| Previous changeset 0:a41d96fc0b20 (2019-07-15) Next changeset 2:8353f3cc03db (2019-08-29) |
|
Commit message:
"planemo upload for repository https://github.com/jsh58/Genrich commit 85e0bb6eaeaf1b82357cb95abf6ebad6dd4ab492" |
|
modified:
genrich.xml |
| b |
| diff -r a41d96fc0b20 -r db50f51a2952 genrich.xml --- a/genrich.xml Mon Jul 15 09:43:27 2019 -0400 +++ b/genrich.xml Sat Aug 17 16:24:04 2019 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="genrich" name="Genrich" version="0.5"> +<tool id="genrich" name="Genrich" version="0.5+galaxy1"> <description>Detecting sites of genomic enrichment</description> <requirements> <requirement type="package" version="0.5">genrich</requirement> @@ -38,7 +38,7 @@ #################### #if $filter_options.duplicates: - '$filter_options.duplicates' '${out_dups}' + -r -R '${out_dups}' #end if #if $filter_options.exclude_chr: @@ -118,10 +118,13 @@ <option value="Yes">Yes</option> </param> <when value="No" > - <param name="input_treatment_file" argument="-t" type="data" format="qname_sorted.bam" label="Treatment File(s)" /> + <param name="input_treatment_file" argument="-t" type="data" format="qname_sorted.bam" label="Treatment File" + help="This file should be a name-sorted BAM file. 'samtools sort' can do this with the 'name (-n)' parameter." /> </when> <when value="Yes"> - <param name="input_treatment_file" argument="-t" type="data" format="qname_sorted.bam" multiple="true" label="Treatment Files" /> + <param name="input_treatment_file" argument="-t" type="data" format="qname_sorted.bam" multiple="true" + label="Treatment Files." + help="These files should be a name-sorted BAM file. 'samtools sort' can do this with the 'name (-n)' parameter." /> </when> </conditional> @@ -137,10 +140,12 @@ <option value="Yes">Yes</option> </param> <when value="No" > - <param name="input_control_file" argument="-c" type="data" format="qname_sorted.bam" label="Control File(s)" /> + <param name="input_control_file" argument="-c" type="data" format="qname_sorted.bam" label="Control File" + help="This file should be a name-sorted BAM file. 'samtools sort' can do this with the 'name (-n)' parameter." /> </when> <when value="Yes"> - <param name="input_control_file" argument="-c" type="data" format="qname_sorted.bam" multiple="true" label="Control Files" /> + <param name="input_control_file" argument="-c" type="data" format="qname_sorted.bam" multiple="true" label="Control Files" + help="These files should be a name-sorted BAM file. 'samtools sort' can do this with the 'name (-n)' parameter." /> </when> </conditional> </when> |