Merge pull request #161 from ccedmendoza/yac

The output file label has been modified as requested in issue #7

tools/yac_clipper/.shed.yml

@@ -1,5 +1,5 @@
 # .shed.yml supporting automatic pushes.
-owner: drosofff
+owner: artbio
 name: yac_clipper
 description: Clips 3' adapters for small RNA sequencing reads.
 long_description: |

tools/yac_clipper/yac.xml

@@ -1,4 +1,4 @@
-<tool id="yac" name="Clip adapter" version="1.3.6">
+<tool id="yac" name="Clip adapter" version="2.0.0">
     <description />
     <command interpreter="python">yac.py --input $input
                                        --output $output
@@ -39,7 +39,7 @@
         </conditional>
     </inputs>
     <outputs>
-        <data format="fasta" metadata_source="input" name="output">
+        <data format="fasta" metadata_source="input" name="output" label="Clipping of ${input.name}">
           <change_format>
               <when input="out_format" value="fastq" format="fastq" />
           </change_format>
@@ -67,15 +67,29 @@
         </test>
     </tests>
     <help>
-This tool clips adapter sequences from a fasta or fastq file and
-outputs either a fasta or fastq file of clipped reads with
-renumbered fasta/fastq headers.
 
-By default clipped sequences with unknown nucleotides are kept, but 
-can be discarded by setting "Accept reads containing N?" to reject.
+**What it does**
 
-Min size and max size filter clipped reads on their size.
++ Clips adapter sequences
++ Renumbers sequence headers
++ Filters sequences on their size
++ Filters sequences containing unknown nucleotides (optional)
+
+-------
+
+**Inputs**
+
+1. A fastq file of reads to be clipped
+2. Select the size of the reads to be kept
+3. Select an output format when input is a fastq file (this may be fastq or fastq)
+4. Select whether you wish or do not wish to keep clipped sequences with unknown nucleotides (N)
+5. Select a pre-built adapter sequence or enter your own sequence (at least 7 nucleotides long)
+
+-------
+
+**Output**
+
+A fastq or fasta file containing clipped sequences satisfying the selected criteria.
 
-Note that unclipped reads that satisfy the min and max size conditions are kept.
   </help>
 </tool>