Mercurial > repos > iuc > anndata_import

comparison import.xml @ 5:9f277f08bd8f draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 5744259254d4254a29cb7a6687fbbfd103301064"
author iuc
date Thu, 06 Feb 2020 00:16:56 +0000
parents b68022a5c83f
children 546e3c9d261c
comparison
equal deleted inserted replaced
4:3257312867cd 5:9f277f08bd8f
1 <tool id="anndata_import" name="Import Anndata and loom" version="@VERSION@+@GALAXY_VERSION@"> 1 <tool id="anndata_import" name="Import Anndata and loom" version="@VERSION@+@GALAXY_VERSION@" profile="18.01">
2 <description>from different format</description> 2 <description>from different format</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"/> 6 <param name="barcodes" type="data" format="tabular,txt" label="Barcodes"/>
75 adata = ad.read_csv( 75 adata = ad.read_csv(
76 '$hd5_format.in.input', 76 '$hd5_format.in.input',
77 delimiter='$delimiter', 77 delimiter='$delimiter',
78 first_column_names=$hd5_format.in.first_column_names) 78 first_column_names=$hd5_format.in.first_column_names)
79 79
80 #else if $hd5_format.in.adata_format == '10x_h5'
81 import scanpy as sc
82 adata = sc.read_10x_h5('$hd5_format.in.input')
83
80 #else if $hd5_format.in.adata_format == 'mtx' 84 #else if $hd5_format.in.adata_format == 'mtx'
81 #if $hd5_format.in.tenx.use == 'no' 85 #if $hd5_format.in.tenx.use == 'no'
82 adata = ad.read_mtx(filename='$hd5_format.in.matrix') 86 adata = ad.read_mtx(filename='$hd5_format.in.matrix')
83 #else 87 #else
84 import scanpy as sc 88 import scanpy as sc
107 <when value="anndata"> 111 <when value="anndata">
108 <conditional name="in"> 112 <conditional name="in">
109 <param name="adata_format" type="select" label="Format for the annotated data matrix"> 113 <param name="adata_format" type="select" label="Format for the annotated data matrix">
110 <option value="loom">Loom</option> 114 <option value="loom">Loom</option>
111 <option value="tabular">Tabular, CSV, TSV</option> 115 <option value="tabular">Tabular, CSV, TSV</option>
116 <option value="10x_h5">H5 format from Cell ranger or not</option>
112 <option value="mtx">Matrix Market (mtx), from Cell ranger or not</option> 117 <option value="mtx">Matrix Market (mtx), from Cell ranger or not</option>
113 <option value="umi_tools">UMI tools</option> 118 <option value="umi_tools">UMI tools</option>
114 </param> 119 </param>
115 <when value="loom"> 120 <when value="loom">
116 <param name="input" type="data" format="loom" label="Annotated data matrix"/> 121 <param name="input" type="data" format="loom" label="Annotated data matrix"/>
121 <param name="var_names" type="text" value="Gene" label="var_names"/> 126 <param name="var_names" type="text" value="Gene" label="var_names"/>
122 </when> 127 </when>
123 <when value="tabular"> 128 <when value="tabular">
124 <param name="input" type="data" format="tabular,csv,tsv" label="Annotated data matrix"/> 129 <param name="input" type="data" format="tabular,csv,tsv" label="Annotated data matrix"/>
125 <param name="first_column_names" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Does the first column store the row names?"/> 130 <param name="first_column_names" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Does the first column store the row names?"/>
131 </when>
132 <when value="10x_h5" >
133 <param name="input" type="data" format="h5" label="Data matrix"/>
126 </when> 134 </when>
127 <when value="mtx"> 135 <when value="mtx">
128 <param name="matrix" type="data" format="mtx" label="Matrix"/> 136 <param name="matrix" type="data" format="mtx" label="Matrix"/>
129 <conditional name="tenx"> 137 <conditional name="tenx">
130 <param name="use" type="select" label="Use 10x Genomics formatted mtx"> 138 <param name="use" type="select" label="Use 10x Genomics formatted mtx">
265 <param name="other_files" value="secondlayer.tsv"/> 273 <param name="other_files" value="secondlayer.tsv"/>
266 <param name="coldata" value="cols.tsv"/> 274 <param name="coldata" value="cols.tsv"/>
267 <param name="rowdata" value="rows.tsv"/> 275 <param name="rowdata" value="rows.tsv"/>
268 <output name="loomdata" value="converted.loom.test" ftype="loom" compare="sim_size"/> 276 <output name="loomdata" value="converted.loom.test" ftype="loom" compare="sim_size"/>
269 </test> 277 </test>
278 <test expect_num_outputs="1"><!-- 10x h5 test -->
279 <conditional name="hd5_format">
280 <param name="filetype" value="anndata"/>
281 <conditional name="in">
282 <param name="adata_format" value="10x_h5"/>
283 <param name="input" value="dropletutils_input.h5"/>
284 </conditional>
285 </conditional>
286 <output name="anndata">
287 <assert_contents>
288 <has_text text="HDF"/>
289 <has_text text="ENSG00000258728" />
290 <has_text text="GCGAGAAAGTTGTAGA" />
291 </assert_contents>
292 </output>
293 </test>
270 </tests> 294 </tests>
271 <help><![CDATA[ 295 <help><![CDATA[
272 **What it does** 296 **What it does**
273 297
274 This tool creates an AnnData or loom dataset from several input types: 298 This tool creates an AnnData or loom dataset from several input types: