diff macs2_predictd.xml @ 18:640d3af5d833 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e8307adcc6ee9245fa2bb9ecb6de1cbe008dc2c3"

--- a/macs2_predictd.xml	Thu Apr 25 17:49:05 2019 -0400
+++ b/macs2_predictd.xml	Sat Apr 02 21:37:38 2022 +0000
@@ -1,5 +1,6 @@
-<tool id="macs2_predictd" name="MACS2 predictd" version="@VERSION_STRING@.1">
+<tool id="macs2_predictd" name="MACS2 predictd" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
     <description>Predict 'd' or fragment size from alignment results</description>
+    <expand macro="bio_tools"/>
     <macros>
         <import>macs2_macros.xml</import>
     </macros>
@@ -15,6 +16,8 @@
         @effective_genome_size@
         --bw '${ band_width }'
         @mfold_command@
+        --d-min $d_min
+        @buffer_size@
 
         ## remove the timepoint and strip the output
         2>&1 | awk -F: '{print $4}' | awk '{$1=$1}1'
@@ -33,6 +36,8 @@
         <expand macro="tag_size" />
         <expand macro="band_width" />
         <expand macro="mfold_options" />
+        <expand macro="fragment_size"/>
+        <expand macro="buffer_size"/>
     </inputs>
 
     <outputs>
@@ -48,12 +53,16 @@
             <param name="band_width" value="300"/>
             <param name="lower" value="5"/>
             <param name="upper" value="50"/>
+            <assert_command>
+                <has_text text="--buffer-size"/>
+                <has_text text="--d-min"/>
+            </assert_command>
             <output name="outfile">
                 <assert_contents>
                     <has_line line="# predicted fragment length is 284 bps" />
                 </assert_contents>
             </output>
-            <output name="outfile_image" file="predictd_on_ChIP_200K_and_Control_200K.pdf" compare="sim_size"/>
+            <output name="outfile_image" file="predictd_on_ChIP_200K_and_Control_200K.pdf" compare="sim_size" ftype="pdf"/>
         </test>
     </tests>
     <help>