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comparison import.xml @ 15:bfac01f0393b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 08ce25c9b0ae236d3c0c352119de9db6b56c2925
author iuc
date Sat, 29 Mar 2025 07:35:15 +0000
parents 47ecd3ed0564
children
comparison
equal deleted inserted replaced
14:b08778769c73 15:bfac01f0393b
1 <tool id="anndata_import" name="Import Anndata" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 1 <tool id="anndata_import" name="Import Anndata" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
2 <description>from different formats</description> 2 <description>from different formats</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 <xml name="params_10x"> 5 <xml name="params_10x">
6 <param name="barcodes" type="data" format="tabular,txt" label="Barcodes (whitelist) file with one barcode per line"/> 6 <param name="barcodes" type="data" format="tabular,txt" label="Barcodes (whitelist) file with one barcode per line"/>
83 gex_only=$in.tenx.gex_only) 83 gex_only=$in.tenx.gex_only)
84 #end if 84 #end if
85 85
86 #else if $in.adata_format == 'umi_tools' 86 #else if $in.adata_format == 'umi_tools'
87 adata = ad.read_umi_tools('umi_tools_input.gz') 87 adata = ad.read_umi_tools('umi_tools_input.gz')
88
89 #else if $in.adata_format == 'custom'
90 import pandas as pd
91
92 adata = ad.read_mtx(filename='$in.mtx')
93 adata = adata.transpose().copy()
94
95 obs = pd.read_csv('$in.obs', sep='\t', index_col=0)
96 var = pd.read_csv('$in.var', sep='\t', index_col=0)
97
98 if adata.shape[0] != obs.shape[0]:
99 raise ValueError(f"Mismatch: adata has {adata.shape[0]} cells, but obs has {obs.shape[0]} rows.")
100
101 if adata.shape[1] != var.shape[0]:
102 raise ValueError(f"Mismatch: adata has {adata.shape[1]} genes, but var has {var.shape[0]} rows.")
103
104
105 adata.obs = obs
106 adata.var = var
107
88 #end if 108 #end if
89 adata.write('anndata.h5ad', compression='gzip') 109 adata.write('anndata.h5ad', compression='gzip')
90 print(adata) 110 print(adata)
91 ]]></configfile> 111 ]]></configfile>
92 </configfiles> 112 </configfiles>
96 <option value="loom">Loom data</option> 116 <option value="loom">Loom data</option>
97 <option value="tabular">Tabular, CSV, TSV</option> 117 <option value="tabular">Tabular, CSV, TSV</option>
98 <option value="10x_h5">H5 format from Cell ranger or not</option> 118 <option value="10x_h5">H5 format from Cell ranger or not</option>
99 <option value="mtx">Matrix Market (mtx), from Cell ranger or not</option> 119 <option value="mtx">Matrix Market (mtx), from Cell ranger or not</option>
100 <option value="umi_tools">UMI tools count matrix</option> 120 <option value="umi_tools">UMI tools count matrix</option>
121 <option value="custom">custom (with annotated cells and genes tables)</option>
101 </param> 122 </param>
102 <when value="loom"> 123 <when value="loom">
103 <param name="input" type="data" format="loom" label="Annotated data matrix"/> 124 <param name="input" type="data" format="loom" label="Annotated data matrix"/>
104 <param name="sparse" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Is the data matrix to read sparse?"/> 125 <param name="sparse" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Is the data matrix to read sparse?"/>
105 <param name="cleanup" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Cleanup?"/> 126 <param name="cleanup" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Cleanup?"/>
134 </conditional> 155 </conditional>
135 </when> 156 </when>
136 <when value="umi_tools"> 157 <when value="umi_tools">
137 <param name="input" type="data" format="tabular" label="condensed count matrix from UMI tools"/> 158 <param name="input" type="data" format="tabular" label="condensed count matrix from UMI tools"/>
138 </when> 159 </when>
160 <when value="custom">
161 <param name="mtx" type="data" format="mtx" label="Matrix in Matrix Market format"/>
162 <param name="obs" type="data" format="tabular,tabular.gz" label="Annotated cells (first column will be obs_index)"/>
163 <param name="var" type="data" format="tabular,tabular.gz" label="Annotated genes (first column will be var_index)"/>
164 </when>
139 </conditional> 165 </conditional>
140 </inputs> 166 </inputs>
141 <outputs> 167 <outputs>
142 <data name="anndata" format="h5ad" from_work_dir="anndata.h5ad" label="Anndata import on ${on_string}"/> 168 <data name="anndata" format="h5ad" from_work_dir="anndata.h5ad" label="Anndata import on ${on_string}"/>
143 </outputs> 169 </outputs>
271 <has_text text="ENSG00000258728" /> 297 <has_text text="ENSG00000258728" />
272 <has_text text="GCGAGAAAGTTGTAGA" /> 298 <has_text text="GCGAGAAAGTTGTAGA" />
273 </assert_contents> 299 </assert_contents>
274 </output> 300 </output>
275 </test> 301 </test>
302 <test expect_num_outputs="1">
303 <conditional name="in">
304 <param name="adata_format" value="custom"/>
305 <param name="mtx" value="trimmed_matrix.mtx"/>
306 <param name="obs" value="trimmed_barcode.tabular"/>
307 <param name="var" value="trimmed_gene.tabular"/>
308 </conditional>
309 <assert_stdout>
310 <has_text_matching expression="1000 × 500"/>
311 </assert_stdout>
312 <output name="anndata" ftype="h5ad">
313 <assert_contents>
314 <has_h5_keys keys="var/symbol,var/mito"/>
315 </assert_contents>
316 </output>
317 </test>
276 </tests> 318 </tests>
277 <help><![CDATA[ 319 <help><![CDATA[
278 320
279 **What it does** 321 **What it does**
280 322