| Previous changeset 9:acbd3fb47f90 (2018-01-25) Next changeset 11:cb785e26207c (2018-03-06) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e9415c8ba21c77f848a57d60ee6be78dff4b49a6 |
|
modified:
macs2_callpeak.xml |
| b |
| diff -r acbd3fb47f90 -r f0b351e734b8 macs2_callpeak.xml --- a/macs2_callpeak.xml Thu Jan 25 02:11:52 2018 -0500 +++ b/macs2_callpeak.xml Wed Jan 31 15:12:13 2018 -0500 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="macs2_callpeak" name="MACS2 callpeak" version="@VERSION_STRING@.2"> +<tool id="macs2_callpeak" name="MACS2 callpeak" version="@VERSION_STRING@.3"> <description>Call peaks from alignment results</description> <macros> <import>macs2_macros.xml</import> @@ -102,7 +102,7 @@ #end if ## run R to create pdf from model script - #if $nomodel_type.nomodel_type_selector == "create_model" and "pdf" in str($outputs).split(','): + #if $nomodel_type.nomodel_type_selector == "create_model" and "pdf" in str($outputs).split(',') and $format != "BAMPE": && Rscript MACS2_model.r > MACS2_model.r.log #end if @@ -206,7 +206,7 @@ <option value="summits">Peak summits</option> <option value="bdg" >Scores in bedGraph files (--bdg)</option> <option value="html">Summary page (html)</option> - <option value="pdf">Plot in PDF</option> + <option value="pdf">Plot in PDF (only available if a model is created and if BAMPE is not used)</option> </param> <section name="advanced_options" title="Advanced Options"> @@ -274,7 +274,8 @@ <filter> (( outputs and 'pdf' in outputs and - nomodel_type['nomodel_type_selector'] == "create_model" + nomodel_type['nomodel_type_selector'] == "create_model" and + format != "BAMPE" )) </filter> </data> @@ -335,6 +336,8 @@ <param name="gsize" value="3300000000"/> <param name="nomodel_type_selector" value="nomodel"/> <param name="nolambda" value="True"/> + <!-- we select PDF as output, but since we are in BAMPE mode, this will not ignored and the expect_num_outputs stays one. --> + <param name="outputs" value="pdf"/> <output name="output_narrowpeaks" file="callpeak_bampe_narrow.bed"/> </test> </tests> |