Mercurial > repos > florianbegusch > qiime2_suite
diff qiime2/qiime_fragment-insertion_filter-features.xml @ 29:3ba9833030c1 draft
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author | florianbegusch |
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date | Fri, 04 Sep 2020 13:12:49 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_fragment-insertion_filter-features.xml Fri Sep 04 13:12:49 2020 +0000 @@ -0,0 +1,79 @@ +<?xml version="1.0" ?> +<tool id="qiime_fragment-insertion_filter-features" name="qiime fragment-insertion filter-features" + version="2020.8"> + <description>Filter fragments in tree from table.</description> + <requirements> + <requirement type="package" version="2020.8">qiime2</requirement> + </requirements> + <command><![CDATA[ +qiime fragment-insertion filter-features + +--i-table=$itable + +--i-tree=$itree + +--o-filtered-table=ofilteredtable + +--o-removed-table=oremovedtable + +#if str($examples) != 'None': +--examples=$examples +#end if + +; +cp oremovedtable.qza $oremovedtable + + ]]></command> + <inputs> + <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] A feature-table which needs to filtered down to those fragments that are contained in the tree, e.g. result of a Deblur or DADA2 run. [required]" name="itable" optional="False" type="data" /> + <param format="qza,no_unzip.zip" label="--i-tree: ARTIFACT The tree resulting from inserting fragments into a Phylogeny[Rooted] reference phylogeny, i.e. the output of function \'sepp\' [required]" name="itree" optional="False" type="data" /> + <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" /> + + </inputs> + + <outputs> + <data format="qza" label="${tool.name} on ${on_string}: filteredtable.qza" name="ofilteredtable" /> + <data format="qza" label="${tool.name} on ${on_string}: removedtable.qza" name="oremovedtable" /> + + </outputs> + + <help><![CDATA[ +Filter fragments in tree from table. +############################################################### + +Filters fragments not inserted into a phylogenetic tree from a feature- +table. Some fragments computed by e.g. Deblur or DADA2 are too remote to +get inserted by SEPP into a reference phylogeny. To be able to use the +feature-table for downstream analyses like computing Faith's PD or UniFrac, +the feature-table must be cleared of fragments that are not part of the +phylogenetic tree, because their path length can otherwise not be +determined. Typically, the number of rejected fragments is low (<= 10), but +it might be worth to inspect the ratio of reads assigned to those rejected +fragments. + +Parameters +---------- +table : FeatureTable[Frequency] + A feature-table which needs to filtered down to those fragments that + are contained in the tree, e.g. result of a Deblur or DADA2 run. +tree : Phylogeny[Rooted] + The tree resulting from inserting fragments into a reference phylogeny, + i.e. the output of function 'sepp' + +Returns +------- +filtered_table : FeatureTable[Frequency] + The input table minus those fragments that were not part of the tree. + This feature-table can be used for downstream analyses like + phylogenetic alpha- or beta- diversity computation. +removed_table : FeatureTable[Frequency] + Those fragments that got removed from the input table, because they + were not part of the tree. This table is mainly used for quality + control, e.g. to inspect the ratio of removed reads per sample from the + input table. You can ignore this table for downstream analyses. + ]]></help> + <macros> + <import>qiime_citation.xml</import> + </macros> + <expand macro="qiime_citation"/> +</tool> \ No newline at end of file