annotate scanpy-multiplet-scrublet.xml @ 0:9f8381c5d808 draft

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
author ebi-gxa
date Thu, 22 Jul 2021 20:57:12 +0000
parents
children 8ca3ab8300ce
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
1 <?xml version="1.0" encoding="utf-8"?>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
2 <tool id="scanpy_multiplet_scrublet" name="Scanpy Scrublet" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
3 <description>remove multiplets from annData objects with Scrublet</description>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
4 <macros>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
5 <import>scanpy_macros2.xml</import>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
6 </macros>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
7 <expand macro="requirements"/>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
8 <command detect_errors="exit_code"><![CDATA[
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
9 ln -s '${input_obj_file}' input.h5 &&
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
10 PYTHONIOENCODING=utf-8 scanpy-multiplet scrublet
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
11 #if $threshold
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
12 --threshold '${threshold}'
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
13 #end if
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
14 #if $batch_key
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
15 --batch-key '${batch_key}'
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
16 #end if
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
17 $filter
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
18 #if $settings.default == "false"
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
19 #if $settings.n_neighbors
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
20 --n-neighbours '${settings.n_neighbors}'
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
21 #end if
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
22 --sim-doublet-ratio '${settings.sim_doublet_ratio}'
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
23 --synthetic-doublet-umi-subsampling '${settings.synthetic_doublet_umi_subsampling}'
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
24 --expected-doublet-rate '${settings.expected_doublet_rate}'
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
25 --stdev-doublet-rate '${settings.stdev_doublet_rate}'
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
26 --knn-dist-metric "${settings.knn_dist_metric}"
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
27 --n-pcs '${settings.n_pcs}'
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
28 --random-state '${settings.random_state}'
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
29 ${settings.normalise_variance} ${settings.log_transform} ${settings.mean_center}
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
30 ${settings.approx} ${settings.get_doublet_neighbor_parents}
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
31 #end if
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
32 @INPUT_OPTS@
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
33 @OUTPUT_OPTS@
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
34 ]]></command>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
35
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
36 <inputs>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
37 <expand macro="input_object_params"/>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
38 <expand macro="output_object_params"/>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
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."/>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
40 <param name="filter" argument="--filter" type="boolean" truevalue="--filter" falsevalue="" checked="False"
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
41 label="Remove predicted multiplets?" help="By default, the output object is annotated but not filtered according to the scrublet status."/>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
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."/>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
43 <conditional name="settings">
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
44 <param name="default" type="boolean" checked="true" label="Use programme defaults"/>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
45 <when value="true"/>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
46 <when value="false">
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
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."/>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
48 <param name="synthetic_doublet_umi_subsampling" argument="--synthetic-doublet-umi-subsampling" type="float" value="1.0" label="Rate for sampling UMIs when creating synthetic doublets." help="If 1.0, each doublet is created by simply adding the UMI counts from two randomly sampled observed transcriptomes. For values less than 1, the UMI counts are added and then randomly sampled at the specified rate."/>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
49 <param name="expected_doublet_rate" argument="--expected-doublet-rate" type="float" value="0.05" label="Estimated doublet rate for the experiment."/>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
50 <param name="stdev_doublet_rate" argument="--stdev-doublet-rate" type="float" value="0.02" label="Uncertainty in the expected doublet rate."/>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
51 <param name="knn_dist_metric" argument="--knn-dist-metric" type="select" label="A known metric’s name.">
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
52 <option value="euclidean" selected="true">Euclidean</option>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
53 <option value="angular">angular</option>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
54 <option value="cityblock">cityblock</option>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
55 <option value="cosine">cosine</option>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
56 <option value="l1">l1</option>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
57 <option value="l2">l2</option>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
58 <option value="manhattan">manhattan</option>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
59 <option value="braycurtis">braycurtis</option>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
60 <option value="canberra">canberra</option>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
61 <option value="chebyshev">chebyshev</option>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
62 <option value="correlation">correlation</option>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
63 <option value="dice">dice</option>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
