Mercurial > repos > ebi-gxa > scater_calculate_cpm
comparison scater-calculate-cpm.xml @ 0:66e18f77e161 draft default tip
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
author | ebi-gxa |
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date | Wed, 03 Apr 2019 11:44:15 -0400 |
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-1:000000000000 | 0:66e18f77e161 |
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1 <tool id="scater_calculate_cpm" name="Scater CalculateCPM" version="@TOOL_VERSION@+galaxy0"> | |
2 <description>from raw counts</description> | |
3 <macros> | |
4 <import>scater_macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements" /> | |
7 <command detect_errors="exit_code"><![CDATA[ | |
8 scater-calculate-cpm.R -i '${R_scater_serialized}' | |
9 -s '$size_factors' | |
10 -o '$R_scater_cpm' | |
11 -t '$cpm_matrix' | |
12 ]]></command> | |
13 | |
14 <inputs> | |
15 <param name="R_scater_serialized" type="data" format="rdata" label="Serialized SingleCellExperiment in RDS format" | |
16 help="File name in which a serialized R SingleCellExperiment object where object matrix found"/> | |
17 <param name="size_factors" argument="--size-factors" type="boolean" label="Use pre-calculated size factors in the input object if available"/> | |
18 | |
19 </inputs> | |
20 | |
21 <outputs> | |
22 <data name="R_scater_cpm" format="rdata" label="${tool.name} on ${on_string}: serialized SingeleCellExperiment object holding CPM"/> | |
23 <data name="cpm_matrix" format="txt" label="${tool.name} on ${on_string}: CPM matrix in text format"/> | |
24 </outputs> | |
25 | |
26 <tests> | |
27 <test> | |
28 <param name="R_scater_serialized" ftype="rdata" value="R_scater_serialized.rds"/> | |
29 <output name="R_scater_cpm" ftype="rdata" file="R_scater_cpm.rds"/> | |
30 <output name="cpm_matrix" ftype="txt" file="cpm_matrix.txt"/> | |
31 </test> | |
32 </tests> | |
33 | |
34 <help><![CDATA[ | |
35 @HELP@ | |
36 | |
37 @VERSION_HISTORY@ | |
38 ]]></help> | |
39 <expand macro="citations" /> | |
40 </tool> |