Mercurial > repos > ebi-gxa > garnett_get_std_output

annotate garnett_get_std_output.xml @ 3:5f05e2901299 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 660486ba0e1ef2f0195e7c6f75448221ba4640f7"
author ebi-gxa
date Tue, 28 Apr 2020 11:32:08 -0400
parents 1023eae1b147
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
5f05e2901299 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 660486ba0e1ef2f0195e7c6f75448221ba4640f7"
ebi-gxa
parents: 1
diff changeset
1 <tool id="garnett_get_std_output" name="Garnett - get standard output" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
0
40b587883bd9 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
2 <description>Get 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>
40b587883bd9 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
3 <macros>
40b587883bd9 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
4 <import>garnett_macros.xml</import>
40b587883bd9 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
5 </macros>
40b587883bd9 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
6 <expand macro="requirements" />
40b587883bd9 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
7 <command detect_errors="exit_code"><![CDATA[
1
1023eae1b147 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
ebi-gxa
parents: 0
diff changeset
8 garnett_get_std_output.R --input-object '${input_object}' --classifier '${classifier}' --output-file-path '${output_file_path}'
0
40b587883bd9 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
9 ]]></command>
40b587883bd9 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
10 <inputs>
40b587883bd9 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
11 <param type="data" name="input_object" label="input CDS object" format="rdata" help="CDS object with predicted labels" />
1
1023eae1b147 "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="Classifier object in rdata format" />
0
40b587883bd9 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
13 </inputs>
40b587883bd9 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
14 <outputs>
40b587883bd9 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
15 <data name="output_file_path" format="txt" />
40b587883bd9 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
16 </outputs>
40b587883bd9 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
17 <tests>
40b587883bd9 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
18 <test>
40b587883bd9 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
19 <param name="input_object" value="cds_pred_labs.rds" />
40b587883bd9 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
20 <output name="output_file_path" value="garnett_output_tbl.txt" compare="sim_size" />
40b587883bd9 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
21 </test>
40b587883bd9 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
22 </tests>
40b587883bd9 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
23 <help><![CDATA[
40b587883bd9 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
24 @HELP@
40b587883bd9 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
25
40b587883bd9 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
26 @VERSION_HISTORY@
40b587883bd9 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
27 ]]></help>
40b587883bd9 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
28 <expand macro="citations" />
40b587883bd9 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
diff changeset
29 </tool>