--- 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: