view skewer.xml @ 3:1731a1cca226 draft

v1.1.0

<tool id="tool_1" name="Aurora Skewer" version="1.0.0">
  <description>A fast and accurate adapter trimmer for next-generation sequencing paired-end reads&#xD;
    </description>
  <requirements>
        <requirement type="package" version="1.15.0.6-0">pandoc</requirement><requirement type="package" version="1.20.0">r-getopt</requirement><requirement type="package" version="1.6">r-rmarkdown</requirement><requirement type="package" version="0.2.2">skewer</requirement></requirements>
  <stdio>
        <regex match="XXX" source="stderr" level="warning" description="Check the warnings_and_errors.txt file for more details."/></stdio>
  <command><![CDATA[export TOOL_DIR='${__tool_directory__}' &&

Rscript '${__tool_directory__}/'skewer_render.R

	-o '$report'
	-d '$report.files_path'
	-s '$sink_message'
	-A '$first_reads'
	-B '$second_reads'
	-x '$adapter_first_reads'
	-y '$adapter_second_reads'
	-m '$trimming_mode'
	-r '$maximum_allowed_error_rate'
	-D '$maximum_allowed_indel_error_rate'
	-q '$quality_trimming_3_end'
	-Q '$mean_quality'
	-l '$minimum_read_length'
	-j '$advanced_options.junction_adapter'
	-M '$advanced_options.tab_adapter'
	-b '$advanced_options.barcode'
	-c '$advanced_options.cut'
	-n '$advanced_options.filter_degenerative_reads'
	-u '$advanced_options.filter_undetermined_mate_pair_reads'
	-f '$advanced_options.format'
	-z '$advanced_options.compress'
	-E '$advanced_options.qiime'
	-F '$advanced_options.quiet'
	-i '$advanced_options.intelligent'
	-1 '$trimmed_r1'
	-2 '$trimmed_r2'
	-3 '$trimmed_s'
]]></command>
  <inputs>
        <param type="data" name="first_reads" label="First reads" optional="False" format="fastq,fastqsanger" multiple="False"/><param type="data" name="second_reads" label="Second reads" help="If it is single end reads, ignore this input field and use the &quot;first reads&quot; field only." optional="True" format="fastq,fastqsanger" multiple="False"/><param type="data" name="adapter_first_reads" argument="-x" label="Adapter sequence/file for the first reads." optional="True" format="fasta,fa" multiple="False"/><param type="data" name="adapter_second_reads" argument="-y" label="Adapter sequence/file for the second reads" optional="True" format="fasta,fa" multiple="False"/><param type="select" name="trimming_mode" argument="-m" label="trimming mode" optional="False" multiple="False"><option value="None" selected="true">--select a model--</option><option value="head" selected="false">5&#x2019; end trimming (single end reads)</option><option value="tail" selected="false">3&#x2019; end trimming (single end reads)</option><option value="any" selected="false">anywhere adapter detection and trimming (single end reads)</option><option value="pe" selected="false">paired-end trimming</option><option value="mp" selected="false">mate-pair trimming</option><option value="ap" selected="false">amplicon trimming</option></param><param type="float" name="maximum_allowed_error_rate" argument="-r" label="Maximum allowed error rate" optional="False" value="0.1" min="0" max="0.5"/><param type="float" name="maximum_allowed_indel_error_rate" argument="-d" label="Maximum allowed indel error rate" help="The valid range of indel error rate is [0,  maximum allowed error rate]" optional="False" value="0.03" min="0"/><param type="integer" name="quality_trimming_3_end" argument="-q" label="3&#x2019; end quality trimming" optional="False" value="0"/><param type="integer" name="mean_quality" argument="-Q" label="Reads filtering by average quality" optional="False" value="0"/><param type="integer" name="minimum_read_length" argument="-l" label="Minimum read length allowed after trimming" optional="False" value="18"/><section name="advanced_options" title="Advanced options" expanded="False"><param type="data" name="junction_adapter" argument="-j" label="Junction adapter sequence/file for Nextera Mate Pair reads" optional="True" format="fasta,fa" multiple="False"/><param type="text" name="tab_adapter" argument="-M" label="TAB delimited file indicates valid forward/reverse adapter pairing" optional="True"/><param type="boolean" name="barcode" argument="-b" label="Whether to demultiplex reads according to adapters/primers" optional="False" checked="False" truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/><param type="text" name="cut" argument="-c" label="To hard clip off the 5&#x2019; leading bases of the forward primer and reverse primer respectively as the barcodes in amplicon mode" optional="False" value="0, 0"/><param type="boolean" name="filter_degenerative_reads" argument="-n" label="Whether to filter out highly degenerative reads" optional="False" checked="False" truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/><param type="boolean" name="filter_undetermined_mate_pair_reads" argument="-u" label="Whether to filter out undetermined mate-pair reads" optional="False" checked="False" truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/><param type="select" name="format" argument="-f" label="Format of FASTQ quality value" optional="False" multiple="False"><option value="sanger" selected="false">sanger</option><option value="solexa" selected="false">solexa</option><option value="auto" selected="true">auto</option></param><param type="boolean" name="compress" argument="-z" label="Whether to compress output in GZIP format" optional="False" truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/><param type="boolean" name="qiime" argument="-qiime" label="Whether to prepare files required by QIIME" optional="False" truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/><param type="boolean" name="quiet" argument="--quiet" label="Whether in quiet mode" optional="False" truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/><param type="boolean" name="intelligent" argument="-i" label="Whether to intelligently redistribute reads" optional="False" checked="False" truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/></section></inputs>
  <outputs>
        <data name="report" format="html" label="${tool.name} report on ${on_string}" hidden="false"/><data name="sink_message" format="txt" label="${tool.name} log" from_work_dir="warnings_and_errors.txt" hidden="false"/><data name="trimmed_r1" format="fastq" label="${tool.name} trimmed first reads on ${on_string}" hidden="false"/><data name="trimmed_r2" format="fastq" label="${tool.name} trimmed second reads on ${on_string}" hidden="false"/><data name="trimmed_s" format="fastq" label="${tool.name} trimmed single end reads on ${on_string}" hidden="false"/></outputs>
  <help><![CDATA[Read the `tool manual <http://download2.nust.na/pub4/sourceforge/s/project/sk/skewer/skewer_manual.pdf>`_ if you are not sure what parameter values to use.]]></help>
  <citations>
        <citation type="bibtex"><![CDATA[
            @article{allaire2016rmarkdown,
            title={rmarkdown: Dynamic Documents for R, 2016},
            author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
            and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
            journal={R package version 0.9},
            volume={6},
            year={2016}
            }
        ]]></citation><citation type="bibtex"><![CDATA[
            @book{xie2015dynamic,
            title={Dynamic Documents with R and knitr},
            author={Xie, Yihui},
            volume={29},
            year={2015},
            publisher={CRC Press}
            }
        ]]></citation><citation type="bibtex"><![CDATA[@article{jiang2014skewer,
  title={Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads},
  author={Jiang, Hongshan and Lei, Rong and Ding, Shou-Wei and Zhu, Shuifang},
  journal={BMC bioinformatics},
  volume={15},
  number={1},
  pages={182},
  year={2014},
  publisher={BioMed Central}
}]]></citation></citations>
</tool>