Mercurial > repos > petr-novak > repeatexplorer2

changeset 4:fe2220ee2fd1 draft

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Uploaded
author petr-novak
date Fri, 24 Apr 2020 08:44:45 -0400
parents f99da6158dae
children febc137b9826
files repex_full_clustering.xml repex_tarean.xml tool_dependencies.xml
diffstat 3 files changed, 33 insertions(+), 29 deletions(-) [+]
line wrap: on
line diff
--- a/repex_full_clustering.xml	Wed Apr 22 02:27:53 2020 -0400
+++ b/repex_full_clustering.xml	Fri Apr 24 08:44:45 2020 -0400
@@ -83,13 +83,13 @@
   <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." />
  
   <conditional name="read_sampling">
-    <param name="do_sampling" type="boolean" truevalue="true" falsevalue="false" checked="True" label="Use maximum processable sequence reads" />
-    <when value="true">
+    <param name="do_sampling" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Read sampling" help="Use this option if you want to analyze only a part of the reads" />
+    <when value="false">
       <!-- pass -->
-      <param name="sample" label="Sample size" hidden="True" type="integer" value="0" help="Number of sequence reads for clustering"/>
+      <param name="sample" label="Sample size" hidden="True" type="integer" value="0" help="Number of analyzed reads"/>
     </when>
-    <when value="false">
-      <param name="sample" label="Sample size" type="integer" value="500000" min="10000" help="Number of reads for clustering"/>
+    <when value="true">
+      <param name="sample" label="Sample size" type="integer" value="500000" min="10000" help="Number of analyzed reads"/>
     </when>
   </conditional>
 
@@ -127,14 +127,15 @@
       </conditional>
 
       <conditional name="options">
-        <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, optimized for read length 100 nt or more (search parameters: mgblast, min PID 90, W18) </option>
-          <option value="ILLUMINA_DUST_OFF" selected="false">Illumina reads, no masking of low complexity repeats (search parameters: mgblast, min PID 90, -W18, -F F) </option>
-          <option value="ILLUMINA_SENSITIVE_MGBLAST" selected="false">Illumina reads, sensitive search (search parameters: mgblast,  min PID 80, -W8) slow, experimental feature!</option>
-          <option value="ILLUMINA_SENSITIVE_BLASTPLUS" selected="false">Illumina reads, more sensitive search (search parameters: blastn,  min PID 80, -W6) extremely slow, experimental feature!</option>
-          <option value="OXFORD_NANOPORE" selected="false">
-            Pseudo short reads simulated from Oxford Nanopore data, experimental feature!
-          </option>
+        <param name="options" type="select" label="Similarity search options">
+          <option value="ILLUMINA" selected="true">Default </option>
+          <option value="ILLUMINA_DUST_OFF" selected="false">Masking of low complexity repeats disabled </option>
+
+          <!-- <option value="ILLUMINA_SENSITIVE_MGBLAST" selected="false">Illumina reads, sensitive search (search parameters: mgblast,  min PID 80, -W8) slow, experimental feature!</option> -->
+          <!-- <option value="ILLUMINA_SENSITIVE_BLASTPLUS" selected="false">Illumina reads, more sensitive search (search parameters: blastn,  min PID 80, -W6) extremely slow, experimental feature!</option> -->
+          <!-- <option value="OXFORD_NANOPORE" selected="false"> -->
+          <!--   Pseudo short reads simulated from Oxford Nanopore data, experimental feature! -->
+          <!-- </option> -->
         </param>
       </conditional>
       
--- a/repex_tarean.xml	Wed Apr 22 02:27:53 2020 -0400
+++ b/repex_tarean.xml	Fri Apr 24 08:44:45 2020 -0400
@@ -76,18 +76,17 @@
 	  <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."/>
 
-	  <conditional name="read_sampling">
-      <param name="do_sampling" type="boolean" truevalue="true" falsevalue="false" checked="True" label="Use maximum processable sequence reads" />
-      <when value="true">
+    <conditional name="read_sampling">
+      <param name="do_sampling" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Read sampling" help="Use this option if you want to analyze only a part of the reads" />
+      <when value="false">
         <!-- pass -->
-        <param name="sample" label="Sample size" hidden="True" type="integer" value="0" help="Number of sequence reads for clustering"/>
+        <param name="sample" label="Sample size" hidden="True" type="integer" value="0" help="Number of analyzed reads"/>
       </when>
-      <when value="false">
-            <param name="sample" label="Sample size" type="integer" value="500000" min="10000" help="Number of reads for clustering"/>
+      <when value="true">
+        <param name="sample" label="Sample size" type="integer" value="500000" min="10000" help="Number of analyzed reads"/>
       </when>
     </conditional>
 
-
     <conditional name="advanced_options">
       <param name="advanced" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Advanced options" />
       <when value="false">
@@ -107,14 +106,18 @@
         <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 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 input data to adjust search to differences in read length and error rate">
-             <option value="ILLUMINA" selected="true">Illumina reads, optimized for read length 100 nt or more (parameters: mgblast, min PID 90, W18) </option>
-             <option value="ILLUMINA_DUST_OFF" selected="false">Illumina reads, no masking of low complexity repeats (parameters: mgblast, min PID 90, -W18, -F F) </option>
-             <option value="ILLUMINA_SENSITIVE_MGBLAST" selected="false">Illumina reads, sensitive search (parameters: mgblast,  min PID 80, -W8) slow, experimental feature!</option>
-             <option value="ILLUMINA_SENSITIVE_BLASTPLUS" selected="false">Illumina reads, more sensitive search (parameters: blastn,  min PID 80, -W6) extremely slow, experimental feature!</option>
-           </param>
-         </conditional>
+        <conditional name="options">
+          <param name="options" type="select" label="Similarity search options">
+            <option value="ILLUMINA" selected="true">Default </option>
+            <option value="ILLUMINA_DUST_OFF" selected="false">Masking of low complexity repeats disabled </option>
+
+            <!-- <option value="ILLUMINA_SENSITIVE_MGBLAST" selected="false">Illumina reads, sensitive search (search parameters: mgblast,  min PID 80, -W8) slow, experimental feature!</option> -->
+          <!-- <option value="ILLUMINA_SENSITIVE_BLASTPLUS" selected="false">Illumina reads, more sensitive search (search parameters: blastn,  min PID 80, -W6) extremely slow, experimental feature!</option> -->
+          <!-- <option value="OXFORD_NANOPORE" selected="false"> -->
+          <!--   Pseudo short reads simulated from Oxford Nanopore data, experimental feature! -->
+          <!-- </option> -->
+          </param>
+        </conditional>
       </when>
     </conditional>
 
--- a/tool_dependencies.xml	Wed Apr 22 02:27:53 2020 -0400
+++ b/tool_dependencies.xml	Fri Apr 24 08:44:45 2020 -0400
@@ -1,7 +1,7 @@
 <?xml version="1.0" ?>
 <tool_dependency>
     <package name="repex_tarean" version="2.3.8">
-        <repository changeset_revision="18380033c742" name="package_repex_tarean_1_0" owner="petr-novak" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"/>
+        <repository changeset_revision="db7bc058aeca" 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>