Mercurial > repos > iuc > mothur_chimera_check
diff chimera.check.xml @ 0:8e874c18a298 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author | iuc |
---|---|
date | Fri, 19 May 2017 05:07:56 -0400 |
parents | |
children | 37bd32018025 |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/chimera.check.xml Fri May 19 05:07:56 2017 -0400 @@ -0,0 +1,110 @@ +<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.template" alignment.template.dat && + #if $svg.gen == "yes": + ln -s "$svg.name" svg.name.dat && + #end if + + echo 'chimera.check( + fasta=fasta.dat, + reference=alignment.template.dat, + #if $svg.gen == "yes": + svg=yes, + name=svg.name.dat, + #end if + increment=$increment, + ksize=$ksize, + processors='\${GALAXY_SLOTS:-8}' + )' + | sed 's/ //g' ## mothur trips over whitespace + | mothur + | tee mothur.out.log + ]]></command> + <inputs> + <param name="fasta" type="data" format="mothur.align" argument="fasta" label="fasta - Candiate Aligned Sequences"/> + <conditional name="alignment"> + <param name="source" type="select" label="Select Reference Template from" help=""> + <option value="hist">History</option> + <option value="ref">Cached Reference</option> + </param> + <when value="ref"> + <param name="template" type="select" argument="reference" label="reference - Select an alignment database" help=""> + <options from_data_table="mothur_aligndb"> + </options> + </param> + </when> + <when value="hist"> + <param name="template" type="data" format="fasta" argument="reference" label="reference - Reference to align with" help=""/> + </when> + </conditional> + <param name="ksize" type="integer" value="7" argument="ksize" label="ksize - kmer length to determine differences between sequence fragments (uses default if < 1)"/> + <param name="increment" type="integer" value="10" argument="increment" label="increment - Increment for window slide on each iteration (uses default if < 1)" help="Default is 10, but you may set it up to sequence length minus twice the window."/> + <conditional name="svg"> + <param name="gen" type="select" label="svg - Generate a SVG plot for each query sequence" help=""> + <option value="no" selected="true">No</option> + <option value="yes">Yes</option> + </param> + <when value="no"/> + <when value="yes"> + <param name="name" type="data" format="mothur.names" optional="true" argument="name" label="name - Names of queries for which to generate SVG plot"/> + </when> + </conditional> + </inputs> + <outputs> + <expand macro="logfile-output"/> + <data name="out_file" format="txt" from_work_dir="fasta.chimeracheck.chimeras" label="${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="template" value="HMP_MOCK.v35.align"/> + <output name="out_file" file="Mock_S280_L001_R1_001_small.trim.contigs.good.chimeracheck.chimeras" ftype="txt"/> + <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="template" value="HMP_MOCK.v35.align"/> + <param name="gen" value="yes"/> + <param name="name" value="Mock_S280_L001_R1_001_small.trim.contigs.good.names_tiny"/> + <output name="out_file" 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> + <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>