comparison mageck_mle.xml @ 1:93f268840b0c draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 2eea865fe331694058922292e5681b96f4f0b4c7

0:eab37e8fea75

<?xml version="1.0"?>
<tool id="mageck_mle" name="MAGeCK mle" version="@VERSION@" >
    <description>- perform maximum-likelihood estimation of gene essentiality scores</description>
    <macros>
        <import>mageck_macros.xml</import>
    </macros>
    <expand macro="requirements" />

                <option value="median" selected="True">Median</option>
                <option value="total">Total</option>
                <option value="control">Control</option>
            </param>
            <param name="genes_var" argument="--genes-varmodeling" type="integer" value="1000" label="Number of genes for mean-variance modeling" help="Default: 1000" />
            <param name="permutation" argument="--permutation-round" type="integer" value="10" label="Number of permutations" help="The rounds for permutation. The permutation time is (# genes) * x for x rounds of permutation. Suggested value: 100 (may take longer time). Default: 10" />
            <param name="remove_outliers" argument="--remove-outliers" type="boolean" truevalue="--remove-outliers" falsevalue="" checked="false" optional="true" label="Try to remove outliers" help="Turning this option on will slow the algorithm" />
            <param name="adjust_method" argument="--adjust-method" type="select" label="P-Value Adjustment Method" help="Method for sgRNA-level p-value adjustment, including False Discovery Rate (FDR), Holm's method (Holm), or Pounds's method (Pounds). Default: FDR">
                <option value="fdr" selected="True">FDR</option>
                <option value="holm">Holm</option>
                <option value="pounds">Pounds</option>

            <param name="sgrnaeff_name_col" argument="--sgrna-eff-score-column" type="data_column" data_ref="sgrnaeff_file" value="1" optional="true" label="sgRNA score column" help="The sgRNA efficiency prediction column in sgRNA efficiency prediction file (specified by the --sgrna-efficiency option). Default is 1 (the second column)." />
            <param name="sgrnaeff_score_col" argument="--sgrna-eff-name-column" type="data_column" data_ref="sgrnaeff_file" value="0" optional="true" label="sgRNA ID column" help="The sgRNA ID column in sgRNA efficiency prediction file (specified by the --sgrna-efficiency option). Default is 0 (the first column)" />
            <param name="update_eff" argument="--update-efficiency" type="boolean" truevalue="--update-efficiency" falsevalue="" checked="false" optional="true"
                label="Update efficiency" help="Iteratively update sgRNA efficiency during EM iteration" />
            <param name="out_log" type="boolean" truevalue="True" falsevalue="" checked="false"
                label="Output logfile" help="This file includes the logging information during the execution. For count command, it will list some basic statistics of the dataset at the end, including the number of reads, the number of reads mapped to the library, the number of zero-count sgRNAs, etc. Default: No" />
        </section>
    </inputs>
    <outputs>
        <data name="gene_summary" format="tabular" from_work_dir="*.gene_summary.txt" label="${tool.name} on ${on_string}: Gene Summary (MLE)" />
        <data name="sgrna_summary" format="tabular" from_work_dir="*.sgrna_summary.txt" label="${tool.name} on ${on_string}: sgRNA Summary (MLE)" />

1:93f268840b0c

<?xml version="1.0"?>
<tool id="mageck_mle" name="MAGeCK mle" version="@VERSION@.1" >
    <description>- perform maximum-likelihood estimation of gene essentiality scores</description>
    <macros>
        <import>mageck_macros.xml</import>
    </macros>
    <expand macro="requirements" />

                <option value="median" selected="True">Median</option>
                <option value="total">Total</option>
                <option value="control">Control</option>
            </param>
            <param name="genes_var" argument="--genes-varmodeling" type="integer" value="1000" label="Number of genes for mean-variance modeling" help="Default: 1000" />
            <param name="permutation" argument="--permutation-round" type="integer" value="2" label="Number of permutations" help="The rounds for permutation. The permutation time is (# genes) * x for x rounds of permutation. Default: 2" />
            <param name="remove_outliers" argument="--remove-outliers" type="boolean" truevalue="--remove-outliers" falsevalue="" checked="false" optional="true" label="Try to remove outliers" help="Turning this option on will slow the algorithm" />
            <param name="adjust_method" argument="--adjust-method" type="select" label="P-Value Adjustment Method" help="Method for sgRNA-level p-value adjustment, including False Discovery Rate (FDR), Holm's method (Holm), or Pounds's method (Pounds). Default: FDR">
                <option value="fdr" selected="True">FDR</option>
                <option value="holm">Holm</option>
                <option value="pounds">Pounds</option>

            <param name="sgrnaeff_name_col" argument="--sgrna-eff-score-column" type="data_column" data_ref="sgrnaeff_file" value="1" optional="true" label="sgRNA score column" help="The sgRNA efficiency prediction column in sgRNA efficiency prediction file (specified by the --sgrna-efficiency option). Default is 1 (the second column)." />
            <param name="sgrnaeff_score_col" argument="--sgrna-eff-name-column" type="data_column" data_ref="sgrnaeff_file" value="0" optional="true" label="sgRNA ID column" help="The sgRNA ID column in sgRNA efficiency prediction file (specified by the --sgrna-efficiency option). Default is 0 (the first column)" />
            <param name="update_eff" argument="--update-efficiency" type="boolean" truevalue="--update-efficiency" falsevalue="" checked="false" optional="true"
                label="Update efficiency" help="Iteratively update sgRNA efficiency during EM iteration" />
            <param name="out_log" type="boolean" truevalue="True" falsevalue="" checked="false"
                label="Output Log file" help="This file includes the logging information during the execution. For count command, it will list some basic statistics of the dataset at the end, including the number of reads, the number of reads mapped to the library, the number of zero-count sgRNAs, etc. Default: No" />
        </section>
    </inputs>
    <outputs>
        <data name="gene_summary" format="tabular" from_work_dir="*.gene_summary.txt" label="${tool.name} on ${on_string}: Gene Summary (MLE)" />
        <data name="sgrna_summary" format="tabular" from_work_dir="*.sgrna_summary.txt" label="${tool.name} on ${on_string}: sgRNA Summary (MLE)" />