Mercurial > repos > iuc > anndata_import
comparison import.xml @ 12:93dd15e13e6a draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 656ce7ff596a8870b77848469e85b406c7bd9344
| author | iuc |
|---|---|
| date | Sun, 12 Nov 2023 16:42:57 +0000 |
| parents | fb9e030ffae4 |
| children |
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| 11:fb9e030ffae4 | 12:93dd15e13e6a |
|---|---|
| 11 <param name="make_unique" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Make the variable index unique by appending '-1', '-2'?"/> | 11 <param name="make_unique" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Make the variable index unique by appending '-1', '-2'?"/> |
| 12 <param name="gex_only" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Keep only 'Gene Expression' data and ignore other feature types?"/> | 12 <param name="gex_only" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Keep only 'Gene Expression' data and ignore other feature types?"/> |
| 13 </xml> | 13 </xml> |
| 14 </macros> | 14 </macros> |
| 15 <expand macro="requirements"> | 15 <expand macro="requirements"> |
| 16 <requirement type="package" version="1.7.0">scanpy</requirement> | 16 <requirement type="package" version="1.9.6">scanpy</requirement> |
| 17 </expand> | 17 </expand> |
| 18 <expand macro="version_command"/> | 18 <expand macro="version_command"/> |
| 19 <command detect_errors="exit_code"><![CDATA[ | 19 <command detect_errors="exit_code"><![CDATA[ |
| 20 #if $hd5_format.filetype == 'anndata' | 20 #if $hd5_format.filetype == 'anndata' |
| 21 #if $hd5_format.in.adata_format == 'mtx' | 21 #if $hd5_format.in.adata_format == 'mtx' |
| 227 <param name="use" value="no"/> | 227 <param name="use" value="no"/> |
| 228 </conditional> | 228 </conditional> |
| 229 </conditional> | 229 </conditional> |
| 230 <output name="anndata" value="import.mtx.no_10x.h5ad" ftype="h5ad" compare="sim_size"/> | 230 <output name="anndata" value="import.mtx.no_10x.h5ad" ftype="h5ad" compare="sim_size"/> |
| 231 </test> | 231 </test> |
| 232 <!--<test> | 232 <test expect_num_outputs="1"> |
| 233 <conditional name="in"> | 233 <conditional name="in"> |
| 234 <param name="adata_format" value="mtx"/> | 234 <param name="adata_format" value="mtx"/> |
| 235 <param name="matrix" value="matrix_10x_v1.2.0.mtx"/> | 235 <param name="matrix" value="matrix_10x_v1.2.0.mtx"/> |
| 236 <conditional name="tenx"> | 236 <conditional name="tenx"> |
| 237 <param name="use" value="legacy_10x"/> | 237 <param name="use" value="legacy_10x"/> |
| 242 <param name="gex_only" value="true"/> | 242 <param name="gex_only" value="true"/> |
| 243 </conditional> | 243 </conditional> |
| 244 </conditional> | 244 </conditional> |
| 245 <output name="anndata" value="import.mtx.legacy_10x.h5ad" ftype="h5ad" compare="sim_size"/> | 245 <output name="anndata" value="import.mtx.legacy_10x.h5ad" ftype="h5ad" compare="sim_size"/> |
| 246 </test> | 246 </test> |
| 247 <test> | 247 <test expect_num_outputs="1"> |
| 248 <conditional name="in"> | 248 <conditional name="in"> |
| 249 <param name="adata_format" value="mtx"/> | 249 <param name="adata_format" value="mtx"/> |
| 250 <param name="matrix" value="matrix_10x_v3.0.0.mtx"/> | 250 <param name="matrix" value="matrix_10x_v3.0.0.mtx"/> |
| 251 <conditional name="tenx"> | 251 <conditional name="tenx"> |
| 252 <param name="use" value="v3_10x"/> | 252 <param name="use" value="v3_10x"/> |
| 256 <param name="make_unique" value="true"/> | 256 <param name="make_unique" value="true"/> |
| 257 <param name="gex_only" value="true"/> | 257 <param name="gex_only" value="true"/> |
| 258 </conditional> | 258 </conditional> |
| 259 </conditional> | 259 </conditional> |
| 260 <output name="anndata" value="import.mtx.v3_10x.h5ad" ftype="h5ad" compare="sim_size"/> | 260 <output name="anndata" value="import.mtx.v3_10x.h5ad" ftype="h5ad" compare="sim_size"/> |
| 261 </test>!--> | 261 </test> |
| 262 <test expect_num_outputs="1"> | 262 <test expect_num_outputs="1"> |
| 263 <param name="filetype" value="anndata"/> | 263 <param name="filetype" value="anndata"/> |
| 264 <conditional name="in"> | 264 <conditional name="in"> |
| 265 <param name="adata_format" value="umi_tools"/> | 265 <param name="adata_format" value="umi_tools"/> |
| 266 <param name="input" value="umi_tools.tsv"/> | 266 <param name="input" value="umi_tools.tsv"/> |