Mercurial > repos > iuc > mothur_filter_shared
diff filter.shared.xml @ 2:644b7baba854 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
| author | iuc |
|---|---|
| date | Tue, 20 Mar 2018 22:11:33 -0400 |
| parents | bccb5efbc4ee |
| children | e44c38a17c7a |
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--- a/filter.shared.xml Tue Sep 05 16:54:33 2017 -0400 +++ b/filter.shared.xml Tue Mar 20 22:11:33 2018 -0400 @@ -7,50 +7,64 @@ <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ - @SHELL_OPTIONS@ +@SHELL_OPTIONS@ - ## create symlinks to input datasets - ln -s "$otu" otu.dat && +## create symlinks to input datasets +ln -s '$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 +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"> + <param name="otu" argument="shared" type="data" format="mothur.shared" label="shared - specify your shared file"/> + <param argument="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"> + <param argument="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)"/> + <param argument="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"/> + <param argument="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"/> + <param argument="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"/> + <param argument="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"/> + <param argument="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"/> + <param argument="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 argument="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"/> + <param argument="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"/> + <expand macro="param-savelog"/> </inputs> <outputs> <expand macro="logfile-output"/> @@ -60,11 +74,16 @@ </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"/> + <param name="otu" value="esophagus.fn.shared" ftype="mothur.shared"/> + <output_collection name="filter_shared" count="4"> + <element name="0.03" ftype="mothur.shared"> + <assert_contents> + <expand macro="test-shared-format"/> + <has_text text="0.03"/> + </assert_contents> + </element> </output_collection> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <test><!-- test with label and group select --> @@ -73,13 +92,18 @@ <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"/> + <element name="0.29" ftype="mothur.shared"> + <assert_contents> + <expand macro="test-shared-format"/> + <has_text text="0.29"/> + </assert_contents> + </element> </output_collection> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ @@ -89,8 +113,7 @@ .. _filter.shared: https://www.mothur.org/wiki/Filter.shared -]]> - </help> + ]]></help> <citations> <citation type="doi">10.1128/AEM.01541-09</citation> </citations>