Mercurial > repos > ebi-gxa > scanpy_multiplet_scrublet

comparison scanpy-multiplet-scrublet.xml @ 5:b8126b3bf5d0 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6c9d530aa653101e9e21804393ec11f38cddf027-dirty
author ebi-gxa
date Thu, 16 Feb 2023 13:29:18 +0000
parents 8ca3ab8300ce
children fadc4fbf8025
comparison
equal deleted inserted replaced
4:8ca3ab8300ce 5:b8126b3bf5d0
1 <?xml version="1.0" encoding="utf-8"?> 1 <?xml version="1.0" encoding="utf-8"?>
2 <tool id="scanpy_multiplet_scrublet" name="Scanpy Scrublet" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> 2 <tool id="scanpy_multiplet_scrublet" name="Scanpy Scrublet" version="@TOOL_VERSION@+galaxy9" profile="@PROFILE@">
3 <description>remove multiplets from annData objects with Scrublet</description> 3 <description>remove multiplets from annData objects with Scrublet</description>
4 <macros> 4 <macros>
5 <import>scanpy_macros2.xml</import> 5 <import>scanpy_macros2.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
11 #if $threshold 11 #if $threshold
12 --threshold '${threshold}' 12 --threshold '${threshold}'
13 #end if 13 #end if
14 #if $batch_key 14 #if $batch_key
15 --batch-key '${batch_key}' 15 --batch-key '${batch_key}'
16 #else if $sample_key
17 --batch-key '${sample_key}'
16 #end if 18 #end if
17 $filter 19 $filter
18 #if $settings.default == "false" 20 #if $settings.default == "false"
19 #if $settings.n_neighbors 21 #if $settings.n_neighbors
20 --n-neighbours '${settings.n_neighbors}' 22 --n-neighbours '${settings.n_neighbors}'
37 <expand macro="input_object_params"/> 39 <expand macro="input_object_params"/>
38 <expand macro="output_object_params"/> 40 <expand macro="output_object_params"/>
39 <param name="threshold" argument="--threshold" type="float" optional="true" label="Doublet score threshold." help="Threshold for calling a transcriptome a doublet. If not set, this is set automatically by looking for the minimum between the two modes of the doublet_scores_sim_ histogram. It is best practice to check the threshold visually using the doublet_scores_sim_ histogram and/or based on co-localization of predicted doublets in a 2-D embedding."/> 41 <param name="threshold" argument="--threshold" type="float" optional="true" label="Doublet score threshold." help="Threshold for calling a transcriptome a doublet. If not set, this is set automatically by looking for the minimum between the two modes of the doublet_scores_sim_ histogram. It is best practice to check the threshold visually using the doublet_scores_sim_ histogram and/or based on co-localization of predicted doublets in a 2-D embedding."/>
40 <param name="filter" argument="--filter" type="boolean" truevalue="--filter" falsevalue="" checked="False" 42 <param name="filter" argument="--filter" type="boolean" truevalue="--filter" falsevalue="" checked="False"
41 label="Remove predicted multiplets?" help="By default, the output object is annotated but not filtered according to the scrublet status."/> 43 label="Remove predicted multiplets?" help="By default, the output object is annotated but not filtered according to the scrublet status."/>
42 <param name="batch_key" type="text" argument="--batch-key" optional="true" label="Where batches are present, the name of the column in adata.obs that differentiates among experiments/batches."/> 44 <param name="batch_key" type="text" argument="--batch-key" optional="true" label="Where batches are present, the name of the column in adata.obs that differentiates among experiments/batches."/>
45 <param name="sample_key" type="text" argument="--batch-key" optional="true" label="The name of the column in adata.obs that differentiates among samples. This is a convenience for workflows, this is overriden if the batch key is set. It is an Scrubblet best practice to operate per samples rather than on the complete dataset (and it should use less memory)."/>
43 <conditional name="settings"> 46 <conditional name="settings">
44 <param name="default" type="boolean" checked="true" label="Use programme defaults"/> 47 <param name="default" type="boolean" checked="true" label="Use programme defaults"/>
45 <when value="true"/> 48 <when value="true"/>
46 <when value="false"> 49 <when value="false">
47 <param name="sim_doublet_ratio" argument="--sim-doublet-ratio" type="float" value="2.0" label="Number of doublets to simulate relative to the number of observed transcriptomes."/> 50 <param name="sim_doublet_ratio" argument="--sim-doublet-ratio" type="float" value="2.0" label="Number of doublets to simulate relative to the number of observed transcriptomes."/>