Mercurial > repos > iuc > mothur_chimera_check
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit dfdd4c590370ecb3a9806314d43eb5668e36a01a"
author | iuc |
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date | Fri, 22 Jan 2021 02:03:35 +0000 |
parents | 37bd32018025 |
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<tool profile="16.07" id="mothur_chimera_check" name="Chimera.check" version="@WRAPPER_VERSION@.0"> <description>Find putative chimeras using chimeraCheck</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ @SHELL_OPTIONS@ ## create symlinks to input datasets ln -s '$fasta' fasta.dat && ln -s '$alignment.reference' alignment.reference.dat && #if $svg_cond.svg == "yes": ln -s '$svg_cond.name' svg.name.dat && #end if echo 'chimera.check( fasta=fasta.dat, reference=alignment.reference.dat, #if $svg_cond.svg == "yes": svg=yes, name=svg.name.dat, #end if increment=$increment, ksize=$ksize, processors='\${GALAXY_SLOTS:-8}' )' | sed 's/ //g' ## mothur trips over whitespace | mothur | tee mothur.out.log ]]></command> <inputs> <param argument="fasta" type="data" format="mothur.align" label="fasta - Candiate Aligned Sequences"/> <conditional name="alignment"> <param name="source" type="select" label="Select Reference Template from"> <option value="hist">History</option> <option value="ref">Cached Reference</option> </param> <when value="ref"> <param argument="reference" type="select" label="reference - Select an alignment database"> <options from_data_table="mothur_aligndb"/> </param> </when> <when value="hist"> <param argument="reference" type="data" format="fasta" label="reference - Reference to align with"/> </when> </conditional> <param argument="ksize" type="integer" value="7" label="ksize - kmer length to determine differences between sequence fragments" help="uses default if < 1"/> <param argument="increment" type="integer" value="10" label="increment - Increment for window slide on each iteration" help="Default is 10, but you may set it up to sequence length minus twice the window."/> <conditional name="svg_cond"> <param argument="svg" type="select" label="svg - Generate a SVG plot for each query sequence"> <option value="no" selected="true">No</option> <option value="yes">Yes</option> </param> <when value="no"/> <when value="yes"> <param argument="name" type="data" format="mothur.names" optional="true" label="name - Names of queries for which to generate SVG plot"/> </when> </conditional> <expand macro="param-savelog"/> </inputs> <outputs> <expand macro="logfile-output"/> <data name="chimeracheck.chimeras" format="txt" from_work_dir="fasta.chimeracheck.chimeras" label="${tool.name} on ${on_string}: chimeracheck.chimeras"/> <collection name="images" type="list" label="${tool.name} on ${on_string}: SVG images"> <discover_datasets pattern="(?P<designation>.*)\.chimeracheck\.svg"/> <filter>svg['gen'] == 'yes'</filter> </collection> </outputs> <tests> <test> <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/> <param name="source" value="hist"/> <param name="reference" value="HMP_MOCK.v35.align"/> <output name="chimeracheck.chimeras" file="Mock_S280_L001_R1_001_small.trim.contigs.good.chimeracheck.chimeras" ftype="txt"/> <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <test> <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/> <param name="source" value="hist"/> <param name="reference" value="HMP_MOCK.v35.align"/> <param name="svg" value="yes"/> <param name="name" value="Mock_S280_L001_R1_001_small.trim.contigs.good.names_tiny"/> <output name="chimeracheck.chimeras" file="Mock_S280_L001_R1_001_small.trim.contigs.good.chimeracheck.chimeras" ftype="txt"/> <output_collection name="images" count="2"> <element name="M00967_43_000000000-A3JHG_1_1101_14010_4122" file="M00967_43_000000000-A3JHG_1_1101_14010_4122.chimeracheck.svg"/> <element name="M00967_43_000000000-A3JHG_1_1101_13293_4703" md5="0d99dc17c183dab4efc75c697060a9a5"/> </output_collection> <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> </tests> <help><![CDATA[ @MOTHUR_OVERVIEW@ **Command Documentation** The chimera.check_ command identifies putative chimeras using the chimeraCheck approach. It looks at distance of left side of query to it's closest match + distance of right side of query to it's closest match - distance of whole query and its closest match over several windows. Note: following the RDP model this method does not determine whether or not a sequence is chimeric, but allows you to determine that based on the IS values produced. .. _chimera.check: https://www.mothur.org/wiki/Chimera.check ]]></help> <expand macro="citations"/> </tool>