Mercurial > repos > ebi-gxa > sccaf_regress_out
comparison sccaf_regress_out.xml @ 1:5ef0610e9f50 draft default tip
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 7034937deaaf56b2e6f585bb28234a86a5b5fa2e
author | ebi-gxa |
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date | Mon, 25 Nov 2019 06:28:23 -0500 |
parents | 885db50f1bc1 |
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0:885db50f1bc1 | 1:5ef0610e9f50 |
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1 <?xml version="1.0" encoding="utf-8"?> | 1 <?xml version="1.0" encoding="utf-8"?> |
2 <tool id="sccaf_regress_out" name="SCCAF mulitple regress out" version="@TOOL_VERSION@+galaxy0"> | 2 <tool id="sccaf_regress_out" name="SCCAF mulitple regress out" version="@TOOL_VERSION@+galaxy1"> |
3 <description>with multiple categorical keys on an AnnData object.</description> | 3 <description>with multiple categorical keys on an AnnData object.</description> |
4 <macros> | 4 <macros> |
5 <import>sccaf_macros.xml</import> | 5 <import>sccaf_macros.xml</import> |
6 </macros> | 6 </macros> |
7 <expand macro="requirements"/> | 7 <expand macro="requirements"/> |
9 ln -s '${input_obj_file}' input.h5 && | 9 ln -s '${input_obj_file}' input.h5 && |
10 sccaf-regress-out -i input.h5 -o output.h5 -k '${keys_to_regress}' | 10 sccaf-regress-out -i input.h5 -o output.h5 -k '${keys_to_regress}' |
11 ]]></command> | 11 ]]></command> |
12 <inputs> | 12 <inputs> |
13 <param name="input_obj_file" argument="input-object-file" type="data" format="h5" label="Input object in hdf5 AnnData format"/> | 13 <param name="input_obj_file" argument="input-object-file" type="data" format="h5" label="Input object in hdf5 AnnData format"/> |
14 <expand macro="output_object_params"/> | |
14 <param name="keys_to_regress" label="Keys to regress" help="Comma separated keys for regressing out; they need to exist in the observations part of the AnnData object." type="text"/> | 15 <param name="keys_to_regress" label="Keys to regress" help="Comma separated keys for regressing out; they need to exist in the observations part of the AnnData object." type="text"/> |
15 </inputs> | 16 </inputs> |
16 <outputs> | 17 <outputs> |
17 <data name="output" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: regressesed out on ${keys_to_regress}"/> | 18 <expand macro="output_data_obj" description="regressed out on ${keys_to_regress}"/> |
18 </outputs> | 19 </outputs> |
19 | 20 |
20 <tests> | 21 <tests> |
21 <test> | 22 <test> |
22 <param name="input_obj_file" value="find_cluster.h5"/> | 23 <param name="input_obj_file" value="find_cluster.h5"/> |
23 <param name="input_format" value="anndata"/> | 24 <param name="input_format" value="anndata"/> |
24 <param name="color_by" value="louvain"/> | 25 <param name="color_by" value="louvain"/> |
25 <output name="output" file="output.h5" ftype="h5" compare="sim_size"/> | 26 <output name="output_h5ad" file="output.h5" ftype="h5" compare="sim_size"/> |
26 </test> | 27 </test> |
27 </tests> | 28 </tests> |
28 | 29 |
29 <help><![CDATA[ | 30 <help><![CDATA[ |
30 ============================= | 31 ============================= |