Mercurial > repos > ebi-gxa > scpred_preprocess_data

annotate scpred_preprocess_data.xml @ 1:39b208cca9f1 draft

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 59503a4ae6f53a7782336df4f82fbd755cfb2933"
author ebi-gxa
date Wed, 29 Apr 2020 16:35:01 +0000
parents 0cd6c851ccfe
children cb4ebb47c3b9
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
39b208cca9f1 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 59503a4ae6f53a7782336df4f82fbd755cfb2933"
ebi-gxa
parents: 0
diff changeset
1 <tool id="scpred_preprocess_data" name="Scpred pre-process" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
0
0cd6c851ccfe "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c6a3af3aa798c106d1a8f3e2bf1aef5251d0bb7e"
ebi-gxa
parents:
diff changeset
2 <description>Pre-process input dataset (no train/test split)</description>
0cd6c851ccfe "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c6a3af3aa798c106d1a8f3e2bf1aef5251d0bb7e"
ebi-gxa
parents:
diff changeset
3 <macros>
0cd6c851ccfe "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c6a3af3aa798c106d1a8f3e2bf1aef5251d0bb7e"
ebi-gxa
parents:
diff changeset
4 <import>scpred_macros.xml</import>
0cd6c851ccfe "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c6a3af3aa798c106d1a8f3e2bf1aef5251d0bb7e"
ebi-gxa
parents:
diff changeset
5 </macros>
0cd6c851ccfe "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c6a3af3aa798c106d1a8f3e2bf1aef5251d0bb7e"
ebi-gxa
parents:
diff changeset
6 <expand macro="requirements" />
0cd6c851ccfe "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c6a3af3aa798c106d1a8f3e2bf1aef5251d0bb7e"
ebi-gxa
parents:
diff changeset
7 <command detect_errors="exit_code"><![CDATA[
1
39b208cca9f1 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 59503a4ae6f53a7782336df4f82fbd755cfb2933"
ebi-gxa
parents: 0
diff changeset
8 scpred_preprocess_data.R --input-sce-object "${input_sce_object}" --output-matrix-object "${output_mat_object}"
39b208cca9f1 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 59503a4ae6f53a7782336df4f82fbd755cfb2933"
ebi-gxa
parents: 0
diff changeset
9
39b208cca9f1 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 59503a4ae6f53a7782336df4f82fbd755cfb2933"
ebi-gxa
parents: 0
diff changeset
10 #if $norm_counts_slot
39b208cca9f1 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 59503a4ae6f53a7782336df4f82fbd755cfb2933"
ebi-gxa
parents: 0
diff changeset
11 --normalised-counts-slot "${norm_counts_slot}"
39b208cca9f1 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 59503a4ae6f53a7782336df4f82fbd755cfb2933"
ebi-gxa
parents: 0
diff changeset
12 #end if
39b208cca9f1 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 59503a4ae6f53a7782336df4f82fbd755cfb2933"
ebi-gxa
parents: 0
diff changeset
13 #if $output_labels
39b208cca9f1 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 59503a4ae6f53a7782336df4f82fbd755cfb2933"
ebi-gxa
parents: 0
diff changeset
14 --output-labels "${output_labels}"
39b208cca9f1 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 59503a4ae6f53a7782336df4f82fbd755cfb2933"
ebi-gxa
parents: 0
diff changeset
15 #end if
39b208cca9f1 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 59503a4ae6f53a7782336df4f82fbd755cfb2933"
ebi-gxa
parents: 0
diff changeset
16
39b208cca9f1 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 59503a4ae6f53a7782336df4f82fbd755cfb2933"
ebi-gxa
parents: 0
diff changeset
17 ]]></command>
0
0cd6c851ccfe "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c6a3af3aa798c106d1a8f3e2bf1aef5251d0bb7e"
ebi-gxa
parents:
diff changeset
18 <inputs>
0cd6c851ccfe "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c6a3af3aa798c106d1a8f3e2bf1aef5251d0bb7e"
ebi-gxa
parents:
diff changeset
19 <param type="data" name="input_sce_object" label="SCE object containing expression data" format="rdata" help="File with serialized SingleCellExperiment object that contains expression matrix" />
0cd6c851ccfe "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c6a3af3aa798c106d1a8f3e2bf1aef5251d0bb7e"
ebi-gxa
parents:
diff changeset
20 <param type="text" name="norm_counts_slot" value="normcounts" label="Normalised counts slot" help="Slot containing normalised counts in input SCE object" />
0cd6c851ccfe "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c6a3af3aa798c106d1a8f3e2bf1aef5251d0bb7e"
ebi-gxa
parents:
diff changeset
21 </inputs>
0cd6c851ccfe "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c6a3af3aa798c106d1a8f3e2bf1aef5251d0bb7e"
ebi-gxa
parents:
diff changeset
22 <outputs>
0cd6c851ccfe "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c6a3af3aa798c106d1a8f3e2bf1aef5251d0bb7e"
ebi-gxa
parents:
diff changeset
23 <data name="output_mat_object" format="rdata" />
0cd6c851ccfe "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c6a3af3aa798c106d1a8f3e2bf1aef5251d0bb7e"
ebi-gxa
parents:
diff changeset
24 <data name="output_labels" format="txt" />
0cd6c851ccfe "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c6a3af3aa798c106d1a8f3e2bf1aef5251d0bb7e"
ebi-gxa
parents:
diff changeset
25 </outputs>
0cd6c851ccfe "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c6a3af3aa798c106d1a8f3e2bf1aef5251d0bb7e"
ebi-gxa
parents:
diff changeset
26 <help><![CDATA[
0cd6c851ccfe "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c6a3af3aa798c106d1a8f3e2bf1aef5251d0bb7e"
ebi-gxa
parents:
diff changeset
27 @HELP@
0cd6c851ccfe "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c6a3af3aa798c106d1a8f3e2bf1aef5251d0bb7e"
ebi-gxa
parents:
diff changeset
28
0cd6c851ccfe "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c6a3af3aa798c106d1a8f3e2bf1aef5251d0bb7e"
ebi-gxa
parents:
diff changeset
29 @VERSION_HISTORY@
0cd6c851ccfe "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c6a3af3aa798c106d1a8f3e2bf1aef5251d0bb7e"
ebi-gxa
parents:
diff changeset
30 ]]></help>
0cd6c851ccfe "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c6a3af3aa798c106d1a8f3e2bf1aef5251d0bb7e"
ebi-gxa
parents:
diff changeset
31 <expand macro="citations" />
0cd6c851ccfe "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c6a3af3aa798c106d1a8f3e2bf1aef5251d0bb7e"
ebi-gxa
parents:
diff changeset
32 </tool>