diff transit_resampling.xml @ 6:a05b6a392ff0 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 0daaffac75df549583b6d834113608c2dbacb1d3

--- a/transit_resampling.xml	Sat Nov 27 09:49:19 2021 +0000
+++ b/transit_resampling.xml	Tue May 27 19:59:25 2025 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="transit_resampling" name="TRANSIT Resampling" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="transit_resampling" name="TRANSIT Resampling" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>- determine per-gene p-values</description>
     <expand macro="bio_tools"/>
     <macros>
@@ -12,14 +12,13 @@
         #for idx, filename in enumerate(str($controls).split(',')):
             ln -s '$filename' control_file_${idx}.wig &&
         #end for
-        transit resampling $input_files $control_files annotation.dat transit_out.txt
+        transit resampling $control_files $input_files annotation.dat transit_out.txt
         @STANDARD_OPTIONS@
         -s $samples $histogram $adaptive $exclude_zero $pseudo $loess
         ]]>
     </command>
     <inputs>
         <expand macro="standard_inputs">
-            <expand macro="handle_replicates" />
             <param name="controls" type="data" format="wig" multiple="true" label="Control .wig files" />
             <param name="samples" argument="-s" type="integer" value="10000" label="Number of samples" />
             <param name="histogram" argument="-h" type="boolean" truevalue="-h" falsevalue="" label="Output histogram of the permutations" />
@@ -35,11 +34,13 @@
     </outputs>
     <tests>
         <test>
-            <param name="inputs" ftype="wig" value="transit-in1-rep1.wig,transit-in1-rep2.wig" />
+            <conditional name="mode">
+                <param name="replicates" value="Replicates" />
+                <param name="inputs" ftype="wig" value="transit-in1-rep1.wig,transit-in1-rep2.wig" />
+           </conditional>
             <param name="controls" ftype="wig" value="transit-co1-rep1.wig,transit-co1-rep2.wig,transit-co1-rep3.wig" />
             <param name="annotation" ftype="tabular" value="transit-in1.prot" />
             <param name="samples" value="1000" />
-            <param name="replicates" value="Replicates" />
             <output name="sites" file="resampling-sites1.txt" ftype="tabular" compare="sim_size" />
         </test>
     </tests>
@@ -87,7 +88,6 @@
 -ez             :=  Exclude rows with zero accross conditions. Default: Off
 --pc            :=  Pseudocounts to be added at each site. Default: 0
 -l              :=  Perform LOESS Correction; Helps remove possible genomic position bias. Default: Off.
--r <string>     :=  How to handle replicates. Sum, Mean. Default: -r Mean
 --iN <float>     :=  Ignore TAs occuring at given fraction of the N terminus. Default: 0.0
 --iC <float>     :=  Ignore TAs occuring at given fraction of the C terminus. Default: 0.0
 --ctrl_lib      :=  String of letters representing library of control files in order e.g. 'AABB' Default: empty. Letters used must also be used in --exp_lib. If non-empty, resampling will limit permutations to within-libraries.
@@ -144,8 +144,8 @@
 
 See  `TRANSIT documentation`
 
-- TRANSIT: https://transit.readthedocs.io/en/latest/index.html
-- `TRANSIT Gumbel`: https://transit.readthedocs.io/en/latest/transit_methods.html#re-sampling
+- TRANSIT: https://transit.readthedocs.io/en/v@TOOL_VERSION@/index.html
+- `TRANSIT Gumbel`: https://transit.readthedocs.io/en/v@TOOL_VERSION@/transit_methods.html#re-sampling
 ]]></help>
 
     <expand macro="citations" />