Mercurial > repos > iuc > sceasy_convert
comparison sceasy.xml @ 1:2062be7efc84 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sceasy/ commit 49fa5e842137b98ceb314ab1471411785a352bd3
| author | iuc |
|---|---|
| date | Tue, 12 Dec 2023 11:40:19 +0000 |
| parents | d70139524747 |
| children | 5c9b16bdbd5e |
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| 0:d70139524747 | 1:2062be7efc84 |
|---|---|
| 2 <description> | 2 <description> |
| 3 Convert between common single cell formats | 3 Convert between common single cell formats |
| 4 </description> | 4 </description> |
| 5 <macros> | 5 <macros> |
| 6 <token name="@TOOL_VERSION@">0.0.7</token> | 6 <token name="@TOOL_VERSION@">0.0.7</token> |
| 7 <token name="@VERSION_SUFFIX@">1</token> | 7 <token name="@VERSION_SUFFIX@">2</token> |
| 8 <macro name="mac_input_form" token_format="@FORMAT@" > | 8 <macro name="mac_input_form" token_format="@FORMAT@" > |
| 9 <param name="input_object_file" type="data" format="@FORMAT@" label="Input object in @FORMAT@ format"/> | 9 <param name="input_object_file" type="data" format="@FORMAT@" label="Input object in @FORMAT@ format"/> |
| 10 </macro> | 10 </macro> |
| 11 </macros> | 11 </macros> |
| 12 <requirements> | 12 <requirements> |
| 108 <option value="sce2loom" >SingleCellexperiment to Loom</option> | 108 <option value="sce2loom" >SingleCellexperiment to Loom</option> |
| 109 <option value="seurat2anndata">Seurat to AnnData</option> | 109 <option value="seurat2anndata">Seurat to AnnData</option> |
| 110 <option value="seurat2sce" >Seurat to SingleCellexperiment</option> | 110 <option value="seurat2sce" >Seurat to SingleCellexperiment</option> |
| 111 </param> | 111 </param> |
| 112 <when value="anndata2cds" > | 112 <when value="anndata2cds" > |
| 113 <expand macro="mac_input_form" token_format="h5ad" /> | 113 <expand macro="mac_input_form" format="h5ad,h5" /> |
| 114 </when> | 114 </when> |
| 115 <when value="anndata2seurat" > | 115 <when value="anndata2seurat" > |
| 116 <expand macro="mac_input_form" token_format="h5ad" /> | 116 <expand macro="mac_input_form" format="h5ad,h5" /> |
| 117 </when> | 117 </when> |
| 118 <when value="loom2anndata"> | 118 <when value="loom2anndata"> |
| 119 <expand macro="mac_input_form" token_format="h5" /> | 119 <expand macro="mac_input_form" format="h5,loom,rdata" /> |
| 120 </when> | 120 </when> |
| 121 <when value="loom2sce"> | 121 <when value="loom2sce"> |
| 122 <expand macro="mac_input_form" token_format="h5" /> | 122 <expand macro="mac_input_form" format="h5,loom,rdata" /> |
| 123 </when> | 123 </when> |
| 124 <when value="sce2anndata"> | 124 <when value="sce2anndata"> |
| 125 <expand macro="mac_input_form" token_format="sce" /> | 125 <expand macro="mac_input_form" format="sce,rds,rdata.sce" /> |
| 126 </when> | 126 </when> |
| 127 <when value="sce2loom"> | 127 <when value="sce2loom"> |
| 128 <expand macro="mac_input_form" token_format="sce" /> | 128 <expand macro="mac_input_form" format="sce,rds,rdata.sce" /> |
| 129 </when> | 129 </when> |
| 130 <when value="seurat2anndata"> | 130 <when value="seurat2anndata"> |
| 131 <expand macro="mac_input_form" token_format="rds" /> | 131 <expand macro="mac_input_form" format="rds,rdata" /> |
| 132 </when> | 132 </when> |
| 133 <when value="seurat2sce"> | 133 <when value="seurat2sce"> |
| 134 <expand macro="mac_input_form" token_format="rds" /> | 134 <expand macro="mac_input_form" format="rds,rdata" /> |
| 135 </when> | 135 </when> |
| 136 </conditional> | 136 </conditional> |
| 137 </inputs> | 137 </inputs> |
| 138 <outputs> | 138 <outputs> |
| 139 <data name="output_sce" format="rdata" from_work_dir="outfile.rds" label="${tool.name} on ${on_string}: SingleCellExperiment"> | 139 <data name="output_sce" format="rdata" from_work_dir="outfile.rds" label="${tool.name} on ${on_string}: SingleCellExperiment"> |
| 149 <data name="output_loom" format="h5" from_work_dir="outfile.loom" label="${tool.name} on ${on_string}: Loom"> | 149 <data name="output_loom" format="h5" from_work_dir="outfile.loom" label="${tool.name} on ${on_string}: Loom"> |
| 150 <filter> | 150 <filter> |
| 151 conversion['direction'].endswith('loom') | 151 conversion['direction'].endswith('loom') |
| 152 </filter> | 152 </filter> |
| 153 </data> | 153 </data> |
| 154 <data name="output_anndata" format="h5" from_work_dir="outfile.h5ad" label="${tool.name} on ${on_string}: AnnData"> | 154 <data name="output_anndata" format="h5ad" from_work_dir="outfile.h5ad" label="${tool.name} on ${on_string}: AnnData"> |
