comparison goseq.xml @ 1:9d1256d9ef0b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 027e71072ff901d6b9593b37113c7b1f8b77527b

0:ade933eff007

        --category_file '$category_file'
        #if $methods['wallenius']:
        --wallenius_tab '$wallenius_tab'
        #end if
        #if $methods['hypergeometric']:
        --nobias_tab 'nobias_tab'
        #end if
        --repcnt '$methods.repcnt'
        --sampling_tab '$sampling_tab'
        --p_adj_method '$p_adj_method'
        --use_genes_without_cat '$use_genes_without_cat'

        The format of this file is tabular, with gene_id in the first column and length in the second column.
        The "get length and gc content" tool can produce such a file.

        *Gene category file:*
        You will also need a file describing the membership of genes in categories. The format of this file is gene_id in the first column,
        category name in the second column. If you are interested in gene ontology categories you can use the getgo file to retrive
        gene ontologies for model organisms, or you can construct your own file.

        **Method options**

        3 methods, "Wallenius", "Sampling" and "Hypergeometric", can be used to calculate the p-values as follows.

1:9d1256d9ef0b

        --category_file '$category_file'
        #if $methods['wallenius']:
        --wallenius_tab '$wallenius_tab'
        #end if
        #if $methods['hypergeometric']:
        --nobias_tab '$nobias_tab'
        #end if
        --repcnt '$methods.repcnt'
        --sampling_tab '$sampling_tab'
        --p_adj_method '$p_adj_method'
        --use_genes_without_cat '$use_genes_without_cat'

        The format of this file is tabular, with gene_id in the first column and length in the second column.
        The "get length and gc content" tool can produce such a file.

        *Gene category file:*
        You will also need a file describing the membership of genes in categories. The format of this file is gene_id in the first column,
        category identifier in the second column.

        **Method options**

        3 methods, "Wallenius", "Sampling" and "Hypergeometric", can be used to calculate the p-values as follows.