diff chipseeker.xml @ 2:cb133602cd9b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit bae8cc7d7a88154b815acc3cd126010e7e965d5c

--- a/chipseeker.xml	Tue May 29 15:08:04 2018 -0400
+++ b/chipseeker.xml	Wed May 30 06:12:27 2018 -0400
@@ -23,18 +23,18 @@
 
         -i '$peaks'
         -G '$gtf'
-        -u $upstream
-        -d $downstream
-        #if $flankgeneinfo:
-            -F $flankgeneinfo
-            -D $flankgenedist
+        -u $adv.upstream
+        -d $adv.downstream
+        #if $adv.flankgeneinfo:
+            -F $adv.flankgeneinfo
+            -D $adv.flankgenedist
         #end if
         -f $format
         -p $pdf
     ]]>
     </command>
     <inputs>
-        <param name="peaks" type="data" format="bed,interval" label="Peaks file" help="A peaks file in BED format." />
+        <param name="peaks" type="data" format="bed,interval,tabular" label="Peaks file" help="A peaks file in BED format." />
         <conditional name="gtf_source">
             <param name="gtf_source_select" type="select" label="Annotation source" help="Select a GTF to use for annotation source.">
                 <option value="cached" selected="true">Use a built-in GTF</option>
@@ -52,16 +52,19 @@
                 <param name="gtf_hist" type="data" format="gtf" label="Select a history GTF" />
             </when>
         </conditional>
-        <param name="upstream" type="integer" min="0" value="3000" label="TSS upstream region" help="User can define TSS (transcription start site) region, by default TSS is defined from -3kb to +3kb." />
-        <param name="downstream" type="integer" min="0" value="3000" label="TSS downstream region" help="User can define TSS (transcription start site) region, by default TSS is defined from -3kb to +3kb."/>
-        <param name="flankgeneinfo" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Add flanking gene information?" help="If specified all genes within the flanking gene distance are reported for each peak. Default: No."/>
-        <param name="flankgenedist" type="integer" min="0" value="5000" label="Flanking gene distance" help="If flanking gene info is turned on the flanking distance can be specified. Default: 5000."/>
         <param name="format" type="select" label="Output Format">
             <option value="interval" selected="True">Interval</option>
             <option value="tabular">Tabular (tab-separated)</option>
         </param>
         <param name="pdf" type="boolean" truevalue="True" falsevalue="" checked="True" label="Output PDF of plots?" help="Default: Yes" />
         <param name="rscript" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Output Rscript?" help="If this option is set to Yes, the Rscript used to annotate the IDs will be provided as a text file in the output. Default: No" />
+
+        <section name="adv" expanded="false" title="Advanced Options">
+            <param name="upstream" type="integer" min="0" value="3000" label="TSS upstream region" help="User can define TSS (transcription start site) region, by default TSS is defined from -3kb to +3kb." />
+            <param name="downstream" type="integer" min="0" value="3000" label="TSS downstream region" help="User can define TSS (transcription start site) region, by default TSS is defined from -3kb to +3kb."/>
+            <param name="flankgeneinfo" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Add flanking gene information?" help="If specified all genes within the flanking gene distance are reported for each peak. Default: No."/>
+            <param name="flankgenedist" type="integer" min="0" value="5000" label="Flanking gene distance" help="If flanking gene info is turned on the flanking distance can be specified. Default: 5000."/>
+        </section>
     </inputs>
 
         <outputs>
@@ -137,14 +140,23 @@
 
 **What it does**
 
-ChIPseeker_ is a Bioconductor package for annotating ChIP-seq data analysis. See
-the `ChIPseeker vignette`_ for more information.
+ChIPseeker_ is a Bioconductor package for annotating ChIP-seq data analysis. Peak Annotation is performed by the annotatePeak function. The position and strand information of nearest genes are reported, in addition to the distance from the peak to the TSS of its nearest gene. Users can define the TSS (transcription start site) region under **Advanced Options**, by default the TSS region is defined from -3kb to +3kb. The genomic region of the peak is reported in the annotation column. Since some annotations may overlap for a peak, ChIPseeker adopts the following priority in genomic annotation:
+
+* Promoter
+* 5’ UTR
+* 3’ UTR
+* Exon
+* Intron
+* Downstream
+* Intergenic
+
+ChIPseeker also produces plots to help users visualise the overlaps in annotation for peaks, for example, the vennpie and upsetplot. See the `ChIPseeker vignette`_ for more information.
 
 -----
 
 **Inputs**
 
-A peaks file in BED or Interval format e.g from MACS2 or DiffBind.
+A peaks file in BED, Interval or Tabular format e.g from MACS2 or DiffBind.
 
 Example:
 
@@ -167,7 +179,7 @@
 This tool outputs
 
     * a file of annotated peaks in Interval or Tabular format
-    * a PDF of plots
+    * a PDF of plots (plotAnnoPie, vennpie, upsetplot)
     * the R script used by this tool
 
 **Annotated peaks**