| 155 <filter> | 155 <filter> |
| 156 conversion['direction'].endswith('anndata') | 156 conversion['direction'].endswith('anndata') |
| 157 </filter> | 157 </filter> |
| 158 </data> | 158 </data> |
| 159 <data name="output_seurat" format="rdata" from_work_dir="outfile.rds" label="${tool.name} on ${on_string}: Seurat"> | 159 <data name="output_seurat" format="rdata" from_work_dir="outfile.rds" label="${tool.name} on ${on_string}: Seurat"> |
| 174 <output name="output_seurat" file="ad2seurat.rds" ftype="rdata" compare="sim_size"/> | 174 <output name="output_seurat" file="ad2seurat.rds" ftype="rdata" compare="sim_size"/> |
| 175 </test> | 175 </test> |
| 176 <test expect_num_outputs="1"> | 176 <test expect_num_outputs="1"> |
| 177 <param name="direction" value="loom2anndata"/> | 177 <param name="direction" value="loom2anndata"/> |
| 178 <param name="input_object_file" value="sce2loom.rds"/> | 178 <param name="input_object_file" value="sce2loom.rds"/> |
| 179 <output name="output_anndata" file="loom2anndata.h5ad" ftype="h5" compare="sim_size"/> | 179 <output name="output_anndata" file="loom2anndata.h5ad" ftype="h5ad" compare="sim_size"/> |
| 180 </test> | 180 </test> |
| 181 <test expect_num_outputs="1"> | 181 <test expect_num_outputs="1"> |
| 182 <param name="direction" value="loom2sce"/> | 182 <param name="direction" value="loom2sce"/> |
| 183 <param name="input_object_file" value="sce2loom.rds"/> | 183 <param name="input_object_file" value="sce2loom.rds"/> |
| 184 <output name="output_sce" file="loom2sce.rds" ftype="rdata" compare="sim_size"/> | 184 <output name="output_sce" file="loom2sce.rds" ftype="rdata" compare="sim_size"/> |
| 185 </test> | 185 </test> |
| 186 <test expect_num_outputs="1"> | 186 <test expect_num_outputs="1"> |
| 187 <param name="direction" value="sce2anndata"/> | 187 <param name="direction" value="sce2anndata"/> |
| 188 <param name="input_object_file" value="test_sce.rds"/> | 188 <param name="input_object_file" value="test_sce.rds"/> |
| 189 <output name="output_anndata" file="sce2anndata.h5ad" ftype="h5" compare="sim_size"/> | 189 <output name="output_anndata" file="sce2anndata.h5ad" ftype="h5ad" compare="sim_size"/> |
| 190 </test> | 190 </test> |
| 191 <test expect_num_outputs="1"> | 191 <test expect_num_outputs="1"> |
| 192 <param name="direction" value="sce2loom"/> | 192 <param name="direction" value="sce2loom"/> |
| 193 <param name="input_object_file" value="test_sce.rds"/> | 193 <param name="input_object_file" value="test_sce.rds"/> |
| 194 <output name="output_loom" file="sce2loom.rds" ftype="h5" compare="sim_size"/> | 194 <output name="output_loom" file="sce2loom.rds" ftype="h5" compare="sim_size"/> |
| 195 </test> | 195 </test> |
| 196 <test expect_num_outputs="1"> | 196 <test expect_num_outputs="1"> |
| 197 <param name="direction" value="seurat2anndata"/> | 197 <param name="direction" value="seurat2anndata"/> |
| 198 <param name="input_object_file" value="test_seurat.rds"/> | 198 <param name="input_object_file" value="test_seurat.rds"/> |
| 199 <output name="output_seurat" file="test_anndata.h5ad" ftype="h5" compare="sim_size"/> | 199 <output name="output_anndata" file="test_anndata.h5ad" ftype="h5ad" compare="sim_size"/> |
| 200 </test> | 200 </test> |
| 201 <test expect_num_outputs="1"> | 201 <test expect_num_outputs="1"> |
| 202 <param name="direction" value="seurat2sce"/> | 202 <param name="direction" value="seurat2sce"/> |
| 203 <param name="input_object_file" value="test_seurat.rds"/> | 203 <param name="input_object_file" value="test_seurat.rds"/> |
| 204 <output name="output_sce" file="test_sce.rds" ftype="rdata" compare="sim_size"/> | 204 <output name="output_sce" file="test_sce.rds" ftype="rdata" compare="sim_size"/> |
| 205 </test> | 205 </test> |
| 206 </tests> | 206 </tests> |
| 207 <help> | 207 <help><![CDATA[ |
| 208 SCeasy | 208 SCeasy |
| 209 ====== | 209 ====== |
| 210 | 210 |
| 211 Convert scRNA data object between formats `sceasy::convertFormat()` | 211 Convert scRNA data object between formats `sceasy::convertFormat()` |
| 212 | 212 |
| 215 .. image:: $PATH_TO_IMAGES/conv.png | 215 .. image:: $PATH_TO_IMAGES/conv.png |
| 216 :width: 80 % | 216 :width: 80 % |
| 217 :align: center | 217 :align: center |
| 218 | 218 |
| 219 | 219 |
| 220 </help> | 220 ]]></help> |
| 221 <citations> | 221 <citations> |
| 222 <citation type="doi"> doi:10.1093/nargab/lqaa052</citation> | 222 <citation type="doi"> doi:10.1093/nargab/lqaa052</citation> |
| 223 </citations> | 223 </citations> |
| 224 </tool> | 224 </tool> |