Mercurial > repos > iuc > anndata_manipulate
diff manipulate.xml @ 0:0ef28c0963c8 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
| author | iuc |
|---|---|
| date | Wed, 10 Apr 2019 03:25:05 -0400 |
| parents | |
| children | 19592ec717ef |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/manipulate.xml Wed Apr 10 03:25:05 2019 -0400 @@ -0,0 +1,217 @@ +<tool id="anndata_manipulate" name="Manipulate AnnData" version="@VERSION@+@GALAXY_VERSION@"> + <description>object</description> + <macros> + <import>macros.xml</import> + <xml name="param_join"> + <param name="join" type="select" label="The connecting string between name and integer"> + <option value="-">-</option> + <option value="_">_</option> + <option value=" "> </option> + <option value="/">/</option> + </param> + </xml> + </macros> + <expand macro="requirements"/> + <expand macro="version_command"/> + <command detect_errors="exit_code"><![CDATA[ +@CMD@ + ]]></command> + <configfiles> + <configfile name="script_file"><![CDATA[ +@CMD_imports@ + +adata = ad.read('$input') + +#if $manipulate.function == 'concatenate' + #for i, filepath in enumerate($manipulate.other_adatas) +adata_$i = ad.read('$filepath') + #end for +adata.concatenate( + #for i, filepath in enumerate($manipulate.other_adatas) + adata_$i, + #end for + join='$manipulate.join', + #if str($manipulate.index_unique) != '' + index_unique='$manipulate.index_unique', + #else + index_unique=None, + #end if + batch_key='$manipulate.batch_key') + +#else if $manipulate.function == 'var_names_make_unique' +adata.var_names_make_unique(join='$manipulate.join') + +#else if $manipulate.function == 'obs_names_make_unique' +adata.obs_names_make_unique(join='$manipulate.join') + +#else if $manipulate.function == 'rename_categories' + #set $categories = [x.strip() for x in str($manipulate.categories).split(',')] +adata.rename_categories( + key='$manipulate.key', + categories=$categories) + +#else if $manipulate.function == 'transpose' +adata.transpose() + +#else if $manipulate.function == 'strings_to_categoricals' +adata.strings_to_categoricals() +#end if + +adata.write('anndata.h5ad') +]]></configfile> + </configfiles> + <inputs> + <param name="input" type="data" format="h5ad" label="Annotated data matrix"/> + <conditional name="manipulate"> + <param name="function" type="select" label="Function of manipulate the object"> + <option value="concatenate">Concatenate along the observations axis</option> + <option value="obs_names_make_unique">Makes the obs index unique by appending '1', '2', etc</option> + <option value="var_names_make_unique">Makes the var index unique by appending '1', '2', etc</option> + <option value="rename_categories">Rename categories of annotation</option> + <option value="strings_to_categoricals">Transform string annotations to categoricals</option> + <option value="transpose">Transpose the data matrix, leaving observations and variables interchanged</option> + </param> + <when value="concatenate"> + <param name="other_adatas" type="data" format="h5ad" multiple="true" label="Annotated data matrix to add"/> + <param name="join" type="select" label="Join method"> + <option value="inner">Intersection of variables</option> + <option value="outer">Union of variables</option> + </param> + <param name="batch_key" type="text" value="batch" label="Key to add the batch annotation to obs"/> + <param name="index_unique" type="select" label="Separator to join the existing index names with the batch category" help="Leave it empty to keep existing indices"> + <option value="-">-</option> + <option value="_">_</option> + <option value=" "> </option> + <option value="/">/</option> + </param> + </when> + <when value="obs_names_make_unique"> + <expand macro="param_join"/> + </when> + <when value="var_names_make_unique"> + <expand macro="param_join"/> + </when> + <when value="rename_categories"> + <param name="key" type="text" value="" label="Key for observations or variables annotation" help="Annotation key in obs or var"/> + <param name="categories" type="text" value="" label="Comma-separated list of new categories" help="It should be the same number as the old categories"/> + </when> + <when value="strings_to_categoricals"/> + <when value="transpose"/> + </conditional> + </inputs> + <outputs> + <data name="anndata" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} on ${on_string}"/> + </outputs> + <tests> + <test> + <param name="input" value="krumsiek11.h5ad"/> + <conditional name="manipulate"> + <param name="function" value="concatenate"/> + <param name="other_adatas" value="import.csv.h5ad"/> + <param