Mercurial > repos > ebi-gxa > scpred_get_std_output

annotate scpred_get_std_output.xml @ 7:598b1d9dd135 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 a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
author ebi-gxa
date Fri, 27 Nov 2020 13:45:49 +0000
parents c88135c1efb1
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
c88135c1efb1 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit bb88d0eb9c193518eb0d05321e3458a10212d3ab"
ebi-gxa
parents: 4
diff changeset
1 <tool id="scpred_get_std_output" name="Scpred - get output in standard format" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
0
156b1e9cc269 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
ebi-gxa
parents:
diff changeset
2 <description>This method allows to export predicted labels in a standardised format, simplifying downstream analyses.</description>
156b1e9cc269 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
ebi-gxa
parents:
diff changeset
3 <macros>
156b1e9cc269 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
ebi-gxa
parents:
diff changeset
4 <import>scpred_macros.xml</import>
156b1e9cc269 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
ebi-gxa
parents:
diff changeset
5 </macros>
156b1e9cc269 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
ebi-gxa
parents:
diff changeset
6 <expand macro="requirements" />
156b1e9cc269 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
ebi-gxa
parents:
diff changeset
7 <command detect_errors="exit_code"><![CDATA[
7
598b1d9dd135 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
ebi-gxa
parents: 5
diff changeset
8 scpred_get_std_output.R --predictions-object "${predictions_object}" --get-scores "${get_scores}" --classifier '${classifier}' --output-table "${output_table}"
0
156b1e9cc269 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
ebi-gxa
parents:
diff changeset
9 ]]></command>
156b1e9cc269 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
ebi-gxa
parents:
diff changeset
10 <inputs>
7
598b1d9dd135 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
ebi-gxa
parents: 5
diff changeset
11 <param type="data" name="predictions_object" label="Predictions Object" format="rdata" help="Path to the predictions file in text format" />
1
a7bf1d2b310b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
ebi-gxa
parents: 0
diff changeset
12 <param type="data" name="classifier" label="Classifier object" format="rdata" help="Path to the classifier object used to obtain predictions" />
0
156b1e9cc269 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
ebi-gxa
parents:
diff changeset
13 <param type="boolean" checked="false" name="get_scores" label="Get scores" help="Boolean: should the prediction scores be included? default: FALSE" />
156b1e9cc269 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
ebi-gxa
parents:
diff changeset
14 </inputs>
156b1e9cc269 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
ebi-gxa
parents:
diff changeset
15 <outputs>
156b1e9cc269 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
ebi-gxa
parents:
diff changeset
16 <data name="output_table" format="txt" />
156b1e9cc269 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
ebi-gxa
parents:
diff changeset
17 </outputs>
156b1e9cc269 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
ebi-gxa
parents:
diff changeset
18 <tests>
156b1e9cc269 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
ebi-gxa
parents:
diff changeset
19 <test>
7
598b1d9dd135 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
ebi-gxa
parents: 5
diff changeset
20 <param name="predictions_object" value="predicted_data.rds" />
598b1d9dd135 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
ebi-gxa
parents: 5
diff changeset
21 <param name="get_scores" value="True" />
598b1d9dd135 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
ebi-gxa
parents: 5
diff changeset
22 <param name="classifier" value="scPred_trained.rds" />
598b1d9dd135 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
ebi-gxa
parents: 5
diff changeset
23 <output name="output_table" file="scpred_output_tbl.txt" compare="sim_size" />
0
156b1e9cc269 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
ebi-gxa
parents:
diff changeset
24 </test>
156b1e9cc269 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
ebi-gxa
parents:
diff changeset
25 </tests>
7
598b1d9dd135 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
ebi-gxa
parents: 5
diff changeset
26 <help><![CDATA[
0
156b1e9cc269 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
ebi-gxa
parents:
diff changeset
27 @HELP@
156b1e9cc269 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
ebi-gxa
parents:
diff changeset
28
156b1e9cc269 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
ebi-gxa
parents:
diff changeset
29 @VERSION_HISTORY@
156b1e9cc269 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
ebi-gxa
parents:
diff changeset
30 ]]></help>
156b1e9cc269 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
ebi-gxa
parents:
diff changeset
31 <expand macro="citations" />
156b1e9cc269 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
ebi-gxa
parents:
diff changeset
32 </tool>