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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit 6e869b3e13ed7b012b270f14fce812613642e5f2"
author | iuc |
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date | Mon, 04 Apr 2022 08:31:45 +0000 |
parents | 2f804526f5fd |
children | 037f0acc7830 |
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<tool id="iuc_pear" name="Pear" version="@TOOL_VERSION@.@VERSION_SUFFIX@" profile="20.09"> <description>Paired-End read merger</description> <macros> <token name="@TOOL_VERSION@">0.9.6</token> <token name="@VERSION_SUFFIX@">2</token> <xml name="format_action"> <actions> <conditional name="library.type"> <when value="paired"> <action type="format"> <option type="from_param" name="library.forward" param_attribute="ext" /> </action> </when> <when value="paired_collection"> <action type="format"> <option type="from_param" name="library.input_collection" param_attribute="forward.ext" /> </action> </when> </conditional> </actions> </xml> </macros> <xrefs> <xref type="bio.tools">pear</xref> </xrefs> <requirements> <requirement type="package" version="@TOOL_VERSION@">pear</requirement> </requirements> <stdio> <exit_code range="1:" /> <exit_code range=":-1" /> <regex match="Error:" /> <regex match="Exception:" /> </stdio> <command> <![CDATA[ pear #if str( $library.type ) == "paired": -f "$library.forward" -r "$library.reverse" #if $library.forward.is_of_type( 'fastqillumina' ): --phred-base 64 #else: --phred-base 33 #end if #else ## prepare collection -f "$library.input_collection.forward" -r "$library.input_collection.reverse" #if $library.input_collection.forward.is_of_type( 'fastqillumina' ): --phred-base 64 #else: --phred-base 33 #end if #end if --output pear --p-value $pvalue --min-overlap $min_overlap #if int($max_assembly_length) > 0: --max-asm-length $max_assembly_length #end if --min-asm-length $min_assembly_length --min-trim-length $min_trim_length --quality-theshold $quality_threshold --max-uncalled-base $max_uncalled_base --test-method $test_method --empirical-freqs $empirical_freqs -j "\${GALAXY_SLOTS:-8}" --score-method $score_method --cap $cap $nbase ]]> </command> <inputs> <conditional name="library"> <param name="type" type="select" label="Dataset type"> <option value="paired">Paired-end</option> <option value="paired_collection">Paired-end Dataset Collection</option> </param> <when value="paired"> <param name="forward" type="data" format="fastqillumina,fastqsanger" label="Name of file that contains the forward paired-end reads" help="-f" /> <param name="reverse" type="data" format="fastqillumina,fastqsanger" label="Name of file that contains the reverse paired-end reads" help="-r" /> </when> <when value="paired_collection"> <param name="input_collection" format="fastqillumina,fastqsanger" type="data_collection" collection_type="paired" label="FASTQ Paired Dataset" help="Nucleotide-space: Must have PHRED-scaled quality values. (-f and -r)" /> </when> </conditional> <!-- optional --> <param name="pvalue" type="float" value="0.01" min="0" optional="true" max="1" label="Specify a p-value for the statistical test" help="If the computed p-value of a possible assembly exceeds the specified p-value then the paired-end read will not be assembled. Setting 1.0 disables the test. (--p-value)" /> <param name="min_overlap" type="integer" value="10" optional="true" label="Minimum overlap size" help="The minimum overlap may be set to 1 when the statistical test is used. However, further restricting the minimum overlap size to a proper value may reduce false-positive assembles. (--min-overlap)" /> <param name="max_assembly_length" type="integer" value="0" optional="true" label="Maximum possible length of the assembled sequences" help="Setting this value to 0 disables the restriction and assembled sequences may be arbitrary long. (--max-assembly-length)" /> <param name="min_assembly_length" type="integer" value="50" optional="true" label="Minimum possible length of the assembled sequences" help="Setting this value to 0 disables the restriction and assembled sequences may be arbitrary short. (--min-assembly-length)" /> <param name="min_trim_length" type="integer" value="1" optional="true" label="Minimum length of reads after trimming the low quality part" help="See option -q. (--min-trim-length)" /> <param name="quality_threshold" type="integer" value="0" optional="true" label="Quality score threshold for trimming the low quality part of a read" help="If the quality scores of two consecutive bases are strictly less than the specified threshold, the rest of the read will be trimmed. (--quality-threshold)" /> <param name="max_uncalled_base" type="float" value="1.0" min="0" optional="true" max="1" label="Maximal proportion of uncalled bases in a read" help="Setting this value to 0 will cause PEAR to discard all reads containing uncalled bases. The other extreme setting is 1 which causes PEAR to process all reads independent on the number of uncalled bases. (--max-uncalled-base)" /> <param name="cap" type="integer" value="40" optional="true" label="Specify the upper bound for the