diff repex_full_clustering.xml @ 4:fe2220ee2fd1 draft

Uploaded

--- 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>