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comparison mageck_mle.xml @ 1:93f268840b0c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 2eea865fe331694058922292e5681b96f4f0b4c7
author iuc
date Sat, 17 Feb 2018 10:41:41 -0500
parents eab37e8fea75
children 9cd937788131
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0:eab37e8fea75 1:93f268840b0c
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="mageck_mle" name="MAGeCK mle" version="@VERSION@" > 2 <tool id="mageck_mle" name="MAGeCK mle" version="@VERSION@.1" >
3 <description>- perform maximum-likelihood estimation of gene essentiality scores</description> 3 <description>- perform maximum-likelihood estimation of gene essentiality scores</description>
4 <macros> 4 <macros>
5 <import>mageck_macros.xml</import> 5 <import>mageck_macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
72 <option value="median" selected="True">Median</option> 72 <option value="median" selected="True">Median</option>
73 <option value="total">Total</option> 73 <option value="total">Total</option>
74 <option value="control">Control</option> 74 <option value="control">Control</option>
75 </param> 75 </param>
76 <param name="genes_var" argument="--genes-varmodeling" type="integer" value="1000" label="Number of genes for mean-variance modeling" help="Default: 1000" /> 76 <param name="genes_var" argument="--genes-varmodeling" type="integer" value="1000" label="Number of genes for mean-variance modeling" help="Default: 1000" />
77 <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" /> 77 <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" />
78 <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" /> 78 <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" />
79 <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"> 79 <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">
80 <option value="fdr" selected="True">FDR</option> 80 <option value="fdr" selected="True">FDR</option>
81 <option value="holm">Holm</option> 81 <option value="holm">Holm</option>
82 <option value="pounds">Pounds</option> 82 <option value="pounds">Pounds</option>
85 <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)." /> 85 <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)." />
86 <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)" /> 86 <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)" />
87 <param name="update_eff" argument="--update-efficiency" type="boolean" truevalue="--update-efficiency" falsevalue="" checked="false" optional="true" 87 <param name="update_eff" argument="--update-efficiency" type="boolean" truevalue="--update-efficiency" falsevalue="" checked="false" optional="true"
88 label="Update efficiency" help="Iteratively update sgRNA efficiency during EM iteration" /> 88 label="Update efficiency" help="Iteratively update sgRNA efficiency during EM iteration" />
89 <param name="out_log" type="boolean" truevalue="True" falsevalue="" checked="false" 89 <param name="out_log" type="boolean" truevalue="True" falsevalue="" checked="false"
90 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" /> 90 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" />
91 </section> 91 </section>
92 </inputs> 92 </inputs>
93 <outputs> 93 <outputs>
94 <data name="gene_summary" format="tabular" from_work_dir="*.gene_summary.txt" label="${tool.name} on ${on_string}: Gene Summary (MLE)" /> 94 <data name="gene_summary" format="tabular" from_work_dir="*.gene_summary.txt" label="${tool.name} on ${on_string}: Gene Summary (MLE)" />
95 <data name="sgrna_summary" format="tabular" from_work_dir="*.sgrna_summary.txt" label="${tool.name} on ${on_string}: sgRNA Summary (MLE)" /> 95 <data name="sgrna_summary" format="tabular" from_work_dir="*.sgrna_summary.txt" label="${tool.name} on ${on_string}: sgRNA Summary (MLE)" />