# HG changeset patch
# User petr-novak
# Date 1580715286 18000
# Node ID 968f0867acc5618d7d0810cd0d842625f9681d5d
# Parent  e6fb0f2b2097a778878ab81329a3245b54e34b49
documentation and help update

diff -r e6fb0f2b2097 -r 968f0867acc5 repex_full_clustering.xml
--- a/repex_full_clustering.xml	Wed Jan 08 06:31:13 2020 -0500
+++ b/repex_full_clustering.xml	Mon Feb 03 02:34:46 2020 -0500
@@ -6,7 +6,7 @@
       <regex match="Warning" source="stderr" level="warning" description="Unknown error" />
       <exit_code range="1:" level="fatal" description="Error" />
     </stdio>
-    <description>Improved version or repeat discovery and characterization using graph based sequence clustering</description>
+    <description>Improved version or repeat discovery and characterization using graph-based sequence clustering</description>
    <requirements>
      <requirement type="package">last</requirement>
      <requirement type="package">imagemagick</requirement>
@@ -79,8 +79,8 @@
     </command>
  <inputs>
 	<param name="FastaFile" label="NGS reads" type="data" format="fasta"
-	       help="Input file must contain fasta-formatted NGS reads. If paired end reads are used, reads must be interlaced  and all pairs must be complete. Example of input data format is provided in the help below. "/>
-  <param name="paired" type="boolean" truevalue="--paired" falsevalue="" checked="True" label="Paired-end reads" help="Check if you are using pair reads and input sequences contain both read mates and left mates alternate with their right mates" />
+	       help="Input file must contain FASTA-formatted NGS reads. Illumina paired-end reads are recommended."/>
+  <param name="paired" type="boolean" truevalue="--paired" falsevalue="" checked="True" label="Paired-end reads" help="If paired-end reads are used, left- and right-hand reads must be interlaced and all pairs must be complete. Example of the correct format is provided in the help below." />
  
 	<param name="sample" label="Sample size" type="integer" value="500000" min="10000"/>
   <param name="taxon" label="Select taxon and protein domain database version (REXdb)" type="select" help="Reference database of transposable element protein domains - REXdb - is used for annotation of repeats">
@@ -98,12 +98,12 @@
     </when>
     <when value="true">
       <conditional name="comparative">
-        <param name="options_comparative" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Perform comparative analysis" help="Use this options when you want to compare sequences multiple groups"/>
+        <param name="options_comparative" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Perform comparative analysis" help="Use this options to analyze multiple samples simultaneously"/>
 	      <when value="false">
           <!-- do nothing here -->
         </when>
         <when value="true">
-   		    <param name="prefix_length" label="Group code length" type="integer" value="3" min="1" max="10" help="For comparative analysis, sequences are from individial groups distinguished by sample code which must be used as prefix for sequence name. See example below."/>
+   		    <param name="prefix_length" label="Group code length" type="integer" value="3" min="1" max="10" help="For comparative analysis, reads from different samples are distinguished by sample codes included as prefix to the read names. See example below."/>
         </when>
       </conditional>
 
