Mercurial > repos > ebi-gxa > sccaf_asses
annotate sccaf_macros.xml @ 1:37a4c22f600b draft default tip
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 7034937deaaf56b2e6f585bb28234a86a5b5fa2e
| author | ebi-gxa |
|---|---|
| date | Mon, 25 Nov 2019 06:28:06 -0500 |
| parents | 95670267a5b6 |
| children |
| rev | line source |
|---|---|
|
0
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
1 <macros> |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
2 <xml name="requirements"> |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
3 <requirements> |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
4 <requirement type="package" version="@TOOL_VERSION@">sccaf</requirement> |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
5 </requirements> |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
6 </xml> |
|
1
37a4c22f600b
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 7034937deaaf56b2e6f585bb28234a86a5b5fa2e
ebi-gxa
parents:
0
diff
changeset
|
7 <token name="@TOOL_VERSION@">0.0.9</token> |
|
0
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
8 <token name="@SCCAF_INTRO@"> |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
9 SCCAF explained |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
10 =============== |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
11 |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
12 Single Cell Clustering Assessment Framework (SCCAF) is a novel method for |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
13 automated identification of putative cell types from single cell RNA-seq |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
14 (scRNA-seq) data. By iteratively applying clustering and a machine learning |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
15 approach to gene expression profiles of a given set of cells, SCCAF |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
16 simultaneously identifies distinct cell groups and a weighted list of feature |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
17 genes for each group. The feature genes, which are overexpressed in the |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
18 particular cell group, jointly discriminate the given cell group from other |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
19 cells. Each such group of cells corresponds to a putative cell type or state, |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
20 characterised by the feature genes as markers. |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
21 </token> |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
22 <token name="@HELP@">More information can be found at https://github.com/SCCAF/SCCAF</token> |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
23 <token name="@PLOT_OPTS@"> |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
24 #if $do_plotting.plot |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
25 -P output.png |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
26 --projectio $do_plotting.projection |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
27 --components $do_plotting.components |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
28 #if $do_plotting.color_by |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
29 --color-by $do_plotting.color_by |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
30 #end if |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
31 #if $do_plotting.groups |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
32 --group $do_plotting.groups |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
33 #end if |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
34 #if $do_plotting.use_raw |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
35 --use-raw |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
36 #end if |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
37 #if $do_plotting.palette |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
38 --palette $do_plotting.palette |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
39 #end if |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
40 #if $do_plotting.show_edges |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
41 --edges |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
42 #end if |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
43 #if $do_plotting.show_arrows |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
44 --arrows |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
45 #end if |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
46 #if not $do_plotting.color_order |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
47 --no-sort-order |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
48 #end if |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
49 #if $do_plotting.omit_frame |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
50 --frameoff |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
51 #end if |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
52 #end if |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
53 </token> |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
54 <xml name="citations"> |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
55 <citations> |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
56 <citation type="doi"></citation> |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
57 <citation type="bibtex"> |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
58 @misc{githubsccaf, |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
59 author = {Miao, Zhichao}, |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
60 year = {2018}, |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
61 title = {SCCAF}, |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
62 publisher = {GitHub}, |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
63 journal = {GitHub repository}, |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
64 url = {https://github.com/Functional-Genomics/SCCAF}, |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
65 }</citation> |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
66 <yield /> |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
67 </citations> |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
68 </xml> |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
69 <xml name="input_object_params"> |
|
1
37a4c22f600b
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 7034937deaaf56b2e6f585bb28234a86a5b5fa2e
ebi-gxa
parents:
0
diff
changeset
|
70 <param name="input_obj_file" argument="--input-object-file" type="data" format="h5,h5ad" label="Input object in AnnData hdf5 format" help="Normally the result of Scanpy (or equivalent), which already has both a visualisation (either tSNE, UMAP or PCA - needed) and clustering (ideally) pre-computed."/> |
|
0
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
71 </xml> |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
72 <xml name="output_object_params"> |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
73 <param name="output_format" argument="--output-format" type="select" label="Format of output object"> |
|
1
37a4c22f600b
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 7034937deaaf56b2e6f585bb28234a86a5b5fa2e
ebi-gxa
parents:
0
diff
changeset
|
74 <option value="anndata_h5ad" selected="true">AnnData format hdf5</option> |
|
37a4c22f600b
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 7034937deaaf56b2e6f585bb28234a86a5b5fa2e
ebi-gxa
parents:
0
diff
changeset
|
75 <option value="anndata">AnnData format (h5 for older versions)</option> |
|
0
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
76 </param> |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
77 </xml> |
|
1
37a4c22f600b
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 7034937deaaf56b2e6f585bb28234a86a5b5fa2e
ebi-gxa
parents:
0
diff
changeset
|
78 <xml name="output_data_obj" token_description="operation"> |
|
37a4c22f600b
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 7034937deaaf56b2e6f585bb28234a86a5b5fa2e
ebi-gxa
parents:
0
diff
changeset
|
79 <data name="output_h5ad" format="h5ad" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData"> |
|
37a4c22f600b
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 7034937deaaf56b2e6f585bb28234a86a5b5fa2e
ebi-gxa
parents:
0
diff
changeset
|
80 <filter>output_format == 'anndata_h5ad'</filter> |
|
37a4c22f600b
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 7034937deaaf56b2e6f585bb28234a86a5b5fa2e
ebi-gxa
parents:
0
diff
changeset
|
81 </data> |
|
37a4c22f600b
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 7034937deaaf56b2e6f585bb28234a86a5b5fa2e
ebi-gxa
parents:
0
diff
changeset
|
82 <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData"> |
|
37a4c22f600b
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 7034937deaaf56b2e6f585bb28234a86a5b5fa2e
ebi-gxa
parents:
0
diff
changeset
|
83 <filter>output_format == 'anndata'</filter> |
|
37a4c22f600b
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 7034937deaaf56b2e6f585bb28234a86a5b5fa2e
ebi-gxa
parents:
0
diff
changeset
|
84 </data> |
|
37a4c22f600b
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 7034937deaaf56b2e6f585bb28234a86a5b5fa2e
ebi-gxa
parents:
0
diff
changeset
|
85 </xml> |
|
0
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
86 <xml name="output_plot_params"> |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
87 <param name="color_by" argument="--color-by" type="text" value="n_genes" label="Color by attributes, comma separated strings"/> |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
88 <param name="groups" argument="--groups" type="text" optional="ture" label="Restrict plotting to named groups, comma separated strings"/> |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
89 <param name="projection" argument="--projection" type="select" label="Plot projection"> |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
90 <option value="2d" selected="true">2D</option> |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
91 <option value="3d">3D</option> |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
92 </param> |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
93 <param name="components" argument="--components" type="text" value="1,2" label="Components to plot, comma separated integers"/> |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
94 <param name="palette" argument="--palette" type="text" optional="true" label="Palette"/> |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
95 <param name="use_raw" argument="--use-raw" type="boolean" checked="false" label="Use raw attributes if present"/> |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
96 <param name="show_edges" argument="--edges" type="boolean" checked="false" label="Show edges"/> |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
97 <param name="show_arrows" argument="--arrows" type="boolean" checked="false" label="Show arrows"/> |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
98 <param name="color_order" argument="--no-sort-order" type="boolean" checked="true" label="Element with high color-by value plot on top"/> |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
99 <param name="omit_frame" argument="--frameoff" type="boolean" checked="false" label="Show frame"/> |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
100 </xml> |
|
95670267a5b6
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
diff
changeset
|
101 </macros> |