Mercurial > repos > petr-novak > repeatexplorer2

changeset 3:f99da6158dae draft

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Uploaded
author petr-novak
date Wed, 22 Apr 2020 02:27:53 -0400
parents 09747b55badb
children fe2220ee2fd1
files repex_full_clustering.xml repex_tarean.xml tool_dependencies.xml
diffstat 3 files changed, 9 insertions(+), 9 deletions(-) [+]
line wrap: on
line diff
--- a/repex_full_clustering.xml	Tue Apr 21 06:39:40 2020 -0400
+++ b/repex_full_clustering.xml	Wed Apr 22 02:27:53 2020 -0400
@@ -128,10 +128,10 @@
 
       <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, default, all-to-all search uses mgblast, minimal identity 90% </option>
-          <option value="ILLUMINA_DUST_OFF" selected="false">Illumina reads, no masking of low complexity repeats  </option>
-          <option value="ILLUMINA_SENSITIVE_MGBLAST" selected="false">all-to-all search is performed using mgblast (W8, min PID 80) slow, experimental feature!</option>
-          <option value="ILLUMINA_SENSITIVE_BLASTPLUS" selected="false">all-to-all search is performed using blastn (W6, min PID 80) very slow, experimental feature!</option>
+          <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>
--- a/repex_tarean.xml	Tue Apr 21 06:39:40 2020 -0400
+++ b/repex_tarean.xml	Wed Apr 22 02:27:53 2020 -0400
@@ -109,10 +109,10 @@
         <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, default, all-to-all search uses mgblast, minimal identity 90% </option>
-             <option value="ILLUMINA_DUST_OFF" selected="false">Illumina reads, no masking of low complexity repeats  </option>
-             <option value="ILLUMINA_SENSITIVE_MGBLAST" selected="false">all-to-all search is performed using mgblast (W8, min PID 80) slow, experimental feature!</option>
-             <option value="ILLUMINA_SENSITIVE_BLASTPLUS" selected="false">all-to-all search is performed using blastn (W6, min PID 80) very slow, experimental feature!</option>
+             <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>
       </when>
--- a/tool_dependencies.xml	Tue Apr 21 06:39:40 2020 -0400
+++ b/tool_dependencies.xml	Wed Apr 22 02:27:53 2020 -0400
@@ -1,7 +1,7 @@
 <?xml version="1.0" ?>
 <tool_dependency>
     <package name="repex_tarean" version="2.3.8">
-        <repository changeset_revision="75fb7416b106" name="package_repex_tarean_1_0" owner="petr-novak" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"/>
+        <repository changeset_revision="18380033c742" 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>