Mercurial > repos > iuc > freyja_demix
diff freyja_demix.xml @ 0:fc6252e78d5b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
author | iuc |
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date | Thu, 28 Jul 2022 09:26:02 +0000 |
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children | c0a0e79d7196 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/freyja_demix.xml Thu Jul 28 09:26:02 2022 +0000 @@ -0,0 +1,146 @@ +<tool id="freyja_demix" name="Freyja: Demix" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" + profile="@PROFILE@"> + <description> + lineage abundances + </description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="biotools"/> + <expand macro="requirements"> + <requirement type="package" version="4.7">sed</requirement> + </expand> + <expand macro="version"/> + <command detect_errors="exit_code"><![CDATA[ +@RUN_FREYJA_UPDATE_COMMAND@ +#if str($sample_name.source) == 'auto': + #set $sn = $variants_in.element_identifier +#else: + #set $sn = str($sample_name.name) +#end if +#set $in_file = $sn.replace(' ', '_') + '.' + $variants_in.ext +ln -s '$variants_in' $in_file && +freyja demix + '$in_file' + '$depth_file' + #if $eps + --eps $eps + #end if + #if $meta + --meta '$meta' + #end if + $confirmedonly + @CUSTOM_BARCODES_COMMAND@ + --covcut $depth_cutoff + --output abundances_raw.tsv && +sed 's/$in_file/$sn/' abundances_raw.tsv > abundances.tsv + ]]></command> + <inputs> + <param name="variants_in" type="data" format="tabular" + label="Dataset with input variant calls" + help="This can be a VCF dataset, or the tabular calls output of freayja call or ivar variants."/> + <conditional name="sample_name"> + <param name="source" type="select" label="Set sample name" + help="Select autodetect to have the dataset or collection element name used as the sample name, or, for a single input dataset, provide an explicit sample name."> + <option value="auto">Autodetect sample name</option> + <option value="manual">Specify sample name explicitly</option> + </param> + <when value="auto"/> + <when value="manual"> + <param name="name" type="text" label="Name of the sample"/> + </when> + </conditional> + <expand macro="demixing_common_options"/> + <param name="depth_cutoff" argument="--covcut" type="integer" min="0" value="10" + multiple="true" + label="Depth cutoff for coverage estimate" + help="In the result file the coverage value will provide the 10x coverage estimate (percent of sites with 10 or greater reads- 10 is the default but can be modfied in this field. "/> + </inputs> + <outputs> + <data name="abundances" format="tabular" + label="${tool.name} on ${on_string}: Lineages abundances summary" + from_work_dir="abundances.tsv"/> + </outputs> + <tests> + <!-- Test 01: manual name sample --> + <test expect_num_outputs="1"> + <param name="variants_in" value="variants.tsv"/> + <param name="depth_file" value="depths.tsv"/> + <conditional name="usher_update_option"> + <param name="choice" value="repo"/> + </conditional> + <conditional name="sample_name"> + <param name="source" value="manual"/> + <param name="name" value="samplename"/> + </conditional> + <output name="abundances" ftype="tabular"> + <assert_contents> + <has_text text="samplename"/> + </assert_contents> + </output> + </test> + <!-- Test 02: autoname sample --> + <test expect_num_outputs="1"> + <param name="variants_in" value="variants.tsv"/> + <param name="depth_file" value="depths.tsv"/> + <conditional name="usher_update_option"> + <param name="choice" value="repo"/> + </conditional> + <conditional name="sample_name"> + <param name="source" value="auto"/> + </conditional> + <output name="abundances" ftype="tabular"> + <assert_contents> + <has_text text="summarized"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +@HELP_HEADER@ + +**Freyja demix** estimates lineage abundances in a potentially multi-lineage input sample. + +Inputs +====== + +The tool requires as input a dataset with called variants and a dataset with genome-wide sequencing depth information. +Both types of data can be produced with *Freyja call*, but the tool accepts variant calls also in VCF format. + +Note +---- + +For single samples it is recommended to select "Specify sample name explicitly" +under "Set sample name". + +To use this tool on multiple samples in parallel, please provide two +collections in the same sample sort order - one with the variant calls, the +other one with the sequencing depths - and select "Autodetect sample name", +which will use collection element identifiers as the names of the samples. +This will produce a new collection of demixing reports that can be passed to +*Freyja: Aggregate and visualize* with sample names preserved. + +Selection of multiple regular called variants and depth datasets is discouraged +since proper dataset pairing cannot be guaranteed! + +Outputs +======= + +The tool produces tabular output that includes the lineages detected in the sample, their corresponding abundances, and a lineage summary by constellation. + +Example output: + +========== =================================================== + filename +summarized [('Delta', 0.65), ('Other', 0.25), ('Alpha', 0.1')] +lineages ['B.1.617.2' 'B.1.2' 'AY.6' 'Q.3'] +abundances "[0.5 0.25 0.15 0.1]" +resid 3.14159 +coverage 95.8 +========== =================================================== + + +Where *summarized* denotes a sum of all lineage abundances in a particular WHO designation (i.e. B.1.617.2 and AY.6 abundances are summed in the above example), otherwise they are grouped into "Other". The *lineage* array lists the identified lineages in descending order, and *abundances* contains the corresponding abundances estimates. The value of *resid* corresponds to the residual of the weighted least absolute devation problem used to estimate lineage abundances. The *coverage* value provides the 10x coverage estimate (percent of sites with 10 or greater reads- 10 is the default but can be modfied using the *--covcut* option). + ]]></help> + <expand macro="citations"/> +</tool>