comparison manipulate.xml @ 2:a56baceb1900 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 3b41d687ff30583540d055f6995de00530cca81d"

1:19592ec717ef

    #if $manipulate.var_obs == 'var'
adata = adata[:,filtered]
    #else if $manipulate.var_obs == 'obs'
adata = adata[filtered, :]
    #end if
#end if

adata.write('anndata.h5ad')
]]></configfile>
    </configfiles>

                <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>
                <option value="add_annotation">Add new annotation(s) for observations or variables</option>
                <option value="filter">Filter observations or variables</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>

                </param>
                <param name="new_annot" type="data" format="tabular" label="Table with new annotations" 
                    help="The new table should have the same number of rows and same order than obs or var. The key names should be in the header (1st line)"/>
            </when>
            <when value="filter">
                <param name="var_obs" type="select" label="What to annotate?">
                    <option value="var">Variables (var)</option>
                    <option value="obs">Observations (obs)</option>
                </param>
                <conditional name="filter">
                    <param name="filter" type="select" label="Type of filtering?">

                    </conditional>
                </conditional>
            </conditional>
            <output name="anndata" value="manipulate.filter_obs_key.h5ad" ftype="h5ad" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

This tool takes a AnnData dataset, manipulates it and returns it. 

    Data matrix is transposed, observations and variables are interchanged.

- Add annotation for variables or observations 

- Filter data variables or observations, by index or key

@HELP@
    ]]></help>
    <expand macro="citations"/>
</tool>

2:a56baceb1900

    #if $manipulate.var_obs == 'var'
adata = adata[:,filtered]
    #else if $manipulate.var_obs == 'obs'
adata = adata[filtered, :]
    #end if

#else if $manipulate.function == 'save_raw'
adata.raw = adata

#end if

adata.write('anndata.h5ad')
]]></configfile>
    </configfiles>

                <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>
                <option value="add_annotation">Add new annotation(s) for observations or variables</option>
                <option value="filter">Filter observations or variables</option>
                <option value="save_raw">Freeze the current state into the 'raw' attribute</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>

                </param>
                <param name="new_annot" type="data" format="tabular" label="Table with new annotations" 
                    help="The new table should have the same number of rows and same order than obs or var. The key names should be in the header (1st line)"/>
            </when>
            <when value="filter">
                <param name="var_obs" type="select" label="What to filter?">
                    <option value="var">Variables (var)</option>
                    <option value="obs">Observations (obs)</option>
                </param>
                <conditional name="filter">
                    <param name="filter" type="select" label="Type of filtering?">

                    </conditional>
                </conditional>
            </conditional>
            <output name="anndata" value="manipulate.filter_obs_key.h5ad" ftype="h5ad" compare="sim_size"/>
        </test>
        <test>
            <!-- test 11 -->
            <param name="input" value="krumsiek11.h5ad"/>
            <conditional name="manipulate">
                <param name="function" value="save_raw"/>
            </conditional>
            <output name="anndata" value="manipulate.save_raw.h5ad" ftype="h5ad" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

This tool takes a AnnData dataset, manipulates it and returns it. 

    Data matrix is transposed, observations and variables are interchanged.

- Add annotation for variables or observations 

- Filter data variables or observations, by index or key

- Freeze the current state into the 'raw' attribute

@HELP@
    ]]></help>
    <expand macro="citations"/>
</tool>