Mercurial > repos > ebi-gxa > scmap_scmap_cluster
annotate scmap_scmap_cluster.xml @ 4:6651208d890b draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6e7bba7c35bcd8d18c53ca8c51f1699f62e2a836"
| author | ebi-gxa |
|---|---|
| date | Wed, 29 Apr 2020 10:05:16 -0400 |
| parents | 97922339644a |
| children | 40e10f3a1844 |
| rev | line source |
|---|---|
|
4
6651208d890b
"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_cluster" name="Scmap cluster projection" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> |
|
0
5421e01f640a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
2 <description>projects one dataset to another</description> |
|
5421e01f640a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
3 <macros> |
|
5421e01f640a
"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> |
|
5421e01f640a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
5 </macros> |
|
5421e01f640a
"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" /> |
|
5421e01f640a
"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[ |
|
5421e01f640a
"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-cluster.R --index-object-file '$index_single_cell_experiment' --projection-object-file '$project_single_cell_experiment' --threshold '$threshold' --output-object-file '$output_single_cell_experiment' --output-text-file '$output_txt' |
|
5421e01f640a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
9 ]]></command> |
|
5421e01f640a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
10 <inputs> |
|
5421e01f640a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
11 <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." /> |
|
5421e01f640a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
12 <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'" /> |
|
5421e01f640a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
13 <param name="threshold" type="float" label="Threshold" value="0.7" help="Threshold on similarity (or probability for SVM and RF)." /> |
|
5421e01f640a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
14 </inputs> |
|
5421e01f640a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
15 <outputs> |
|
5421e01f640a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
16 <data name="output_single_cell_experiment" format="rdata" /> |
|
5421e01f640a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
17 <data name="output_txt" format="csv" /> |
|
5421e01f640a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
18 </outputs> |
|
5421e01f640a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
19 <tests> |
|
5421e01f640a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
20 <test> |
|
5421e01f640a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
21 <param name="index_single_cell_experiment" value="index_cluster.rds" ftype="rdata"/> |
|
5421e01f640a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
22 <param name="project_single_cell_experiment" value="test_sce.rds" ftype="rdata"/> |
|
2
97922339644a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
ebi-gxa
parents:
0
diff
changeset
|
23 <output name="output_single_cell_experiment" file="project_cluster.rds" compare="sim_size"/> |
|
97922339644a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
ebi-gxa
parents:
0
diff
changeset
|
24 <output name="output_txt" file="project_cluster.csv" compare="sim_size"/> |
|
0
5421e01f640a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
25 </test> |
|
5421e01f640a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
26 </tests> |
|
5421e01f640a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
27 <help><![CDATA[ |
|
5421e01f640a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
28 @HELP@ |
|
5421e01f640a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
29 |
|
5421e01f640a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
30 @VERSION_HISTORY@ |
|
5421e01f640a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
31 ]]></help> |
|
5421e01f640a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
32 <expand macro="citations" /> |
|
5421e01f640a
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff
changeset
|
33 </tool> |