annotate scmap_get_std_output.xml @ 3:3370352d1f85 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 09:55:17 -0400
parents 0cb98597934b
children 0d713384d8d8
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
3370352d1f85 "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_get_std_output" name="Scmap get standard output" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
0
5f95950c3959 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
ebi-gxa
parents:
diff changeset
2 <description>Create final output in standard format to allow for downstream analysis of predicted labels by tools of the EBI gene expression group's cell-types-analysis package</description>
5f95950c3959 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
ebi-gxa
parents:
diff changeset
3 <macros>
5f95950c3959 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
ebi-gxa
parents:
diff changeset
4 <import>scmap_macros.xml</import>
5f95950c3959 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
ebi-gxa
parents:
diff changeset
5 </macros>
5f95950c3959 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
ebi-gxa
parents:
diff changeset
6 <expand macro="requirements" />
5f95950c3959 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
ebi-gxa
parents:
diff changeset
7 <command detect_errors="exit_code"><![CDATA[
1
656c588b718c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
ebi-gxa
parents: 0
diff changeset
8 scmap_get_std_output.R --predictions-file "${input_predictions_file}" --output-table "${output_predictions_file}" --include-scores "${include_scores}" --index '${index}' --tool '${tool}' --sim-col-name "${sim_col_name}"
0
5f95950c3959 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
ebi-gxa
parents:
diff changeset
9 ]]></command>
5f95950c3959 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
ebi-gxa
parents:
diff changeset
10 <inputs>
5f95950c3959 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
ebi-gxa
parents:
diff changeset
11 <param type="data" name="input_predictions_file" label="Scmap predictions file in text format" format="txt" help="Path to the predictions file in text format" />
5f95950c3959 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
ebi-gxa
parents:
diff changeset
12 <param type="boolean" name="include_scores" checked="false" label="Should prediction scores be included?" help="Boolean indicating whether similarity scores should be included in the final output" />
1
656c588b718c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
ebi-gxa
parents: 0
diff changeset
13 <param type="data" name="index" label="Scmap index object" format="rdata" help="Scmap index object in rdata format" />
656c588b718c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
ebi-gxa
parents: 0
diff changeset
14 <param type="select" name="tool" label="Tool used (cell/cluster)" help="What tool was used - scmap-cell or scmap-cluster?">
656c588b718c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
ebi-gxa
parents: 0
diff changeset
15 <option value="scmap-cell">Scmap-cell</option>
656c588b718c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
ebi-gxa
parents: 0
diff changeset
16 <option value="scmap-cluster">Scmap-cluster</option>
656c588b718c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
ebi-gxa
parents: 0
diff changeset
17 </param>
0
5f95950c3959 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
ebi-gxa
parents:
diff changeset
18 <param type="text" name="sim_col_name" value="scmap_cluster_siml" label="Column name of similarity scores" help="Name of column that contains distances between clusters/cells" />
5f95950c3959 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
ebi-gxa
parents:
diff changeset
19 </inputs>
5f95950c3959 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
ebi-gxa
parents:
diff changeset
20 <outputs>
5f95950c3959 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
ebi-gxa
parents:
diff changeset
21 <data name="output_predictions_file" format="txt" />
5f95950c3959 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
ebi-gxa
parents:
diff changeset
22 </outputs>
5f95950c3959 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
ebi-gxa
parents:
diff changeset
23 <tests>
5f95950c3959 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
ebi-gxa
parents:
diff changeset
24 <test>
5f95950c3959 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
ebi-gxa
parents:
diff changeset
25 <param name="input_predictions_file" value="project_cluster.csv" />
5f95950c3959 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
ebi-gxa
parents:
diff changeset
26 <param name="include_scores" value="TRUE" />
5f95950c3959 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
ebi-gxa
parents:
diff changeset
27 <output name="output_predictions_file" value="scmap_output_tbl.txt" compare="sim_size" />
5f95950c3959 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
ebi-gxa
parents:
diff changeset
28 </test>
5f95950c3959 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
ebi-gxa
parents:
diff changeset
29 </tests>
5f95950c3959 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
ebi-gxa
parents:
diff changeset
30 <help><![CDATA[
5f95950c3959 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
ebi-gxa
parents:
diff changeset
31 Generate output tables in tab-separated format compatible with input specified in cell-types-analysis package: https://github.com/ebi-gene-expression-group/cell-types-analysis.
5f95950c3959 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
ebi-gxa
parents:
diff changeset
32 See the example snippet below:
5f95950c3959 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
ebi-gxa
parents:
diff changeset
33 ________________________________________
5f95950c3959 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
ebi-gxa
parents:
diff changeset
34 | cell_id | predicted_label | score |
5f95950c3959 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
ebi-gxa
parents:
diff changeset
35 | ERR2632411 | memory B cell | 0.8 |
5f95950c3959 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
ebi-gxa
parents:
diff changeset
36 ...
5f95950c3959 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
ebi-gxa
parents:
diff changeset
37
5f95950c3959 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
ebi-gxa
parents:
diff changeset
38 @VERSION_HISTORY@
5f95950c3959 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
ebi-gxa
parents:
diff changeset
39 ]]></help>
5f95950c3959 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
ebi-gxa
parents:
diff changeset
40 <expand macro="citations" />
5f95950c3959 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
ebi-gxa
parents:
diff changeset
41 </tool>
5f95950c3959 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
ebi-gxa
parents:
diff changeset
42
5f95950c3959 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
ebi-gxa
parents:
diff changeset
43