Mercurial > repos > ebi-gxa > scpred_get_std_output
annotate scpred_get_std_output.xml @ 6:9f3ce66cd91f draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit e2e8344bd707659bcb2bdfcfdda648179884bd53"
author | ebi-gxa |
---|---|
date | Fri, 14 Aug 2020 11:08:13 -0400 |
parents | c88135c1efb1 |
children | 598b1d9dd135 |
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[ |
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
|
8 scpred_get_std_output.R --predictions-file "${predictions_file}" --get-scores "${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> |
156b1e9cc269
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
ebi-gxa
parents:
diff
changeset
|
11 <param type="data" name="predictions_file" label="Predictions file" format="txt" 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> |
156b1e9cc269
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
ebi-gxa
parents:
diff
changeset
|
20 <param name="predictions_file" value="predictions_table.txt" /> |
156b1e9cc269
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
ebi-gxa
parents:
diff
changeset
|
21 <param name="get_scores" value="TRUE" /> |
156b1e9cc269
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
ebi-gxa
parents:
diff
changeset
|
22 <output name="output_table" file="scpred_output_tbl.txt" compare="sim_size"/> |
156b1e9cc269
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
ebi-gxa
parents:
diff
changeset
|
23 </test> |
156b1e9cc269
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
ebi-gxa
parents:
diff
changeset
|
24 </tests> |
156b1e9cc269
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
ebi-gxa
parents:
diff
changeset
|
25 <help><![CDATA[ |
156b1e9cc269
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
ebi-gxa
parents:
diff
changeset
|
26 @HELP@ |
156b1e9cc269
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
ebi-gxa
parents:
diff
changeset
|
27 |
156b1e9cc269
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
ebi-gxa
parents:
diff
changeset
|
28 @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
|
29 ]]></help> |
156b1e9cc269
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
ebi-gxa
parents:
diff
changeset
|
30 <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
|
31 </tool> |