name="join" value="inner"/> + <param name="batch_key" value="batch"/> + <param name="index_unique" value="-"/> + </conditional> + <assert_stdout> + <has_text_matching expression="adata_0"/> + <has_text_matching expression="adata.concatenate"/> + <has_text_matching expression="join='inner'"/> + <has_text_matching expression="index_unique='-'"/> + <has_text_matching expression="batch_key='batch'"/> + </assert_stdout> + <output name="anndata" value="manipulate.concatenate.h5ad" ftype="h5ad" compare="sim_size"/> + </test> + <test> + <param name="input" value="krumsiek11.h5ad"/> + <conditional name="manipulate"> + <param name="function" value="obs_names_make_unique"/> + <param name="join" value="-"/> + </conditional> + <assert_stdout> + <has_text_matching expression="adata.obs_names_make_unique\(join='-'\)"/> + </assert_stdout> + <output name="anndata" value="manipulate.obs_names_make_unique.h5ad" ftype="h5ad" compare="sim_size"/> + </test> + <test> + <param name="input" value="krumsiek11.h5ad"/> + <conditional name="manipulate"> + <param name="function" value="var_names_make_unique"/> + <param name="join" value="-"/> + </conditional> + <assert_stdout> + <has_text_matching expression="adata.var_names_make_unique\(join='-'\)"/> + </assert_stdout> + <output name="anndata" value="manipulate.var_names_make_unique.h5ad" ftype="h5ad" compare="sim_size"/> + </test> + <test> + <param name="input" value="krumsiek11.h5ad"/> + <conditional name="manipulate"> + <param name="function" value="rename_categories"/> + <param name="key" value="cell_type"/> + <param name="categories" value="Er,Ml,Mt, Ne, pr"/> + </conditional> + <assert_stdout> + <has_text_matching expression="adata.rename_categories"/> + <has_text_matching expression="key='cell_type'"/> + <has_text_matching expression="categories=\['Er', 'Ml', 'Mt', 'Ne', 'pr'\]"/> + </assert_stdout> + <output name="anndata" value="manipulate.rename_categories.h5ad" ftype="h5ad" compare="sim_size"/> + </test> + <test> + <param name="input" value="krumsiek11.h5ad"/> + <conditional name="manipulate"> + <param name="function" value="strings_to_categoricals"/> + </conditional> + <assert_stdout> + <has_text_matching expression="adata.strings_to_categoricals"/> + </assert_stdout> + <output name="anndata" value="manipulate.strings_to_categoricals.h5ad" ftype="h5ad" compare="sim_size"/> + </test> + <test> + <param name="input" value="krumsiek11.h5ad"/> + <conditional name="manipulate"> + <param name="function" value="transpose"/> + </conditional> + <assert_stdout> + <has_text_matching expression="adata.transpose"/> + </assert_stdout> + <output name="anndata" value="manipulate.transpose.h5ad" ftype="h5ad" compare="sim_size"/> + </test> + </tests> + <help><![CDATA[ +**What it does** + +This tool takes a AnnData dataset, manipulates it and returns it. + +The possible manipulations are: + +- Concatenate along the observations axis (`concatenate method <https://anndata.readthedocs.io/en/latest/anndata.AnnData.concatenate.html>`__) + + The `uns`, `varm` and `obsm` attributes are ignored. + + If you use `join='outer'` this fills 0s for sparse data when variables are absent in a batch. Use this with care. Dense data is filled with `NaN` + +- Makes the obs index unique by appending '1', '2', etc (`obs_names_make_unique method <https://anndata.readthedocs.io/en/latest/anndata.AnnData.obs_names_make_unique.html>`__) + + The first occurance of a non-unique value is ignored. + +- Makes the var index unique by appending '1', '2', etc (`var_names_make_unique method <https://anndata.readthedocs.io/en/latest/anndata.AnnData.var_names_make_unique.html>`__) + + The first occurance of a non-unique value is ignored. + +- Rename categories of annotation `key` in `obs`, `var` and `uns` (`rename_categories method <https://anndata.readthedocs.io/en/latest/anndata.AnnData.rename_categories.html>`__) + + Besides calling `self.obs[key].cat.categories = categories` - similar for `var` - this also renames categories in unstructured annotation that uses the categorical annotation `key` + +- Transform string annotations to categoricals (`strings_to_categoricals method <https://anndata.readthedocs.io/en/latest/anndata.AnnData.strings_to_categoricals.html>`__) + + Only affects string annotations that lead to less categories than the total number of observations. + +- Transpose the data matrix, leaving observations and variables interchanged (`transpose method <https://anndata.readthedocs.io/en/latest/anndata.AnnData.transpose.html>`__) + + Data matrix is transposed, observations and variables are interchanged. + +@HELP@ + ]]></help> + <expand macro="citations"/> +</tool>