| Previous changeset 0:b8da4d41aa1d (2018-02-14) Next changeset 2:81bbbddcf285 (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_test.xml test-data/out.count.bam.txt test-data/out.count.fastq.txt |
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| diff -r b8da4d41aa1d -r 5e2a28bee02d mageck_test.xml --- a/mageck_test.xml Wed Feb 14 06:42:55 2018 -0500 +++ b/mageck_test.xml Sat Feb 17 10:41:53 2018 -0500 |
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| @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="mageck_test" name="MAGeCKs test" version="@VERSION@" > +<tool id="mageck_test" name="MAGeCKs test" version="@VERSION@.1" > <description>- given a table of read counts, perform the sgRNA and gene ranking</description> <macros> <import>mageck_macros.xml</import> @@ -31,14 +31,21 @@ --adjust-method $adv.adjust_method $adv.var_samples --sort-criteria $adv.sort_criteria + --remove-zero $adv.remove_zero +#if $adv.remove_zero_threshold: + --remove-zero-threshold $adv.remove_zero_threshold +#end if + --gene-lfc-method $adv.lfc_method #if $adv.control_sgrna: --control-sgrna $adv.control_sgrna #end if + #if $adv.cnv_norm: --cnv-norm $adv.cnv_norm #end if + #if $adv.cell_line: --cell-line $adv.cell_line #end if @@ -65,7 +72,7 @@ <param name="normcounts" argument="--normcounts-to-file" type="boolean" truevalue="--normcounts-to-file" falsevalue="" checked="false" optional="true" label="Output normalized counts file" help="Default: No" /> <param name="pdfreport" argument="--pdf-report" type="boolean" truevalue="--pdf-report" falsevalue="" checked="false" optional="true" label="Output PDF report" help="Generate pdf report of the input file. Default: No" /> <param name="rscriptOpt" type="boolean" truevalue="True" falsevalue="" checked="false" optional="true" label="Output R script" help="Output the R script used to generate the plots in the pdf report. Default: No" /> - <param name="out_log" type="boolean" truevalue="True" falsevalue="" checked="false" label="Output logfile" help="This file includes the logging information during the execution. Default: No" /> + <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. Default: No" /> </section> <section name="adv" title="Advanced Options"> @@ -84,12 +91,14 @@ </param> <param name="var_samples" argument="--variance-from-all-samples" type="boolean" truevalue="--variance-from-all-samples" falsevalue="" checked="false" optional="true" label="Estimate the variance from all samples, instead of from only control samples" help="Use this option only if you believe there are relatively few essential sgRNAs or genes between control and treatment samples" /> <expand macro="sort_criteria" /> - <param name="remove_zero" argument="--remove-zero" type="select" help="Whether to remove zero-count sgRNAs in control and/or treatment experiments {none,control,treatment,both}. Default: None (do not remove those zero-count sgRNAs)" > - <option value="none" selected="True">None</option> + <param name="remove_zero" argument="--remove-zero" type="select" label="Remove zero" help="Remove sgRNAs whose mean value is zero in Control, Treatment, Both control/treatment, or Any control/treatment sample. Default: Both (remove those sgRNAs that are zero in both control and treatment samples)" > + <option value="none" >None</option> <option value="control">Control</option> <option value="treatment">Treatment</option> - <option value="both">Both</option> + <option value="both" selected="True">Both</option> + <option value="any">Any</option> </param> + <param name="remove_zero_threshold" argument="--remove-zero-threshold" type="float" value="0" label="Remove zero Threshold" help="sgRNA normalized count threshold to be considered removed in the --remove-zero option. Default: 0"/> <param name="lfc_method" argument="--gene-lfc-method" type="select" label="Gene Log-Fold Change Method." help="Method to calculate gene log fold changes (LFC) from sgRNA LFCs. Available methods include the median/mean of all sgRNAs (median/mean), or the median/mean sgRNAs that are ranked in front of the alpha cutoff in RRA (alphamedian/alphamean), or the sgRNA that has the second strongest LFC (secondbest). In the alphamedian/alphamean case, the number of sgRNAs correspond to the goodsgrna column in the output, and the gene LFC will be set to 0 if no sgRNA is in front of the alpha cutoff. Default: Median. (new since v0.5.5)"> <option value="median" selected="True">Median</option> <option value="alphamedian">Alphamedian</option> |
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| diff -r b8da4d41aa1d -r 5e2a28bee02d test-data/out.count.bam.txt --- a/test-data/out.count.bam.txt Wed Feb 14 06:42:55 2018 -0500 +++ b/test-data/out.count.bam.txt Sat Feb 17 10:41:53 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 b8da4d41aa1d -r 5e2a28bee02d test-data/out.count.fastq.txt --- a/test-data/out.count.fastq.txt Wed Feb 14 06:42:55 2018 -0500 +++ b/test-data/out.count.fastq.txt Sat Feb 17 10:41:53 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 |