# HG changeset patch
# User davidecangelosi
# Date 1557917699 14400
# Node ID d6e062f6d462e45078d8fb6fa1c7845e1bcb11c9
# Parent  bc5697f4172072726868d35c6fa64bfdb9e6b417
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit bbd56a469f814565939ff5467a35121658f26133

diff -r bc5697f41720 -r d6e062f6d462 pipe-t.xml
--- a/pipe-t.xml	Mon May 13 05:34:38 2019 -0400
+++ b/pipe-t.xml	Wed May 15 06:54:59 2019 -0400
@@ -128,9 +128,8 @@
 </command>
 <inputs>
 <section name="dp" title="File uploading and parsing" expanded="true">
-  <param name="list_files" type="data_collection" collection_type="list" value="" label="Select a collection list of TaqMan
-  Low Density Array files in the history tab" help="Collection should be of category List. "/>
- 	<param name="files" type="data" format="txt" label="Select one of the files in the history tab" help="File should contains only the fields: sampleName and Treatment." />
+  <param name="list_files" type="data_collection" collection_type="list" value="" label="Select a collection list from the history tab" help="Collection should be of category List. "/>
+ 	<param name="files" type="data" format="txt" label="Select one of the files from the history tab" help="File should contains only the columns: sampleName and Treatment." />
   <param name="formatFile" type="select"  label="Select one of the file formats from the list below." help="">
       <option value="EDS" selected="true">EDS</option>
       <option value="plain">Plain</option>
@@ -154,7 +153,7 @@
 </section>
 <section name="dn" title="Normalization" expanded="true">
   <conditional name="condNorm">
-    <param name="normMethod" type="select" label="Select one of the normalization methods from the list below." help="Normalization is important to reduce technical variability from the data.">
+    <param name="normMethod" type="select" label="Select one of the normalization methods from the list below." help="Normalization is important to reduce technical variability in the data.">
       <option value="globalmean" selected="true">Global mean</option>
       <option value="deltaCt">DeltaCt method (housekeeping genes)</option>
       <option value="geometric.mean">Modified global mean</option>
@@ -170,13 +169,13 @@
           <option value="normfinder">NormFinder</option>
         </param>
         <when value="userdefined">
-          <param name="normalizers" type="text" label="Type a comma separated list of housekeeping transcript identifiers that will be used as normalizers." value="U6 snRNA-001973"></param>
+          <param name="normalizers" type="text" label="Type a comma separated list of housekeeping transcripts that will be used as normalizers." value="U6 snRNA-001973"></param>
         </when>
         <when value="genorm">
-          <param name="minhkgenorm" type="integer" label="Type the minimum number of housekeeping transcripts that should be considered." value="2"></param>
+          <param name="minhkgenorm" type="integer" label="Type the minimum number of housekeeping transcripts that will be considered by geNorm method." value="2"></param>
         </when>
         <when value="normfinder">
-          <param name="minhknormfinder" type="integer" label="Type the minimum number of housekeeping transcripts that should be considered." value="1"></param>
+          <param name="minhknormfinder" type="integer" label="Type the minimum number of housekeeping transcripts that will be considered by NormFinder method." value="1"></param>
         </when>
         </conditional>
     </when>
@@ -184,8 +183,8 @@
 </section>
 <section name="df" title="Transcript filtering and imputation" expanded="true">
   <param name="percent" type="integer" min="0" max="100" value="0" label="Set up a percentage of NAs."
