Mercurial > repos > iuc > mothur_filter_shared
diff filter.shared.xml @ 0:bccb5efbc4ee draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
| author | iuc |
|---|---|
| date | Fri, 19 May 2017 05:47:34 -0400 |
| parents | |
| children | 644b7baba854 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/filter.shared.xml Fri May 19 05:47:34 2017 -0400 @@ -0,0 +1,97 @@ +<tool profile="16.07" id="mothur_filter_shared" name="Filter.shared" version="@WRAPPER_VERSION@.0"> + <description>remove OTUs based on various critieria</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 "$otu" otu.dat && + + echo 'filter.shared( + shared=otu.dat, + #if $label: + label=${ str($label).replace(",","-") }, + #end if + #if $label: + groups=${ str($groups).replace(",","-") }, + #end if + minabund=$minabund, + minpercent=$minpercent, + rarepercent=$rarepercent, + keepties=$keepties, + minnumsamples=$minnumsamples, + minpercentsamples=$minpercentsamples, + mintotal=$mintotal, + makerare=$makerare + )' + | sed 's/ //g' ## mothur trips over whitespace + | mothur + | tee mothur.out.log + ]]></command> + <inputs> + <param name="otu" type="data" format="mothur.shared" label="shared - specify your shared file"/> + <param name="label" type="select" optional="true" multiple="true" label="label - OTU Labels" help="If none selected, all labels will be output"> + <expand macro="labeloptions"/> + </param> + <param name="groups" type="select" optional="true" multiple="true" label="Select groups for to include in this grouping"> + <options> + <filter type="data_meta" ref="otu" key="groups"/> + </options> + </param> + <param name="minabund" type="integer" value="0" min="0" label="minabund - indicate the minimum abundance required for each sample in a given OTU" help="If any samples abundance falls below the minimum, the OTU is removed. Default=0"/> + <param name="minpercent" type="integer" value="0" min="0" max="100" label="minpercent - indicate the minimum relative abundance of an OTU" help="For example, if the OTUs total abundance across all samples is 8, and the total abundance across all OTUs is 1000, and minpercent=1. The OTU's relative abundance is 0.008, the minimum is 0.01, so the OTU will be removed (Default=0)"/> + <param name="rarepercent" type="integer" value="0" min="0" max="100" label="rarepercent - indicate the percentage of otus to remove" help="The OTUs chosen to be removed are the rarest. For example if you have 1000 OTUs, rarepercent=20 would remove the 200 OTUs with the lowest abundance (Default=0)"/> + <param name="keepties" type="boolean" truevalue="true" falsevalue="false" checked="true" label="keepties - indicate you want to keep the OTUs with the same abundance as the first 'not rare' OTU" help="For example if you have 10 OTUs, rarepercent=20 abundances of 20, 18, 15, 15, 10, 5, 3, 3, 3, 1. keepties=t, would remove the 10th OTU, but keep the 9th because its abundance ties the 8th OTU. keepties=f would remove OTUs 9 and 10 (Default=T)"/> + <param name="minnumsamples" type="integer" value="0" min="0" label="minnumsamples - indicate the minimum number of samples present in an OTU" help="If the number of samples present falls below the minimum, the OTU is removed (Default=0)"/> + <param name="minpercentsamples" type="integer" value="0" min="0" max="100" label="minpercentsamples - indicate the minimum percent of sample present in an OTU" help="For example, if the total number of samples is 10, the number present is 3, and the minpercentsamples=50. The OTU's precent of samples is 0.333, the minimum is 0.50, so the OTU will be removed (Default=0)"/> + <param name="mintotal" type="integer" value="0" min="0" max="100" label="mintotal - indicate the minimum abundance required for a given OTU" help="If abundance across all samples falls below the minimum, the OTU is removed (Default=0)"/> + <param name="makerare" type="boolean" truevalue="true" falsevalue="false" checked="true" label="makerare - indicate you want the abundances of any removed OTUs to be saved and a new rare OTU created with its abundances equal to the sum of the OTUs removed" help="This will preserve the number of reads in your dataset (Default=T)"/> + </inputs> + <outputs> + <expand macro="logfile-output"/> + <collection name="filter_shared" type="list" label="${tool.name} on ${on_string}: filter.shared"> + <discover_datasets pattern=".*?\.(?P<designation>.*)\.filter\.dat" format="mothur.shared"/> + </collection> + </outputs> + <tests> + <test><!-- test with defaults --> + <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> + <param name="minabund" value="1"/> + <output_collection name="filter_shared" count="36"> + <element name="0.29" md5="db8387475c126110f2ac21066344c933" ftype="mothur.shared"/> + </output_collection> + <expand macro="logfile-test"/> + </test> + <test><!-- test with label and group select --> + <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> + <param name="label" value="0.05,0.29,0.33"/> + <param name="groups" value="forest,pasture"/> + <param name="minabund" value="1"/> + <output_collection name="filter_shared" count="3"> + <element name="0.29" md5="db8387475c126110f2ac21066344c933" ftype="mothur.shared"/> + </output_collection> + <expand macro="logfile-test"/> + </test> + </tests> + <help> +<![CDATA[ + +@MOTHUR_OVERVIEW@ + +**Command Documentation** + +The filter.shared_ is used to remove OTUs based on various critieria. + +.. _filter.shared: https://www.mothur.org/wiki/Filter.shared + +]]> + </help> + <citations> + <citation type="doi">10.1128/AEM.01541-09</citation> + </citations> +</tool>