comparison preprocessing.xml @ 2:48d9421bf176 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b

1:cec3e76eaf05

    count_frag_as_reads = $method.count_frag_as_reads,
    n_jobs = int(os.getenv("GALAXY_SLOTS", 4))
)

#else if $method.method == 'pp.make_gene_matrix'
sa.pp.make_gene_matrix(
    adata,
    gene_anno = '$method.gene_anno',
    chunk_size = $method.chunk_size,
    use_x = $method.use_x,
    id_type = '$method.id_type',

                    <has_text_matching expression="gene_name_key = 'gene_name'"/>
                    <has_text_matching expression="gene_id_key = 'gene_id'"/>
                    <has_text_matching expression="count_frag_as_reads = True"/>
                </assert_contents>
            </output>
            <output name="anndata_out" location="https://zenodo.org/records/11260316/files/pp.make_gene_matrix.pbmc_500_chr21.h5ad" ftype="h5ad" compare="sim_size" delta_frac="0.1" />
        </test>
        <test expect_num_outputs="2">
            <!-- metrics.tsse -->
            <conditional name="method">
                <param name="method" value="metrics.tsse"/>

2:48d9421bf176

    count_frag_as_reads = $method.count_frag_as_reads,
    n_jobs = int(os.getenv("GALAXY_SLOTS", 4))
)

#else if $method.method == 'pp.make_gene_matrix'
adata = sa.pp.make_gene_matrix(
    adata,
    gene_anno = '$method.gene_anno',
    chunk_size = $method.chunk_size,
    use_x = $method.use_x,
    id_type = '$method.id_type',

                    <has_text_matching expression="gene_name_key = 'gene_name'"/>
                    <has_text_matching expression="gene_id_key = 'gene_id'"/>
                    <has_text_matching expression="count_frag_as_reads = True"/>
                </assert_contents>
            </output>
            <output name="anndata_out" location="https://zenodo.org/records/12548681/files/pp.make_gene_matrix.pbmc_500_chr21.h5ad" ftype="h5ad" compare="sim_size" delta_frac="0.1" />
        </test>
        <test expect_num_outputs="2">
            <!-- metrics.tsse -->
            <conditional name="method">
                <param name="method" value="metrics.tsse"/>