diff edena_ovl_wrapper.xml @ 1:cd6cc6d76708 draft

Simplify passing repeated params to Python script. Add more info to help sections.

--- a/edena_ovl_wrapper.xml	Mon Sep 09 05:44:31 2013 -0400
+++ b/edena_ovl_wrapper.xml	Fri Oct 18 14:09:11 2013 -0400
@@ -8,44 +8,18 @@
     edena_ovl_wrapper.py
     \${EDENA_SITE_OPTIONS:---nThreads 2}
     #if $input_selection.input == "unpaired_file"
-      #for $i, $unpaired_file in enumerate( $input_selection.unpaired_input ):
-        #if $i == 0
-          #echo "--unpaired_input="
-        #end if
-        #echo $unpaired_file.unpaired_file
-        #echo '+'
+      #for $ui in $input_selection.unpaired_input
+        --unpaired_input=${ui.unpaired_file}
       #end for
     #elif $input_selection.input == "dr_pairs"
-      #for $i, $dr_pair_1 in enumerate( $input_selection.dr_pairs_input ):
-        #if $i == 0
-          #echo "--dr_pair_1="
-        #end if
-        #echo $dr_pair_1.dr_pair_1
-        #echo '+'
-      #end for
-      #echo ' '
-      #for $i, $dr_pair_2 in enumerate( $input_selection.dr_pairs_input ):
-        #if $i == 0
-          #echo "--dr_pair_2="
-        #end if
-        #echo $dr_pair_2.dr_pair_2
-        #echo '+'
+      #for $dpi in $input_selection.dr_pairs_input
+        --dr_pair_1=${dpi.dr_pair_1}
+        --dr_pair_2=${dpi.dr_pair_2}
       #end for
     #elif $input_selection.input == "rd_pairs"
-      #for $i, $rd_pair_1 in enumerate( $input_selection.rd_pairs_input ):
-        #if $i == 0
-          #echo "--rd_pair_1="
-        #end if
-        #echo $rd_pair_1.rd_pair_1
-        #echo '+'
-      #end for
-      #echo ' '
-      #for $i, $rd_pair_2 in enumerate( $input_selection.rd_pairs_input ):
-        #if $i == 0
-          #echo "--rd_pair_2="
-        #end if
-        #echo $rd_pair_2.rd_pair_2
-        #echo '+'
+      #for $rpi in $input_selection.rd_pairs_input
+        --rd_pair_1=${rpi.rd_pair_1}
+        --rd_pair_2=${rpi.rd_pair_2}
       #end for
     #end if
     #if str($minOlap)
@@ -61,7 +35,7 @@
   <inputs>
     <conditional name="input_selection">
       <param name="input" type="select" label="Select input type">
-        <option value="unpaired_file" selected="True">Unpaired files</option>
+        <option value="unpaired_file">Unpaired files</option>
         <option value="dr_pairs">Direct-reverse paired-end files</option>
         <option value="rd_pairs">Reverse-direct paired-end files</option>
       </param>
@@ -104,7 +78,13 @@
   <help>
 **What it does**
 
-Edena can accept both unpaired and paired files, FASTQ and FASTA format. Note that for technical reasons, all reads are required to be of the same length. You can however provide the program with different files containing different reads length. In such case, Edena will trim the 3’ ends of the longer reads so that they fit the shorter length. It is however required that reads within each individual file are of the same length (as Illumina GA reads are). By default all overlaps with a minimum size corresponding to half of the reads length are computed. This is quite conservative. Provided enough coverage, this value can be increased (option -M) to reduce the memory requirements. For reads longer than 100bp, you may consider the reads truncation option, which could help in discarding 3’ base calling errors.
+Edena is an overlaps graph based short reads assembler and is suited to Illumina GA reads. An assembly with Edena is a two step process: overlapping and assembling.
+
+In the overlapping step, the reads files are provided to the program which computes the transitively reduced overlaps graph. This structure is then stored together with the sequence reads in the overlapping file.
+
+Edena can accept both unpaired and paired files, FASTQ and FASTA format. Note that for technical reasons, all reads are required to be of the same length. You can however provide the program with different files containing different reads length. In such case, Edena will trim the 3’ ends of the longer reads so that they fit the shorter length. It is however required that reads within each individual file are of the same length (as Illumina GA reads are). By default all overlaps with a minimum size corresponding to half of the reads length are computed. This is quite conservative. Provided enough coverage, this value can be increased (option -M) to reduce the memory requirements.
+
+For reads longer than 100bp, you may consider the reads truncation option, which could help in discarding 3’ base calling errors.
 
 **License and citation**