| Previous changeset 0:eab37e8fea75 (2018-02-14) Next changeset 2:9cd937788131 (2018-04-04) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 2eea865fe331694058922292e5681b96f4f0b4c7 |
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modified:
mageck_mle.xml test-data/out.count.bam.txt test-data/out.count.fastq.txt |
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| diff -r eab37e8fea75 -r 93f268840b0c mageck_mle.xml --- a/mageck_mle.xml Wed Feb 14 06:42:36 2018 -0500 +++ b/mageck_mle.xml Sat Feb 17 10:41:41 2018 -0500 |
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| @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="mageck_mle" name="MAGeCK mle" version="@VERSION@" > +<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> @@ -74,7 +74,7 @@ <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="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> @@ -87,7 +87,7 @@ <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" /> + 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> |
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| diff -r eab37e8fea75 -r 93f268840b0c test-data/out.count.bam.txt --- a/test-data/out.count.bam.txt Wed Feb 14 06:42:36 2018 -0500 +++ b/test-data/out.count.bam.txt Sat Feb 17 10:41:41 2018 -0500 |
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| @@ -1,4 +1,4 @@ -sgRNA Gene sample1 +sgRNA Gene test1.bam s_10007 CCNA1 0 s_10008 CCNA1 0 s_10027 CCNC 0 |
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| diff -r eab37e8fea75 -r 93f268840b0c test-data/out.count.fastq.txt --- a/test-data/out.count.fastq.txt Wed Feb 14 06:42:36 2018 -0500 +++ b/test-data/out.count.fastq.txt Sat Feb 17 10:41:41 2018 -0500 |
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| @@ -1,4 +1,4 @@ -sgRNA Gene sample1 +sgRNA Gene test1.fastq.gz s_47512 RNF111 1 s_24835 HCFC1R1 1 s_14784 CYP4B1 4 |