annotate inspect.xml @ 0:b2a6ce371781 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da

<tool id="anndata_inspect" name="Inspect AnnData" version="@VERSION@+@GALAXY_VERSION@">
    <description>object</description>
    <macros>
        <import>macros.xml</import>
    </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 $inspect.info == 'general'
with open('$general', 'w') as f:
    print(adata, file=f)
#else if $inspect.info == 'X'
adata.to_df().to_csv('$X', sep='\t')
#else if $inspect.info == 'obs'
adata.obs.to_csv('$obs', sep='\t')
#else if $inspect.info == 'var'
adata.var.to_csv('$var', sep='\t')
#else if $inspect.info == 'chunk_X'
import pandas as pd
    #if $inspect.chunk.info == 'random'
X = adata.chunk_X(select=$inspect.chunk.size, replace=$inspect.chunk.replace)
    #else
        #set $select = [int(x.strip()) for x in str($inspect.chunk.list).split(',')]
X = adata.chunk_X(select=$select)
    #end if
pd.DataFrame(X).to_csv('$chunk_X', sep='\t')
#end if
]]></configfile>
    </configfiles>
    <inputs>
        <param name="input" type="data" format="h5ad" label="Annotated data matrix"/>
        <conditional name="inspect">
            <param name="info" type="select" label="What to inspect?">
                <option value="general">General information about the object</option>
                <option value="X">The full data matrix</option>
                <option value="chunk_X">A chunk of the data matrix</option>
                <option value="obs">Key-indexed observations annotation</option>
                <option value="var">Key-indexed annotation of variables/features</option>
                <!--<option value="uns">Unstructured annotation</option>!-->
            </param>
            <when value="general"/>
            <when value="X"/>
            <when value="obs"/>
            <when value="var"/>
            <when value="chunk_X">
                <expand macro="params_chunk_X"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="general" format="txt" label="${tool.name} on ${on_string}: General information">
            <filter>inspect['info'] == 'general'</filter>
        </data>
        <data name="X" format="tabular" label="${tool.name} on ${on_string}: Key-indexed observations annotation (X)">
            <filter>inspect['info'] == 'X'</filter>
        </data>
        <data name="obs" format="tabular" label="${tool.name} on ${on_string}: Key-indexed observations annotation (obs)">
            <filter>inspect['info'] == 'obs'</filter>
        </data>
        <data name="var" format="tabular" label="${tool.name} on ${on_string}: Key-indexed annotation of variables/features (var)">
            <filter>inspect['info'] == 'var'</filter>
        </data>
        <data name="chunk_X" format="tabular" label="${tool.name} on ${on_string}: Observations annotation">
            <filter>inspect['info'] == 'chunk_X'</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="input" value="krumsiek11.h5ad"/>
            <conditional name="inspect">
                <param name="info" value="general"/>
            </conditional>
            <output name="general" value="inspect.general.txt"/>
        </test>
        <test>
            <param name="input" value="krumsiek11.h5ad"/>
            <conditional name="inspect">
                <param name="info" value="X"/>
            </conditional>
            <assert_stdout>
                <has_text_matching expression="adata.to_df\(\).to_csv"/>
            </assert_stdout>
            <output name="X" value="inspect.X.tabular" ftype="tabular"/>
        </test>
        <test>
            <param name="input" value="krumsiek11.h5ad"/>
            <conditional name="inspect">
                <param name="info" value="obs"/>
            </conditional>
            <assert_stdout>
                <has_text_matching expression="adata.obs.to_csv"/>
            </assert_stdout>
            <output name="obs" value="inspect.obs.tabular" ftype="tabular"/>
        </test>
        <test>
            <param name="input" value="krumsiek11.h5ad"/>
            <conditional name="inspect">
                <param name="info" value="var"/>
            </conditional>
            <assert_stdout>
                <has_text_matching expression="adata.var.to_csv"/>
            </assert_stdout>
            <output name="var" value="inspect.var.tabular" ftype="tabular"/>
        </test>
        <test>
            <param name="input" value="krumsiek11.h5ad"/>
            <conditional name="inspect">
                <param name="info" value="chunk_X"/>
                <conditional name="chunk">
                    <param name="info" value="specified"/>
                    <param name="list" value="3,5,8"/>
                </conditional>
            </conditional>
            <assert_stdout>
                <has_text_matching expression="adata.chunk_X"/>
                <has_text_matching expression="select=\[3, 5, 8\]"/>
            </assert_stdout>
            <output name="chunk_X" value="inspect.chunk_X.specified.tabular" ftype="tabular"/>
        </test>
        <test>
            <param name="input" value="krumsiek11.h5ad"/>
            <conditional name="inspect">
                <param name="info" value="chunk_X"/>
                <conditional name="chunk">
                    <param name="info" value="random"/>
                    <param name="list" value="10"/>
                    <param name="replace" value="true"/>
                </conditional>
            </conditional>
            <assert_stdout>
                <has_text_matching expression="adata.chunk_X"/>
                <has_text_matching expression="select=10"/>
                <has_text_matching expression="replace=True"/>
            </assert_stdout>
            <output name="chunk_X">
                <assert_contents>
                    <has_text_matching expression="0\t1\t2\t3\t4\t5\t6\t7\t8\t9\t10"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

This tool inspects a AnnData dataset and returns:

- General information about the object as text
- The full data matrix (`X`) as a Tabular
- A chunk of the data matrix as a Tabular, using the `chunk_X method <https://anndata.readthedocs.io/en/latest/anndata.AnnData.chunk_X.html>`__
- Key-indexed observations annotation (`obs`) as a Tabular
- Key-indexed annotation of variables/features (`var`) as a Tabular

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