64 <option value="hamming">hamming</option>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
65 <option value="jaccard">jaccard</option>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
66 <option value="kulsinski">kulsinski</option>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
67 <option value="mahalanobis">mahalanobis</option>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
68 <option value="minkowski">minkowski</option>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
69 <option value="rogerstanimoto">rogerstanimoto</option>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
70 <option value="russelrao">russelrao</option>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
71 <option value="seuclidan">seuclidian</option>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
72 <option value="sokalmichener">sokalmichener</option>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
73 <option value="sokalsneath">sokalsneath</option>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
74 <option value="sqeuclidean">sqeuclidean</option>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
75 <option value="yule">yule</option>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
76 </param>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
77 <param name="normalise_variance" argument="--no-normalize-variance" type="boolean" truevalue="" falsevalue="--no-normalize-variance" checked="True"
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
78 label="Normalize the data such that each gene has a variance of 1?" help="klearn.decomposition.TruncatedSVD will be used for dimensionality reduction, if --no-mean-center is set. Use this flag to disable that behaviour." />
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
79 <param name="log_transform" argument="--log-transform" type="boolean" truevalue="--log-transform" falsevalue="" checked="False"
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
80 label="Apply log transform?" help="Whether to use :func:~scanpy.pp.log1p to log-transform the data prior to PCA."/>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
81 <param name="mean_center" argument="--no-mean-center" type="boolean" truevalue="" falsevalue="--no-mean-center" checked="True"
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
82 label="Center the data such that each gene has a mean of 0" help="sklearn.decomposition.PCA will be used for dimensionality reduction."/>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
83 <param name="n_pcs" argument="--n-pcs" type="integer" value="30" optional="true" label="Number of principal components." help="Used to embed the transcriptomes prior to k-nearest-neighbor graph construction."/>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
84 <param name="approx" argument="--no-approx" type="boolean" truevalue="" falsevalue="--no-approx" checked="True"
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
85 label="Use approximate nearest neighbor (annoy) method for the KNN classifier"/>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
86 <param name="get_doublet_neighbor_parents" argument="--get-doublet-neighbor-parents" type="boolean" truevalue="--get-doublet-neighbor-parents " falsevalue="" checked="False"
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
87 label="Get doublet neighbor parents" help="Return (in .uns) the parent transcriptomes that generated the doublet neighbors of each observed transcriptome. This information can be used to infer the cell states that generated a given doublet state."/>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
88 <param name="n_neighbors" argument="--n-neighbors" type="integer" optional="true" label="Number of neighbors." help="Used to construct the KNN graph of observed transcriptomes and simulated doublets. If not set, this is automatically set to np.round(0.5 * np.sqrt(n_obs))."/>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
89 <param name="random_state" argument="--random-state" type="integer" value="0" label="Seed for random number generator." />
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
90 </when>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
91 </conditional>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
92 </inputs>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
93
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
94 <outputs>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
95 <expand macro="output_data_obj" description="Scrublet-processed annData"/>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
96 </outputs>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
97
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
98 <tests>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
99 <test>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
100 <param name="input_obj_file" value="read_10x.h5"/>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
101 <param name="input_format" value="anndata"/>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
102 <param name="output_format" value="anndata"/>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
103 <output name="output_h5" file="scrublet.h5" ftype="h5" compare="sim_size"/>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
104 </test>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
105 </tests>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
106
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
107 <help><![CDATA[
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
108 .. class:: infomark
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
109
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
110 **What it does**
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
111
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
112 Predict cell doublets using a nearest-neighbor classifier of observed transcriptomes and simulated doublets. Works best if the input is a raw (unnormalized) counts matrix from a single sample or a collection of similar samples from the same experiment. This function is a wrapper around functions that pre-process using Scanpy and directly call functions of Scrublet().
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
113
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
114 This is a wrapper around the Scanpy wrapper for Scrublet- see https://scanpy.readthedocs.io/en/docsearch/external/scanpy.external.pp.scrublet.html.
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
115
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
116 @HELP@
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
117
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
118 @VERSION_HISTORY@
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
119 ]]></help>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
120 <expand macro="citations"/>
9f8381c5d808 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
ebi-gxa
parents:
diff changeset
121 </tool>