Mercurial > repos > ebi-gxa > scanpy_integrate_harmony
comparison scanpy-integrate-harmony.xml @ 1:f1298838e93b draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9028e8fa3761fd640dcace5d36bf9b7d558319f7-dirty"
author | ebi-gxa |
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date | Thu, 10 Sep 2020 08:45:34 +0000 |
parents | 8b3a52fbb482 |
children | 3f61bf17ca50 |
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0:8b3a52fbb482 | 1:f1298838e93b |
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1 <?xml version="1.0" encoding="utf-8"?> | 1 <?xml version="1.0" encoding="utf-8"?> |
2 <tool id="scanpy_integrate_harmony" name="Scanpy Harmony" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> | 2 <tool id="scanpy_integrate_harmony" name="Scanpy Harmony" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> |
3 <description>adjust principal components for variables that might introduce batch effect</description> | 3 <description>adjust principal components for variables that might introduce batch effect</description> |
4 <macros> | 4 <macros> |
5 <import>scanpy_macros2.xml</import> | 5 <import>scanpy_macros2.xml</import> |
6 </macros> | 6 </macros> |
7 <expand macro="requirements"/> | 7 <expand macro="requirements"/> |
50 #end if | 50 #end if |
51 #end if | 51 #end if |
52 @INPUT_OPTS@ | 52 @INPUT_OPTS@ |
53 @OUTPUT_OPTS@ | 53 @OUTPUT_OPTS@ |
54 #else | 54 #else |
55 echo "No batch variables passed, simply passing original input as output unchanged."; | 55 echo "No batch variables passed, simply passing original input as output unchanged." && cp '${input_obj_file}' output.h5 |
56 cp '${input_obj_file}' '${output_h5}' | |
57 #end if | 56 #end if |
58 ]]></command> | 57 ]]></command> |
59 | 58 |
60 <inputs> | 59 <inputs> |
61 <expand macro="input_object_params"/> | 60 <expand macro="input_object_params"/> |
115 <param name="input_format" value="anndata"/> | 114 <param name="input_format" value="anndata"/> |
116 <param name="output_format" value="anndata"/> | 115 <param name="output_format" value="anndata"/> |
117 <param name="batch_key" value="louvain"/> | 116 <param name="batch_key" value="louvain"/> |
118 <output name="output_h5" file="harmony.h5" ftype="h5" compare="sim_size"/> | 117 <output name="output_h5" file="harmony.h5" ftype="h5" compare="sim_size"/> |
119 </test> | 118 </test> |
119 <test> | |
120 <param name="input_obj_file" value="find_cluster.h5"/> | |
121 <param name="input_format" value="anndata"/> | |
122 <param name="output_format" value="anndata"/> | |
123 <output name="output_h5" file="harmony_copy.h5" ftype="h5" compare="sim_size"/> | |
124 </test> | |
120 </tests> | 125 </tests> |
121 | 126 |
122 <help><![CDATA[ | 127 <help><![CDATA[ |
123 .. class:: infomark | 128 .. class:: infomark |
124 | 129 |