Mercurial > repos > iuc > pear
diff pear.xml @ 3:2f6e6d74144e draft
Uploaded
| author | iuc |
|---|---|
| date | Tue, 28 Apr 2015 22:56:51 -0400 |
| parents | |
| children | 5bbdf641a2d5 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pear.xml Tue Apr 28 22:56:51 2015 -0400 @@ -0,0 +1,160 @@ +<tool id="iuc_pear" name="Pear" version="0.9.6.0"> + <description>Paired-End read merger</description> + <!--<version_command>bismark version</version_command>--> + <requirements> + <requirement type="package" version="0.9.6">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" + #else + ## prepare collection + -f $library.input_collection.forward + -r $library.input_collection.reverse + #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, fastq" + label="Name of file that contains the forward paired-end reads" help="-f" /> + <param name="reverse" type="data" format="fastqillumina, fastqsanger, fastq" + 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, fastq" + type="data_collection" collection_type="paired" + label="FASTQ Paired Dataset" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33. (-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" display="checkboxes" optional="False" multiple="True" label="Output files"> + <option value="assembled" selected="True">Assembled reads</option> + <option value="forward">Forward unassembled reads</option> + <option value="reverse">Reverse unassembled reads</option> + <option value="discarded">Discarded reads</option> + </param> + </inputs> + <outputs> + <data format="fastq" name="assembled_reads" from_work_dir="pear.assembled.fastq" label="${tool.name} on ${on_string}: Assembled reads"> + <filter>'assembled' in outputs</filter> + </data> + <data format="fastq" name="unassembled_forward_reads" from_work_dir="pear.unassembled.forward.fastq" label="${tool.name} on ${on_string}: Unassembled forward reads"> + <filter>'forward' in outputs</filter> + </data> + <data format="fastq" name="unassembled_reverse_reads" from_work_dir="pear.unassembled.reverse.fastq" label="${tool.name} on ${on_string}: Unassembled reverse reads"> + <filter>'reverse' in outputs</filter> + </data> + <data format="fastq" name="discarded_reads" from_work_dir="pear.discarded.fastq" label="${tool.name} on ${on_string}: Discarded reads"> + <filter>'discarded' in outputs</filter> + </data> + </outputs> + <tests> + <test> + <param name="forward" value="forward.fastq" ftype="fastq" /> + <param name="reverse" value="reverse.fastq" ftype="fastq" /> + <param name="min_overlap" value="10" /> + <param name="min_assembly_length" value="50" /> + <param name="cap" value="0" /> + <param name="outputs" value="assembled,forward" /> + <output name="assembled_reads" file="pear_assembled_results1.fastq" ftype="fastq"/> + <output name="unassembled_forward_reads" file="pear_unassembled_forward_results1.fastq" ftype="fastq"/> + </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: http://sco.h-its.org/exelixis/web/software/pear/ +.. _documentation: http://sco.h-its.org/exelixis/web/software/pear/doc.html +.. _github repository: https://github.com/xflouris/PEAR + + +]]> + </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btt593</citation> + </citations> +</tool>