <when input="fastq_output" value="--fastq-output" format="fastq.gz" /> + </change_format> + </data> + <collection type="paired" name="output_collection" label="${tool.name} on ${on_string}: collection"> + <filter>(library['type'] == 'paired_collection')</filter> + <data name="forward" format="fasta.gz" metadata_source="input_1" from_work_dir="output_1.gz" > + <change_format> + <when input="fastq_output" value="--fastq-output" format="fastq.gz" /> + </change_format> + </data> + <data name="reverse" format="fasta.gz" metadata_source="input_2" from_work_dir="output_2.gz" > + <change_format> + <when input="fastq_output" value="--fastq-output" format="fastq.gz" /> + </change_format> + </data> + </collection> + </outputs> + <tests> + <!-- test Kraken2 input, single input --> + <test expect_num_outputs="1"> + <param name="input_1" value="extract_kraken_reads/R1.fq.gz" ftype="fastqsanger" /> + <param name="library|type" value="single" /> + <param name="results" value="extract_kraken_reads/kraken2.results" ftype="tabular" /> + <param name="taxid" value="11176" /> + <output name="output_1" file="extract_kraken_reads/out1.k2.11176.fa" decompress="true" ftype="fasta.gz" /> + </test> + <!-- test paired input --> + <test expect_num_outputs="2"> + <param name="input_1" value="extract_kraken_reads/R1.fq.gz" ftype="fastqsanger" /> + <param name="input_2" value="extract_kraken_reads/R2.fq.gz" ftype="fastqsanger" /> + <param name="library|type" value="paired" /> + <param name="results" value="extract_kraken_reads/kraken2.results" ftype="tabular" /> + <param name="taxid" value="11176" /> + <output name="output_1" file="extract_kraken_reads/out1.k2.11176.fa" decompress="true" ftype="fasta.gz" /> + <output name="output_2" file="extract_kraken_reads/out2.k2.11176.fa" decompress="true" ftype="fasta.gz" /> + </test> + <!-- test paired collection input --> + <test expect_num_outputs="3"> + <param name="input_1"> + <collection type="paired"> + <element name="forward" value="extract_kraken_reads/R1.fq.gz" ftype="fastqsanger" /> + <element name="reverse" value="extract_kraken_reads/R2.fq.gz" ftype="fastqsanger" /> + </collection> + </param> + <param name="library|type" value="paired_collection" /> + <param name="results" value="extract_kraken_reads/kraken2.results" ftype="tabular" /> + <param name="taxid" value="11176" /> + <output_collection name="output_collection" type="paired"> + <element name="forward" file="extract_kraken_reads/out1.k2.11176.fa" decompress="true" ftype="fasta.gz" /> + <element name="reverse" file="extract_kraken_reads/out2.k2.11176.fa" decompress="true" ftype="fasta.gz" /> + </output_collection> + </test> + <!-- test Kraken1 input, include children --> + <test expect_num_outputs="1"> + <param name="input_1" value="extract_kraken_reads/R1.fq.gz" ftype="fastqsanger" /> + <param name="library|type" value="single" /> + <param name="results" value="extract_kraken_reads/kraken1.results" ftype="tabular" /> + <param name="report" value="extract_kraken_reads/kraken1.report" ftype="tabular" /> + <param name="taxid" value="11176" /> + <param name="include_children" value="True" /> + <output name="output_1" file="extract_kraken_reads/out1.k1.11176.children.fa" decompress="true" ftype="fasta.gz" /> + </test> + <!-- test exclude --> + <test expect_num_outputs="1"> + <param name="input_1" value="extract_kraken_reads/R1.fq.gz" ftype="fastqsanger" /> + <param name="library|type" value="single" /> + <param name="results" value="extract_kraken_reads/kraken1.results" ftype="tabular" /> + <param name="report" value="extract_kraken_reads/kraken1.report" ftype="tabular" /> + <param name="taxid" value="10386" /> + <param name="include_children" value="True" /> + <param name="exclude" value="True" /> + <output name="output_1" file="extract_kraken_reads/out1.k1.e10386.children.fa" decompress="true" ftype="fasta.gz" /> + </test> + <!-- test max --> + <test expect_num_outputs="1"> + <param name="input_1" value="extract_kraken_reads/R1.fq.gz" ftype="fastqsanger" /> + <param name="library|type" value="single" /> + <param name="results" value="extract_kraken_reads/kraken2.results" ftype="tabular" /> + <param name="taxid" value="11176" /> + <param name="max" value="2" /> + <output name="output_1" file="extract_kraken_reads/out1.k2.11176.max2.fa" decompress="true" ftype="fasta.gz" /> + </test> + <!-- test include parents --> + <test expect_num_outputs="1"> + <param name="input_1" value="extract_kraken_reads/R1.fq.gz" ftype="fastqsanger" /> + <param name="library|type" value="single" /> + <param name="results" value="extract_kraken_reads/kraken2.results" ftype="tabular" /> + <param name="taxid" value="11176" /> + <param name="include_parents" value="True" /> + <param name="report" value="extract_kraken_reads/kraken2.report" ftype="tabular" /> + <output name="output_1" file="extract_kraken_reads/out1.k2.11176.parents.fa" decompress="true" ftype="fasta.gz" /> + </test> + <!-- test multiple tax IDs --> + <test expect_num_outputs="1"> + <param name="input_1" value="extract_kraken_reads/R1.fq.gz" ftype="fastqsanger" /> + <param name="library|type" value="single" /> + <param name="results" value="extract_kraken_reads/kraken2.results" ftype="tabular" /> + <param name="taxid" value="10386 11176" /> + <param name="exclude" value="True" /> + <param name="include_parents" value="True" /> + <param name="report" value="extract_kraken_reads/kraken2.report" ftype="tabular" /> + <output name="output_1" file="extract_kraken_reads/out1.k2.exclude_both.fa" decompress="true" ftype="fasta.gz" /> + </test> + <!-- test multiple tax IDs --> + <test expect_failure="true"> + <param name="input_1" value="extract_kraken_reads/R1.fq.gz" ftype="fastqsanger" /> + <param name="library|type" value="single" /> + <param name="results" value="extract_kraken_reads/kraken2.results" ftype="tabular" /> + <param name="taxid" value="10386 f5" /> + </test> + <!-- test FASTQ output --> + <test expect_num_outputs="1"> + <param name="input_1" value="extract_kraken_reads/R1.fq.gz" ftype="fastqsanger" /> + <param name="library|type" value="single" /> + <param name="results" value="extract_kraken_reads/kraken2.results" ftype="tabular" /> + <param name="taxid" value="11176" /> + <param name="fastq_output" value="true" /> + <output name="output_1" file="extract_kraken_reads/out1.k2.11176.fq" decompress="true" ftype="fastq.gz" /> + </test> + </tests> + <help> + <![CDATA[ +**What it does** +------------------- +After running Kraken, Kraken2, or KrakenUniq, users may use the +`extract_kraken_reads.py` program to extract the FASTA or FASTQ reads +classified as a specific taxonomy ID. For example, this program can be used to +extract all bacterial reads or only reads assigned to Escherichia coli. Users +must provide (at minimum) the original sequence file(s), at least one taxonomy +ID, and the Kraken output file. + ]]> + </help> + <expand macro="citations" /> + <creator> + <person givenName="Jeremy" familyName="Volkening" url="https://github.com/jvolkening" /> + <person givenName="Paul" familyName="Zierep" email="zierep@informatik.uni-freiburg.de" /> + </creator> +</tool>