@@ -116,7 +116,7 @@
       </conditional>
 
       <conditional name="options">
-        <param name="options" type="select" label="Similarity search options" help="Different similarity search parameters are used depending on the used input data to adjust search to differences in length and error rate">
+        <param name="options" type="select" label="Similarity search options" help="Different similarity search parameters are used depending on the input data to adjust for differences in read length and error rate">
           <option value="ILLUMINA" selected="true">Illumina reads, read length 100nt or more </option>
           <option value="ILLUMINA_SHORT" selected="false">Illumina reads, shorter than 100nt (Do not use reads shorter than 50nt!) </option>
           <option value="ILLUMINA_DUST_OFF" selected="false">Illumina reads, no masking of low complexity repeats  </option>
@@ -132,21 +132,21 @@
           <!-- do nothing here -->
         </when>
         <when value="true">
-   		    <param name="library" format="fasta" type="data" label="Custom library of repeats" help="Library of repeats as DNA sequences in fasta format. The required format for IDs in a custom library is : '>reapeatname#class/subclass'"/>
+   		    <param name="library" format="fasta" type="data" label="Custom repeat database" help="The database should contain DNA sequences in FASTA format. The required format for sequence IDs is : '>reapeatname#class/subclass'"/>
         </when>
       </conditional>
-	    <param name="size_threshold" label="Cluster size threshold  for detailed analysis" type="float" value="0.01" min="0.0001" max="100" help ="Minimal size (as percentage of input reads) of the smallest cluster which is analyzed, cluster with less than 20 reads are not considered at all."/>
-      <param name="automatic_filtering" label="Perform automatic filtering of abundant satellite repeats" help="Automatic filtering tries to identify the most abundant tandem repeats and remove such sequences partially from analysis. Removal of abundant tandem repeat can enable to analyze higher proportion of other less abundant repeats." type="boolean" truevalue="--automatic_filtering" falsevalue="" checked="false"/>
-      <param name="keep_names" label="Keep original sequences names" type="boolean" truevalue="--keep_names" falsevalue="" checked="false" help="By default sequence are relabeled using  integers. If you want to keep original names, use this option."/>
-      <param name="assembly_min_cluster_size" type="integer" label="min cluster size for assembly" value="5" min="2" max="100"/>
+	    <param name="size_threshold" label="Cluster size threshold  for detailed analysis" type="float" value="0.01" min="0.0001" max="100" help ="Minimal size (as percentage of input reads) of the smallest cluster which is analyzed; clusters with less than 20 reads are not considered."/>
+      <param name="automatic_filtering" label="Perform automatic filtering of abundant satellite repeats" help="Automatic filtering identifies the most abundant tandem repeats and partially removes their reads from the analysis. This enables to analyze higher proportions of other less abundant repeats." type="boolean" truevalue="--automatic_filtering" falsevalue="" checked="false"/>
+      <param name="keep_names" label="Keep original read names" type="boolean" truevalue="--keep_names" falsevalue="" checked="false" help="By default, reads are renamed using integers. Use this option to keep original names."/>
+      <param name="assembly_min_cluster_size" type="integer" label="Minimal cluster size for assembly" value="5" min="2" max="100"/>
     </when>
   </conditional>
 
        <conditional name="queue_definition">
                <param name="queue_select" type="select" label="Select queue">
-                 <option value="basic_fast_queue">basic &amp; fast</option>
-                 <option value="long_slow_queue">long &amp; slow</option>
-                 <option value="extra_long_slow_queue">extra long &amp; slow</option>
+                 <option value="basic_fast_queue">basic (max runtime 2 days, 4 GB RAM)</option>
+                 <option value="long_slow_queue">long (max runtime 2 weeks, 64 GB RAM)</option>
+                 <option value="extra_long_slow_queue">extra long (max runtime 4 weeks, 64 GB RAM)</option>
                </param>
                <when value="basic_fast_queue">
                  <param name="queue_specification" type="text" label="Modify parameters (optional)"
diff -r e6fb0f2b2097 -r 968f0867acc5 repex_tarean.xml
--- a/repex_tarean.xml	Wed Jan 08 06:31:13 2020 -0500
+++ b/repex_tarean.xml	Mon Feb 03 02:34:46 2020 -0500
@@ -73,8 +73,8 @@
   </command>
 
   <inputs>
-	  <param name="FastaFile" label="paired-end NGS reads" type="data" format="fasta"
-	         help="Input file must contain fasta-formatted interlaced read pairs from paired-end sequencing. All pairs must be complete. Example of input data format is provided in the help below."/>
+	  <param name="FastaFile" label="Paired-end Illumina reads" type="data" format="fasta"
+	         help="Input file must contain FASTA-formatted interlaced read pairs from paired-end sequencing. All pairs must be complete. Example of the input data format is provided in the help below."/>
 	  <param name="sample" label="Sample size" type="integer" value="500000" min="10000"/>
 
