Mercurial > repos > iuc > mageck_mle
diff mageck_mle.xml @ 2:9cd937788131 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
| author | iuc |
|---|---|
| date | Wed, 04 Apr 2018 11:03:44 -0400 |
| parents | 93f268840b0c |
| children | b34c9d6373e0 |
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--- a/mageck_mle.xml Sat Feb 17 10:41:41 2018 -0500 +++ b/mageck_mle.xml Wed Apr 04 11:03:44 2018 -0400 @@ -30,10 +30,21 @@ --cnv-norm $adv.cnv_norm #end if ---norm-method $adv.norm_method ---genes-varmodeling $adv.genes_var ---permutation-round $adv.permutation ---adjust-method $adv.adjust_method +#if $adv.norm_method: + --norm-method $adv.norm_method +#end if + +#if $adv.genes_var: + --genes-varmodeling $adv.genes_var +#end if + +#if $adv.permutation: + --permutation-round $adv.permutation +#end if + +#if $adv.adjust_method: + --adjust-method $adv.adjust_method +#end if #if $adv.sgrnaeff_file: --sgrna-efficiency $adv.sgrnaeff_file @@ -58,26 +69,32 @@ <param name="design_matrix" argument="--design-matrix" type="data" format="tabular" label="Design Matrix file" help="Provide a design matrix, either a file name or a quoted string of the design matrix. For example, 1,1;1,0. The row of the design matrix must match the order of the samples in the count table (if --include-samples is not specified), or the order of the samples by the --include-samples option" /> </when> <when value="labels"> - <param name="include_samples" argument="--include-samples" type="text" label="Sample labels" help="Specify the sample labels if the design matrix is not given by file in the --design-matrix option. Sample labels are separated by comma (,) and must match the labels in the count table" /> - <param name="day0_label" argument="--day0-label" type="text" format="tabular" optional="true" value="" label="Control sample" help="Specify the control sample label (usually day 0 or plasmid). For every other sample label, the MLE module will treat it as a single condition and generate an corresponding design matrix" /> - <param name="beta_labels" argument="--beta-labels" type="text" label="Variables" help="Specify the labels of the variables (i.e., beta), if the design matrix is not given by file in the --design-matrix option. Should be separated by commas (,), and the number of labels must equal to the number of columns of design matrix), including baseline labels. Default: bata_0,beta_1,beta_2,...." /> + <param name="include_samples" argument="--include-samples" type="text" label="Sample labels" help="Specify the sample labels if the design matrix is not given by file in the --design-matrix option. Sample labels are separated by comma (,) and must match the labels in the count table"> + <validator type="regex" message="Please only use letters, numbers or underscores in sample labels, and separate labels by commas">^[\w,]+$</validator> + </param> + <param name="day0_label" argument="--day0-label" type="text" format="tabular" optional="true" value="" label="Control sample" help="Specify the control sample label (usually day 0 or plasmid). For every other sample label, the MLE module will treat it as a single condition and generate an corresponding design matrix"> + <validator type="regex" message="Please only use letters, numbers or underscores in sample label">^[\w]+$</validator> + </param> + <param name="beta_labels" argument="--beta-labels" type="text" label="Variables" help="Specify the labels of the variables (i.e., beta), if the design matrix is not given by file in the --design-matrix option. Should be separated by commas (,), and the number of labels must equal to the number of columns of design matrix), including baseline labels. Default: bata_0,beta_1,beta_2,...."> + <validator type="regex" message="Please only use letters, numbers or underscores in labels, and separate labels by commas">^[\w,]+$</validator> + </param> </when> </conditional> <section name="adv" title="Advanced Options"> <param name="control_sgrna" argument="--control-sgrna" type="data" format="tabular" optional="true" label="Control sgRNAs file" help="A list of control sgRNAs for normalization and for generating the null distribution of RRA" /> <param name="cnv_norm" argument="--cnv-norm" type="data" format="tabular" optional="true" label="CNV profile file" help="A matrix of copy number variation data across cell lines to normalize CNV-biased BetaScores" /> - <param name="norm_method" argument="--norm-method" type="select" label="Method for normalization" help="If control is specified, the size factor will be estimated using control sgRNAs specified in --control-sgrna option. Default: Median" > + <param name="norm_method" argument="--norm-method" type="select" optional="true" label="Method for normalization" help="If control is specified, the size factor will be estimated using control sgRNAs specified in --control-sgrna option. Default: Median" > + <option value="median" selected="True">Median</option> <option value="none">None</option> - <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="genes_var" argument="--genes-varmodeling" type="integer" optional="true" label="Number of genes for mean-variance modeling" help="Default: 1000" /> + <param name="permutation" argument="--permutation-round" type="integer" optional="true" 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> + <param name="adjust_method" argument="--adjust-method" type="select" optional="true" 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">FDR</option> <option value="holm">Holm</option> <option value="pounds">Pounds</option> </param> @@ -168,9 +185,18 @@ **Outputs** -If successful, MAGeCK mle will generate two files, the gene_summary file (including gene beta scores), and the sgrna_summary file (including sgRNA efficiency probability predictions). +This tool outputs + + * a ranked sgRNA Summary file + * a ranked Gene Summary file -**Gene summary file (including beta scores)** +Optionally, under **Output Options** you can choose to output + + * a Log file of the analysis + +If successful, MAGeCK mle will generate two files, the Gene Summary file (including gene beta scores), and the sgRNA Summary file (including sgRNA efficiency probability predictions). + +**Gene Summary file (including beta scores)** An example of the gene summary output file is below. This file includes the beta scores in two conditions specified in the design matrix (HL60|beta and KBM7|beta), and the associated statistics. For more information, check the output format specification of the **mageck test** *Gene Summary* file. @@ -183,7 +209,7 @@ ======== ========= ============= ========== ================ ============ ===================== ================= ============= =========== ================ ============ ===================== ================= -**sgRNA summary file (including sgRNA efficiency probability predictions)** +**sgRNA Summary file (including sgRNA efficiency probability predictions)** An example of the sgRNA ranking output is as follows: