--- a/convert_bc_to_binary_RY.xml	Fri Oct 23 07:28:06 2015 -0400
+++ b/convert_bc_to_binary_RY.xml	Wed Nov 04 07:18:06 2015 -0500
@@ -1,5 +1,5 @@
-<tool id="convert_bc_to_binary_RY.py" name="convert_bc_to_binary_RY.py" version="0.1.0">
-  <description>Convert to binary barcodes.</description>
+<tool id="convert_bc_to_binary_RY.py" name="Create binary barcodes" version="0.1.0">
+  <description>from regular barcodes.</description>
   <macros>
     <import>macros.xml</import>
   </macros>
@@ -25,15 +25,21 @@
     </test>
   </tests>
   <help><![CDATA[
-Convert standard nucleotides to IUPAC nucleotide codes used for binary barcodes.
 
+**What it does**
+
+This tool converts standard nucleotides to IUPAC nucleotide codes used for binary barcodes.
 A and G are converted to nucleotide code R. T, U and C are converted to Y.
 
-Author: Daniel Maticzka
-Copyright: 2015
-License: Apache
-Email: maticzkd@informatik.uni-freiburg.de
-Status: Testing
+**Input**
+
+The input for this tool is a fasta file.
+
+**Output**
+
+This tool produces a single fasta file containing the converted barcodes.
+
+** References **
 ]]></help>
   <expand macro="citations" />
 </tool>

--- a/coords2clnt.xml	Fri Oct 23 07:28:06 2015 -0400
+++ b/coords2clnt.xml	Wed Nov 04 07:18:06 2015 -0500
@@ -1,5 +1,5 @@
-<tool id="coords2clnt.py" name="coords2clnt.py" version="0.1.0">
-  <description>Extract crosslinked nucleotide.</description>
+<tool id="coords2clnt.py" name="Get crosslinked nucleotides" version="0.1.0">
+  <description>from full alignments</description>
   <macros>
     <import>macros.xml</import>
   </macros>
@@ -32,6 +32,7 @@
 Crosslinked nts are assumed to be one nt upstream of the 5'-end of the read.
 
 Input:
+
 * bed6 file containing coordinates of aligned reads
 * bed6 file containing coordinates of crosslinking events
 

--- a/extract_aln_ends.xml	Fri Oct 23 07:28:06 2015 -0400
+++ b/extract_aln_ends.xml	Wed Nov 04 07:18:06 2015 -0500
@@ -1,5 +1,5 @@
-<tool id="extract_aln_ends.py" name="extract_aln_ends.py" version="0.1.0">
-  <description>Extract alignment ends from sam file.</description>
+<tool id="extract_aln_ends.py" name="Extract alignment ends" version="0.1.0">
+  <description>from a sam file</description>
   <macros>
     <import>macros.xml</import>
   </macros>
@@ -37,9 +37,11 @@
 ("forward-reverse") direction.
 
 Input:
+
 * sam file containing alignments (paired-end sequencing)
 
 Output:
+
 * bed6 file containing outer coordinates (sorted by read id)
 
 Author: Daniel Maticzka

--- a/extract_bcs.xml	Fri Oct 23 07:28:06 2015 -0400
+++ b/extract_bcs.xml	Wed Nov 04 07:18:06 2015 -0500
@@ -1,5 +1,5 @@
-<tool id="extract_bcs.py" name="extract_bcs.py" version="1.0.0">
-  <description>Extract barcodes using pattern.</description>
+<tool id="extract_bcs.py" name="Extract barcodes" version="1.0.0">
+  <description>using pattern.</description>
   <macros>
     <import>macros.xml</import>
   </macros>

--- a/merge_pcr_duplicates.xml	Fri Oct 23 07:28:06 2015 -0400
+++ b/merge_pcr_duplicates.xml	Wed Nov 04 07:18:06 2015 -0500
@@ -1,5 +1,5 @@
-<tool id="merge_pcr_duplicates.py" name="merge_pcr_duplicates.py" version="0.1.0">
-  <description>Merge PCR duplicates according to random barcode library.</description>
+<tool id="merge_pcr_duplicates.py" name="Merge PCR duplicates" version="0.1.0">
+  <description>according to random barcode library.</description>
   <macros>
     <import>macros.xml</import>
   </macros>
@@ -35,11 +35,13 @@
 
 Barcodes containing uncalled base 'N' are removed.
 
-Input:
+Input::
+
 * bed6 file containing alignments with fastq read-id in name field
 * fasta library with fastq read-id as sequence ids
 
-Output:
+Output::
+
 * bed6 file with random barcode in name field and number of PCR duplicates as score, sorted by fields chrom, start, stop, strand, name
 
 Author: Daniel Maticzka

--- a/remove_tail.xml	Fri Oct 23 07:28:06 2015 -0400
+++ b/remove_tail.xml	Wed Nov 04 07:18:06 2015 -0500
@@ -1,5 +1,5 @@
-<tool id="remove_tail.py" name="remove_tail.py" version="0.1.0">
-  <description>Remove nts from 3'-end.</description>
+<tool id="remove_tail.py" name="Remove 3'-end nts" version="0.1.0">
+  <description>from FASTQ</description>
   <macros>
     <import>macros.xml</import>
   </macros>

--- a/rm_spurious_events.xml	Fri Oct 23 07:28:06 2015 -0400
+++ b/rm_spurious_events.xml	Wed Nov 04 07:18:06 2015 -0500
@@ -1,5 +1,5 @@
-<tool id="rm_spurious_events.py" name="rm_spurious_events.py" version="0.1.0">
-  <description>Remove spurious events.</description>
+<tool id="rm_spurious_events.py" name="Remove spurious" version="0.1.0">
+  <description>crosslinking events</description>
   <macros>
     <import>macros.xml</import>
   </macros>
@@ -32,17 +32,17 @@
   <help><![CDATA[
 Remove spurious events originating from errors in random sequence tags.
 
-This script compares all events sharing the same coordinates. Among each group
+This tool compares all events sharing the same coordinates. Among each group
 of events the maximum number of PCR duplicates is determined. All events that
 are supported by less than 10 percent of this maximum count are removed.
 
-Input:
-* bed6 file containing crosslinking events with score field set to number of PCR
-  duplicates
+Input::
+
+* bed6 file containing crosslinking events with score field set to number of PCR duplicates
 
-Output:
-* bed6 file with spurious crosslinking events removed, sorted by fields chrom,
-  start, stop, strand
+Output::
+
+* bed6 file with spurious crosslinking events removed, sorted by fields chrom, start, stop, strand
 
 Author: Daniel Maticzka
 Copyright: 2015