Mercurial > repos > ebi-gxa > scmap_scmap_cell
annotate scmap_scmap_cell.xml @ 6:35d8f7d62659 draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit f1d792b2db8e09e441cc75629d34a13e4fb19153"
| author | ebi-gxa |
|---|---|
| date | Mon, 04 May 2020 07:14:30 -0400 |
| parents | 19f2fc7a8920 |
| children | 5e6d54e2ab89 |
| rev | line source |
|---|---|
|
4
19f2fc7a8920
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6e7bba7c35bcd8d18c53ca8c51f1699f62e2a836"
ebi-gxa
parents:
2
diff
changeset
|
1 <tool id="scmap_scmap_cell" name="Scmap cell projection" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> |
|
0
cb6b70d45519
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
2 <description>searches each cell in a query dataset for the nearest neighbours by cosine distance within a collection of reference datasets.</description> |
|
cb6b70d45519
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
3 <macros> |
|
cb6b70d45519
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
4 <import>scmap_macros.xml</import> |
|
cb6b70d45519
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
5 </macros> |
|
cb6b70d45519
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
6 <expand macro="requirements" /> |
|
cb6b70d45519
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
7 <command detect_errors="exit_code"><![CDATA[ |
|
cb6b70d45519
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
8 scmap-scmap-cell.R |
|
cb6b70d45519
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
9 -i '$index_single_cell_experiment' |
|
cb6b70d45519
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
10 -p '$project_single_cell_experiment' |
|
cb6b70d45519
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
11 --number-nearest-neighbours '$n_nearest_neighbours' |
|
cb6b70d45519
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
12 --cluster-col '${cluster_projection.cluster_col}' |
|
cb6b70d45519
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
13 --output-object-file '$output_single_cell_experiment' |
|
cb6b70d45519
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
14 --closest-cells-text-file '$closest_cells_text_file' |
|
cb6b70d45519
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
15 --closest-cells-similarities-text-file '$closest_cells_similarities_text_file' |
|
cb6b70d45519
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
16 #if $cluster_projection |
|
cb6b70d45519
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
17 --output-clusters-text-file '$closest_cells_clusters_csv' |
|
cb6b70d45519
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
18 #end if |
|
cb6b70d45519
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
19 ]]></command> |
|
cb6b70d45519
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
20 <inputs> |
|
cb6b70d45519
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
21 <param type="data" name="index_single_cell_experiment" label="Index SingleCellExperiment object" format="rdata" help="File with serialized SingleCellExperiment object as produced by 'scmap select features' and 'scmap index clusters', onto which another dataset will be projected." /> |
|
cb6b70d45519
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
22 <param type="data" name="project_single_cell_experiment" label="SingleCellExperiment object to project" format="rdata" help="File with serialized SingleCellExperiment object to project onto the index'" /> |
|
cb6b70d45519
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
23 <param name="n_nearest_neighbours" type="integer" label="Number of nearest neighbours" value='5' help="A positive integer specifying the number of nearest neighbours to find" /> |
|
cb6b70d45519
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
24 |
|
cb6b70d45519
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
25 <conditional name="cluster_projection"> |
|
cb6b70d45519
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
26 <param name="cluster_projection" type="boolean" checked="false" label="Annotate cells of the projection dataset using labels of the reference?" help="If cell cluster annotation is available for the reference datasets, in addition to finding top 10 nearest neighbours scmap-cell also allows to annotate cells of the projection dataset using labels of the reference."/> |
|
cb6b70d45519
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
27 <when value="true" > |
|
cb6b70d45519
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
28 <param name="cluster_col" type="text" label="Cluster column" value="cell_type1" help="Column name in the 'colData' slot of the SingleCellExperiment object containing the cell classification information." /> |
|
cb6b70d45519
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
29 </when> |
|
cb6b70d45519
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
30 <when value="false" > |
|
cb6b70d45519
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
31 <param name="cluster_col" type="hidden" value="NULL" /> |
|
cb6b70d45519
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
32 </when> |
|
cb6b70d45519
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
33 </conditional> |
|
cb6b70d45519
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
34 </inputs> |
|
cb6b70d45519
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
35 <outputs> |
|
cb6b70d45519
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
36 <data name="output_single_cell_experiment" format="rdata" /> |
|
cb6b70d45519
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
37 <data name="closest_cells_text_file" format="csv" /> |
|
cb6b70d45519
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
38 <data name="closest_cells_similarities_text_file" format="csv" /> |
|
cb6b70d45519
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
39 <data name="closest_cells_clusters_csv" format="csv"> |
|
cb6b70d45519
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
40 <filter>cluster_projection == "true"</filter> |
|
cb6b70d45519
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
41 </data> |
|
cb6b70d45519
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
42 </outputs> |
|
cb6b70d45519
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
43 <tests> |
|
cb6b70d45519
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
44 <test> |
|
cb6b70d45519
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
45 <param name="index_single_cell_experiment" value="index_cell.rds" ftype="rdata"/> |
|
cb6b70d45519
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
46 <param name="project_single_cell_experiment" value="test_sce.rds" ftype="rdata"/> |
|
cb6b70d45519
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
47 <param name="cluster_projection" value="true" ftype="rdata"/> |
|
2
2b85cec412c3
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
ebi-gxa
parents:
0
diff
changeset
|
48 <output name="output_single_cell_experiment" file="closest_cells_clusters.rds" compare="sim_size"/> |
|
2b85cec412c3
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
ebi-gxa
parents:
0
diff
changeset
|
49 <output name="closest_cells_clusters_csv" file="closest_cells_clusters.csv" compare="sim_size" /> |
|
2b85cec412c3
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
ebi-gxa
parents:
0
diff
changeset
|
50 <output name="closest_cells_text_file" file="closest_cells.csv" compare="sim_size"/> |
|
2b85cec412c3
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
ebi-gxa
parents:
0
diff
changeset
|
51 <output name="closest_cells_similarities_text_file" file="closest_cells_similarities.csv" compare="sim_size"/> |
|
0
cb6b70d45519
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
52 </test> |
|
cb6b70d45519
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
53 </tests> |
|
cb6b70d45519
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
54 <help><![CDATA[ |
|
cb6b70d45519
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
55 @HELP@ |
|
cb6b70d45519
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
56 |
|
cb6b70d45519
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
57 @VERSION_HISTORY@ |
|
cb6b70d45519
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
58 ]]></help> |
|
cb6b70d45519
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
59 <expand macro="citations" /> |
|
cb6b70d45519
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
60 </tool> |