Mercurial > repos > iuc > anndata_import

comparison import.xml @ 12:93dd15e13e6a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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 d330b3082107
comparison
equal deleted inserted replaced
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"/>