comparison normalize.xml @ 10:ab55fe8030b6 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 806c15e8f3ae7acea300ebeb83222162c42eca14"

9:51d945eab1e1

<tool id="scanpy_normalize" name="Normalize" version="@galaxy_version@" profile="@profile@">
    <description>with scanpy</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="version_command"/>

                    <has_text_matching expression="sc.pp.recipe_zheng17"/>
                    <has_text_matching expression="n_top_genes=1000"/>
                    <has_text_matching expression="log=True"/>
                </assert_contents>
            </output>
            <output name="anndata_out" file="pp.recipe_zheng17.random-randint.h5ad" ftype="h5ad" compare="sim_size" delta="1000000" delta_frace="0.15"/>
        </test>
        <test>
            <!-- test 2 -->
            <param name="adata" value="paul15_subsample.h5ad" />
            <conditional name="method">

                <assert_contents>
                    <has_text_matching expression="sc.pp.recipe_seurat"/>
                    <has_text_matching expression="log=True"/>
                </assert_contents>
            </output>
            <output name="anndata_out" file="pp.recipe_seurat.recipe_zheng17.h5ad" ftype="h5ad" compare="sim_size" delta="1000000" delta_frace="0.15"/>
        </test>
    </tests>
    <help><![CDATA[
Normalize total counts per cell (`pp.normalize_per_cell`)
=========================================================

10:ab55fe8030b6

<tool id="scanpy_normalize" name="Normalize" version="@galaxy_version@" profile="@profile@">
    <description>with scanpy</description>
    <expand macro="bio_tools"/>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="version_command"/>

                    <has_text_matching expression="sc.pp.recipe_zheng17"/>
                    <has_text_matching expression="n_top_genes=1000"/>
                    <has_text_matching expression="log=True"/>
                </assert_contents>
            </output>
            <output name="anndata_out" file="pp.recipe_zheng17.random-randint.h5ad" ftype="h5ad" compare="sim_size" delta="1000000" delta_frac="0.15"/>
        </test>
        <test>
            <!-- test 2 -->
            <param name="adata" value="paul15_subsample.h5ad" />
            <conditional name="method">

                <assert_contents>
                    <has_text_matching expression="sc.pp.recipe_seurat"/>
                    <has_text_matching expression="log=True"/>
                </assert_contents>
            </output>
            <output name="anndata_out" file="pp.recipe_seurat.recipe_zheng17.h5ad" ftype="h5ad" compare="sim_size" delta="1000000" delta_frac="0.25"/>
        </test>
    </tests>
    <help><![CDATA[
Normalize total counts per cell (`pp.normalize_per_cell`)
=========================================================