Mercurial > repos > ebi-gxa > ct_get_empirical_dist

annotate ct_get_empirical_dist.xml @ 5:a749b4edecd6 draft default tip

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 8c1bd2ab8a3f988e205677a3bb1ffda1e5694fe1"
author ebi-gxa
date Wed, 17 Jun 2020 16:27:54 +0000
parents 44a6618cce59
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
44a6618cce59 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 85476ee7f3b1d96e9d0afb972af1aaa67d990ce4"
ebi-gxa
parents: 3
diff changeset
1 <tool id="ct_get_empirical_dist" name="Cell types - get empirical distribution" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
0
db3efb377894 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
2 <description>Get empirical distribution for tool performance table</description>
db3efb377894 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
3 <macros>
db3efb377894 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
4 <import>ct_macros.xml</import>
db3efb377894 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
5 </macros>
db3efb377894 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
6 <expand macro="requirements" />
db3efb377894 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
7 <command detect_errors="exit_code"><![CDATA[
db3efb377894 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
8
2
1758678269cb "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
ebi-gxa
parents: 0
diff changeset
9 ln -s $'${ontology_graph}' cl-basic.obo;
1758678269cb "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
ebi-gxa
parents: 0
diff changeset
10
1758678269cb "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
ebi-gxa
parents: 0
diff changeset
11 get_empirical_dist.R --input-ref-file "${input_ref_file}" --label-column-ref "${label_col_ref}" --lab-cl-mapping "${lab_cl_mapping}" --num-iterations "${num_iter}" --num-cores \${GALAXY_SLOTS:-1} --ontology-graph cl-basic.obo --output-path "${output_list_path}"
0
db3efb377894 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
12
2
1758678269cb "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
ebi-gxa
parents: 0
diff changeset
13 #if $parallel
1758678269cb "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
ebi-gxa
parents: 0
diff changeset
14 --parallel "${parallel}"
1758678269cb "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
ebi-gxa
parents: 0
diff changeset
15 #end if
5
a749b4edecd6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8c1bd2ab8a3f988e205677a3bb1ffda1e5694fe1"
ebi-gxa
parents: 4
diff changeset
16 #if $sample_labs
a749b4edecd6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8c1bd2ab8a3f988e205677a3bb1ffda1e5694fe1"
ebi-gxa
parents: 4
diff changeset
17 --sample-labs "${sample_labs}"
a749b4edecd6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8c1bd2ab8a3f988e205677a3bb1ffda1e5694fe1"
ebi-gxa
parents: 4
diff changeset
18 #end if
2
1758678269cb "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
ebi-gxa
parents: 0
diff changeset
19 #if $exclusions
1758678269cb "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
ebi-gxa
parents: 0
diff changeset
20 --exclusions "${exclusions}"
1758678269cb "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
ebi-gxa
parents: 0
diff changeset
21 #end if
5
a749b4edecd6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8c1bd2ab8a3f988e205677a3bb1ffda1e5694fe1"
ebi-gxa
parents: 4
diff changeset
22 #if $sem_sim_metric
2
1758678269cb "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
ebi-gxa
parents: 0
diff changeset
23 --semantic-sim-metric "${sem_sim_metric}"
1758678269cb "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
ebi-gxa
parents: 0
diff changeset
24 #end if
1758678269cb "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
ebi-gxa
parents: 0
diff changeset
25 ]]></command>
0
db3efb377894 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
26 <inputs>
3
6fc67b8caa21 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c6a3af3aa798c106d1a8f3e2bf1aef5251d0bb7e"
ebi-gxa
parents: 2
diff changeset
27 <param type="data" name="input_ref_file" label="Input reference file" format="txt" help="Text file with reference cell labels" />
0
db3efb377894 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
28 <param type="data" name="exclusions" format="yml" label="Exclusions file" help="YML file with excluded/unlabelled terms" />
db3efb377894 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
29 <param type="text" name="label_col_ref" label="Reference label column" value="cell_type" help="Label column in reference file" />
5
a749b4edecd6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8c1bd2ab8a3f988e205677a3bb1ffda1e5694fe1"
ebi-gxa
parents: 4
diff changeset
30 <param type="text" name="tmpdir" label="Tmpdir for caching" optional="true" help="Temporary directory for caching" />
0
db3efb377894 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
31 <param type="data" name="lab_cl_mapping" label="Label - CL term mapping" format="rdata" help="Mapping between cell labels and ontology terms" />
db3efb377894 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
32 <param type="boolean" name="parallel" label="Parallel execution" checked="false" help="Should the table values be computed in parallel?" />
db3efb377894 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
33 <param type="integer" name="num_iter" value='5' label="Number of iterations" help="Number of simulations to generate empirical CDF" />
5
a749b4edecd6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8c1bd2ab8a3f988e205677a3bb1ffda1e5694fe1"
ebi-gxa
parents: 4
diff changeset
34 <param type="integer" name="sample_labs" value='50' label="Number of labels to sample" help="Numbre of labels to sample for each permutation" />
a749b4edecd6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8c1bd2ab8a3f988e205677a3bb1ffda1e5694fe1"
ebi-gxa
parents: 4
diff changeset
35 <param type="data" name="ontology_graph" label="Ontology graph" format="obo" optional="true" help="Ontology graph to run semantis similarity computations" />
a749b4edecd6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8c1bd2ab8a3f988e205677a3bb1ffda1e5694fe1"
ebi-gxa
parents: 4
diff changeset
36 <expand macro="sem_siml_options" />
0
db3efb377894 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
37 </inputs>
db3efb377894 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
38 <outputs>
db3efb377894 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
39 <data name="output_list_path" format="rdata" />
db3efb377894 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
40 </outputs>
db3efb377894 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
41 <tests>
db3efb377894 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
42 <test>
db3efb377894 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
43 <param name="input_ref_file" value="reference_sdrf.tsv" />
db3efb377894 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
44 <param name="label_col_ref" value="Sample.Characteristic.cell.type." />
db3efb377894 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
45 <param name="ontology_graph" value="cl-basic.obo" />
db3efb377894 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
46 <param name="exclusions" value="exclusions.yml" />
db3efb377894 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
47 <param name="parallel" value="TRUE" />
db3efb377894 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
48 <param name="lab_cl_mapping" value="label_cl_dict.rds" />
db3efb377894 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
49 <output name="output_list_path" file="empirical_dist_list.rds" compare="sim_size" />
db3efb377894 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
50 </test>
db3efb377894 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
51 </tests>
db3efb377894 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
52 <help><![CDATA[
db3efb377894 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
53 @HELP@
db3efb377894 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
54
db3efb377894 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
55 @VERSION_HISTORY@
db3efb377894 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
56 ]]></help>
db3efb377894 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
57 <expand macro="citations" />
db3efb377894 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
ebi-gxa
parents:
diff changeset
58 </tool>