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chimera.check.xml
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chimera.check.xml
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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="biotools"/>
<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" format="svg">
<discover_datasets pattern="(?P<designation>.*)\.chimeracheck\.svg" format="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>