ok, now last fixes

tools/peakzilla/peakzilla.xml

@@ -42,16 +42,6 @@
                 -l log.txt
             #end if
             '$chip_bed' '$input_bed' > '$results'
-
-            ## copy the log file to the output if it was requested
-            #if $outputs.log
-                && cp log.txt $log
-            #end if
-
-            ## copy the negative peaks file to the output if it was requested
-            #if $outputs.negative
-                && cp negative_peaks.tsv $negative_peaks
-            #end if
         ]]>
     </command>
     <inputs>
@@ -72,10 +62,10 @@
     </inputs>
     <outputs>
         <data name="results" format="tabular" label="${tool.name} on ${on_string}"/>
-        <data name="log" format="txt" label="Log file for ${tool.name} on ${on_string}">
+        <data name="log" format="txt" from_work_dir="log.txt" label="Log file for ${tool.name} on ${on_string}">
             <filter>log</filter>
         </data>
-        <data name="negative_peaks" format="tabular" label="Negative peaks for ${tool.name} on ${on_string}">
+        <data name="negative_peaks" format="tabular" from_work_dir="negative_peaks.tsv" label="Negative peaks for ${tool.name} on ${on_string}">
             <filter>negative</filter>
         </data>
     </outputs>
@@ -109,15 +99,18 @@
     <help><![CDATA[
         **Peakzilla**
 
-        Peakzilla identifies sites of enrichment and transcription factor binding sites from transcription factor ChIP-seq and ChIP-exo experiments at hight accuracy and resolution. It is designed to perform equally well for data from any species. All necessary parameters are estimated from the data. Peakzilla is suitable for both single and paired end data from any sequencing platform.
+        Peakzilla identifies sites of enrichment and transcription factor binding sites from transcription factor ChIP-seq and ChIP-exo experiments at high accuracy and resolution.
+        It is designed to perform equally well for data from any species. All necessary parameters are estimated from the data. Peakzilla is suitable for both single and
+        paired-end data from any sequencing platform.
 
-        Note that peakzilla is not suited for the identification of broad regions of enrichment (e.g. ChIP-seq for histone marks), we recommand using MACS instead: Zhang et al. Model-based Analysis of ChIP-Seq (MACS). Genome Biol (2008) 9(9):R137
+        Note that peakzilla is not suited for the identification of broad regions of enrichment (e.g. ChIP-seq for histone marks), we recommend using MACS instead: Zhang et al.
+        Model-based Analysis of ChIP-Seq (MACS). Genome Biol (2008) 9(9):R137
 
         *INPUT FORMAT*
-        Peakzilla accepts BED formated alignments as input.
+        Peakzilla accepts BED formatted alignments as input.
 
-        For converstion to BED format and working with BED files and alignments in
-        general I highly reccommend:
+        For conversation to BED format and working with BED files and alignments in
+        general I highly recommend:
 
         * bowtie (http://bowtie-bio.sourceforge.net/)
         * SAMtools (http://samtools.sourceforge.net/)
@@ -148,30 +141,20 @@
         #    Overlap significant peaks from chip1 with enriched regions from chip2
         intersectBed -a chip1_s10_peaks.tsv -b chip2_s2_peaks.tsv > intersect_peaks.tsv
 
-        For example datasets as well as an example of a computational pipeline for the comparative analysis of ChIP-seq datasets, please refer to our publication: Bardet AF et al. A computational pipeline for comparative ChIP-seq analyses. Nature Protocols (2011) 7(1):45-61 (http://www.starklab.org/data/bardet_natprotoc_2011/)
+        For example datasets as well as an example of a computational pipeline for the comparative analysis of ChIP-seq datasets, please refer to our
+        publication: Bardet AF et al. A computational pipeline for comparative ChIP-seq analyses. Nature Protocols (2011) 7(1):45-61 (http://www.starklab.org/data/bardet_natprotoc_2011/)
 
         *OPTIONS*
         One of peakzilla's design goals is to learn all the necessary information
         from the data. The usage of the options should therefore not be required.
 
         *OUTPUT FORMAT*
-        * Results are printed as a table of tab delimited values to stdout
+        * Results are printed as a table of tab-delimited values to stdout
         * Logs are appended to logs.txt in the current directory or a custom directory/filename specified by the -l option
         * Enriched regions in the control sample are written to negative_peaks.tsv or a custom directory/filename specified by the -n option
         * Columns represent Chromosome / Start / End / Name / Summit / Score / ChIP / Control / FoldEnrichment / DistributionScore / FDR (%)
     ]]></help>
     <citations>
-        <citation type="bibtex">
-            @article{bardet2012computational,
-              title={A computational pipeline for comparative ChIP-seq analyses},
-              author={Bardet, Ana{\"\i}s F and He, Qiye and Zeitlinger, Julia and Stark, Alexander},
-              journal={Nature protocols},
-              volume={7},
-              number={1},
-              pages={45--61},
-              year={2012},
-              publisher={Nature Publishing Group UK London}
-            }
-        </citation>
+        <citation type="doi">10.1038/nprot.2011.420</citation>
     </citations>
 </tool>