     <conditional name="advanced_options">
@@ -93,11 +93,11 @@
 	          <param name="library" format="fasta" type="data" label="Use custom repeat database" help="Perform additional similarity search to user-provided repeat database. The database should contain FASTA-formatted DNA sequences with headers (sequence names) in the format: '>reapeatname#class/subclass'"/>
           </when>
         </conditional>
-        <param name="size_threshold" label="Cluster size threshold  for detailed analysis" type="float" value="0.01" min="0.0001" max="100" help ="Minimal size (as percentage of input reads) of the smallest cluster which is analyzed, cluster with less than 20 reads are not considered at all."/>
+        <param name="size_threshold" label="Cluster size threshold for detailed analysis" type="float" value="0.01" min="0.0001" max="100" help ="Minimal size (as percentage of input reads) of the smallest cluster which is analyzed; cluster with less than 20 reads are not considered."/>
         <param name="automatic_filtering" label="Perform automatic filtering of abundant satellite repeats" type="boolean" truevalue="--automatic_filtering" falsevalue="" checked="false"/>
-        <param name="keep_names" label="Keep original sequences names" type="boolean" truevalue="--keep_names" falsevalue="" checked="false" help="By default sequence are relabeled using  integers. If you want to keep original names, use this option."/>
+        <param name="keep_names" label="Keep original read names" type="boolean" truevalue="--keep_names" falsevalue="" checked="false" help="By default, reads are renamed using integers. Use this option if you want to keep original names."/>
          <conditional name="options">
-           <param name="options" type="select" label="Similarity search options" help="Different similarity search parameters are used depending on the used input data to adjust search to differences in length and error rate">
+           <param name="options" type="select" label="Similarity search options" help="Different similarity search parameters are used depending on the input data to adjust search to differences in read length and error rate">
              <option value="ILLUMINA" selected="true">Illumina reads, read length 100nt or more </option>
              <option value="ILLUMINA_SHORT" selected="false">Illumina reads, shorter than 100nt (Do not use reads shorter than 50nt!) </option>
              <option value="ILLUMINA_DUST_OFF" selected="false">Illumina reads, no masking of low complexity repeats  </option>
@@ -108,9 +108,9 @@
 
          <conditional name="queue_definition">
                <param name="queue_select" type="select" label="Select queue">
-                 <option value="basic_fast_queue">basic &amp; fast</option>
-                 <option value="long_slow_queue">long &amp; slow</option>
-                 <option value="extra_long_slow_queue">extra long &amp; slow</option>
+                 <option value="basic_fast_queue">basic (max runtime 2 days, 4 GB RAM)</option>
+                 <option value="long_slow_queue">long (max runtime 2 weeks, 64 GB RAM)</option>
+                 <option value="extra_long_slow_queue">extra long (max runtime 4 weeks, 64 GB RAM)</option>
                </param>
                <when value="basic_fast_queue">
                  <param name="queue_specification" type="text" label="Modify parameters (optional)"
diff -r e6fb0f2b2097 -r 968f0867acc5 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Jan 08 06:31:13 2020 -0500
+++ b/tool_dependencies.xml	Mon Feb 03 02:34:46 2020 -0500
@@ -1,7 +1,7 @@
 <?xml version="1.0" ?>
 <tool_dependency>
     <package name="repex_tarean" version="2.3.7">
-        <repository changeset_revision="6f512dfb0c17" name="package_repex_tarean_1_0" owner="petr-novak" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"/>
+        <repository changeset_revision="73dd574fb04f" name="package_repex_tarean_1_0" owner="petr-novak" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"/>
         <readme>
       prepare repex database and scripts
     </readme>