resulting quality score" help="If set to zero, capping is disabled. (--cap)" /> <param name="test_method" type="select" label="Type of statistical test" help="(--test-method)"> <option value="1" selected="true">Given the minimum allowed overlap, test using the highest OES (1)</option> <option value="2">Use the acceptance probability (2)</option> </param> <param name="empirical_freqs" type="boolean" truevalue="-e" falsevalue="" checked="false" label="Disable empirical base frequencies" help="(--empirical-freqs)" /> <param name="nbase" type="boolean" truevalue="--nbase" falsevalue="" checked="false" label="Use N base if uncertain" help="When merging a base-pair that consists of two non-equal bases out of which none is degenerate, set the merged base to N and use the highest quality score of the two bases. (--nbase)" /> <param name="score_method" type="select" label="Scoring method" help="(--score-method)"> <option value="1">OES with +1 for match and -1 for mismatch</option> <option value="2" selected="true">Assembly score (AS) use +1 for match and -1 for mismatch multiplied by base quality scores</option> <option value="3">Ignore quality scores and use +1 for a match and -1 for a mismatch</option> </param> <param name="outputs" type="select" optional="false" multiple="true" label="Output files"> <option value="assembled" selected="true">Assembled reads</option> <option value="unassembled_forward">Forward unassembled reads</option> <option value="unassembled_reverse">Reverse unassembled reads</option> <option value="discarded">Discarded reads</option> </param> </inputs> <outputs> <data name="assembled_reads" from_work_dir="pear.assembled.fastq" label="${tool.name} on ${on_string}: Assembled reads"> <expand macro="format_action"/> <filter>'assembled' in outputs</filter> </data> <data format="auto" name="unassembled_forward_reads" from_work_dir="pear.unassembled.forward.fastq" label="${tool.name} on ${on_string}: Unassembled forward reads"> <expand macro="format_action"/> <filter>'unassembled_forward' in outputs</filter> </data> <data format="auto" name="unassembled_reverse_reads" from_work_dir="pear.unassembled.reverse.fastq" label="${tool.name} on ${on_string}: Unassembled reverse reads"> <expand macro="format_action"/> <filter>'unassembled_reverse' in outputs</filter> </data> <data format="auto" name="discarded_reads" from_work_dir="pear.discarded.fastq" label="${tool.name} on ${on_string}: Discarded reads"> <expand macro="format_action"/> <filter>'discarded' in outputs</filter> </data> </outputs> <tests> <test expect_num_outputs="2"> <conditional name="library"> <param name="type" value="paired"/> <param name="forward" value="forward.fastq" ftype="fastqsanger" /> <param name="reverse" value="reverse.fastq" ftype="fastqsanger" /> </conditional> <param name="min_overlap" value="10" /> <param name="min_assembly_length" value="50" /> <param name="cap" value="0" /> <param name="outputs" value="assembled,unassembled_forward" /> <output name="assembled_reads" file="pear_assembled_results1.fastq" ftype="fastqsanger"/> <output name="unassembled_forward_reads" file="pear_unassembled_forward_results1.fastq" ftype="fastqsanger"/> </test> <!-- same test as before using collection input and fastqillumina (even if it isn't) .. therefore only loose check of outputs --> <test expect_num_outputs="2"> <conditional name="library"> <param name="type" value="paired_collection"/> <param name="input_collection"> <collection type="paired"> <element name="forward" value="forward.fastq" ftype="fastqillumina" /> <element name="reverse" value="reverse.fastq" ftype="fastqillumina" /> </collection> </param> </conditional> <param name="min_overlap" value="10" /> <param name="min_assembly_length" value="50" /> <param name="cap" value="0" /> <param name="outputs" value="assembled,unassembled_forward" /> <output name="assembled_reads" ftype="fastqillumina"> <assert_contents> <has_line_matching expression="@.*"/> </assert_contents> </output> <output name="unassembled_forward_reads" ftype="fastqillumina"> <assert_contents> <has_line_matching expression="@.*"/> </assert_contents> </output> </test> </tests> <help> <![CDATA[ **What it does** PEAR_ is an ultrafast, memory-efficient and highly accurate pair-end read merger. PEAR evaluates all possible paired-end read overlaps and without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results. Together with a highly optimized implementation, it can merge millions of paired end reads within a couple of minutes on a standard desktop computer. For more information please look at the documentation_ and `github repository`_. .. _PEAR: https://sco.h-its.org/exelixis/web/software/pear/ .. _documentation: https://sco.h-its.org/exelixis/web/software/pear/doc.html .. _github repository: https://github.com/tseemann/PEAR Please note that PEAR is released under the [CC Attribution-NonCommercial-ShareAlike](https://creativecommons.org/licenses/by-nc-sa/3.0/) license and that commercial partners should obtain a license. ]]> </help> <citations> <citation type="doi">10.1093/bioinformatics/btt593</citation> </citations> </tool>