Mercurial > repos > ebi-gxa > scmap_index_cell

annotate scmap_index_cell.xml @ 5:db43f55890d9 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6e7bba7c35bcd8d18c53ca8c51f1699f62e2a836"
author ebi-gxa
date Wed, 29 Apr 2020 10:07:28 -0400
parents faa50757208d
children 441df83ffc7c
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
db43f55890d9 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6e7bba7c35bcd8d18c53ca8c51f1699f62e2a836"
ebi-gxa
parents: 4
diff changeset
1 <tool id="scmap_index_cell" name="Scmap index cells" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
0
628a433819c6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
2 <description>creates a cell index for a dataset to enable fast approximate nearest neighbour search</description>
628a433819c6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
3 <macros>
628a433819c6 "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>
628a433819c6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
5 </macros>
628a433819c6 "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" />
628a433819c6 "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[
3
5593b0744de9 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
ebi-gxa
parents: 2
diff changeset
8 scmap-preprocess-sce.R --input-object "${input_single_cell_experiment}" --output-sce-object sce_object_preprocessed.rds &&
5593b0744de9 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
ebi-gxa
parents: 2
diff changeset
9 scmap-index-cell.R --input-object-file sce_object_preprocessed.rds --number-chunks '$n_chunks' --number-clusters '$n_clusters' --output-object-file '$output_single_cell_experiment' --random-seed '$random_seed'
5593b0744de9 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
ebi-gxa
parents: 2
diff changeset
10 #if $train_id
5593b0744de9 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
ebi-gxa
parents: 2
diff changeset
11 --train-id '${train_id}'
5593b0744de9 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
ebi-gxa
parents: 2
diff changeset
12 #end if
0
628a433819c6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
13 ]]></command>
628a433819c6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
14 <inputs>
628a433819c6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
15 <param type="data" name="input_single_cell_experiment" label="SingleCellExperiment object" format="rdata" help="File with serialized SingleCellExperiment object as produced by 'scmap select features'" />
628a433819c6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
16 <param name="n_chunks" type="integer" label="Number of chunks" value='' help="Number of chunks into which the expr matrix is split" />
628a433819c6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
17 <param name="n_clusters" type="integer" label="Number of clusters" value='' help="Number of clusters per group for k-means clustering" />
3
5593b0744de9 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
ebi-gxa
parents: 2
diff changeset
18 <param type="text" name="train_id" label="Dataset ID" help="ID of the training dataset" />
0
628a433819c6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
19 <param name="random_seed" type="integer" label="Random seed" value='1' help="scmap-cell contains k-means step which makes it stochastic, i.e. running it multiple times will provide slightly different results. A fixed random seed ensures reproducibility." />
628a433819c6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
20 </inputs>
628a433819c6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
21 <outputs>
628a433819c6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
22 <data name="output_single_cell_experiment" format="rdata" />
628a433819c6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
23 </outputs>
628a433819c6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
24 <tests>
628a433819c6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
25 <test>
628a433819c6 "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="n_chunks" value="50" />
628a433819c6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
27 <param name="n_clusters" value="9" />
628a433819c6 "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="input_single_cell_experiment" value="select_features.rds" ftype="rdata"/>
2
dd2a84734b87 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
ebi-gxa
parents: 1
diff changeset
29 <output name="output_single_cell_experiment" file="index_cell.rds" compare="sim_size"/>
0
628a433819c6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
30 </test>
628a433819c6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
31 </tests>
628a433819c6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
32 <help><![CDATA[
628a433819c6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
33 @HELP@
628a433819c6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
34
628a433819c6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
35 @VERSION_HISTORY@
628a433819c6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
36 ]]></help>
628a433819c6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
37 <expand macro="citations" />
628a433819c6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
38 </tool>