- help="miRs\genes with more than the specified percentage of NAs across samples will be removed." />
-<param name="filtname" type="text" label="Type a comma separeted list of transcript identifiers to filter out" help="transcript identifiers specified in the List will be removed." value="U6 snRNA-001973,hsa-miR-520a">
+ help="Transcripts with more than the specified percentage of NAs across all samples will be removed." />
+<param name="filtname" type="text" label="Type a comma separeted list of transcript identifiers to filter out" help="Transcript identifiers specified in the List will be removed." value="U6 snRNA-001973,hsa-miR-520a">
     </param>
   <conditional name="condImpute">
     <param name="format" type="select"  label="Select one of the imputation methods from the list below." help="">
@@ -196,8 +195,8 @@
       <option value="cubic">Cubic Spline</option>
     </param>
     <when value="knn">
-      <param name="k" type="integer" min="1" max="100" value="10" label="Type a number of neighbors to use by the KNN imputation method" />
-      <param name="maxp" type="integer" min="1" max="2000" value="1500" label="Type the maximum number of imputed transcript by  KNN method." help="Larger numbers are divided by two-means clustering (recursively)
+      <param name="k" type="integer" min="1" max="100" value="10" label="Type a number of neighbors to use in the KNN imputation method" />
+      <param name="maxp" type="integer" min="1" max="2000" value="1500" label="Type the maximum number of imputed transcripts to use in the  KNN method." help="Larger numbers are divided by two-means clustering (recursively)
       prior to imputation. "/>
     </when>
   </conditional>
@@ -215,15 +214,15 @@
           <option value="greater">Greater</option>
           <option value="less">Lower</option>
         </param>
-        <param name="paired" type="select" label="Select TRUE if you want a paired analysis?" help="Pairing of samples will follow the order of the sampleNames in the input file">
+        <param name="paired" type="select" label="Select TRUE if you want a paired analysis." help="Pairing of samples will follow the order of the sampleNames in the input file">
             <option value="TRUE" >TRUE</option>
             <option value="FALSE" selected="true">FALSE</option>
         </param>
-        <param name="replicates" type="select" label="Select TRUE if you have replicated miR\gene in your data" help="If replicated miRs\genes are present in the data, the statistics will be calculated once for each replicated miR\gene, rather than the separately.">
+        <param name="replicates" type="select" label="Select TRUE if you have replicated transcripts in your data" help="If replicated transcripts are present in the data, the statistics will be calculated once for each replicated transcript, rather than separately.">
             <option value="TRUE" selected="true">TRUE</option>
             <option value="FALSE" >FALSE</option>
         </param>
-        <param name="sort" type="select" label="Select TRUE if you want the output to be sorted by increasing order of p-value?" help="">
+        <param name="sort" type="select" label="Select TRUE if you want that output file is sorted by increasing order of p-value?" help="">
             <option value="TRUE" selected="true">TRUE</option>
             <option value="FALSE" >FALSE</option>
         </param>
@@ -232,7 +231,7 @@
             <option value="TRUE" selected="true">TRUE</option>
             <option value="FALSE" >FALSE</option>
         </param>
-        <param name="padjust" type="select"  label="Select one of the methods to adjust pvalues for multiple hypothesis testing">
+        <param name="padjust" type="select"  label="Select one of the methods for adjusting pvalues in case of multiple hypothesis testing">
           <option value="BH" selected="true">Benjamini-Hochberg</option>
           <option value="bonferroni">Bonferroni</option>
         </param>
@@ -255,15 +254,15 @@
 <help>
 <![CDATA[
 **What it does**
-INPUTS: This tool parses a list of RTqPCR file and a file with the groups
+INPUTS: This tool parses a list of RT-qPCR file and a file associating these files and one of two groups
 OUTPUTS: and returs
 1) A txt file with the raw Ct data
-2) A PNG file with a boxplot of Ct data after data categorization for each sample
-3) A txt file with deltaCt data after data normalization
+2) A PNG file of a boxplot with the Ct data after data categorization for each sample
+3) A txt file with normalized data
 4) A PNG file with the Empirical cumulative distribution before and after data normalization
-5) A PNG file with boxplot of deltaCt data after data normalization
-6) A txt file after imputation of missing values
-7) A txt file with a number statistics about the significance of each miR\gene
+5) A PNG file of a boxplot with the normalzied data for each sample
+6) A txt file with imputed data for each missing value
+7) A txt file with the results of the differntial expression analyis
 ]]>
 </help>
 </tool>