# HG changeset patch
# User rnateam
# Date 1631553630 0
# Node ID 600360da39864a95367267b5f97c37575d8c77f3
# Parent  26304ccaca5726e5f6027cbe8a38aea66cdc1bd5
"planemo upload for repository https://github.com/tbischler/PEAKachu commit 23fac1009bde8648151e533ce12c9f3d2f787a65-dirty"

diff -r 26304ccaca57 -r 600360da3986 peakachu.xml
--- a/peakachu.xml	Wed Jan 16 17:53:50 2019 -0500
+++ b/peakachu.xml	Mon Sep 13 17:20:30 2021 +0000
@@ -1,9 +1,9 @@
-<tool id="peakachu" name="PEAKachu" version="0.1.0.2">
+<tool id="peakachu" name="PEAKachu" version="0.2.0+galaxy0" profile="20.01">
     <description>Calls Peaks in CLIP data</description>
     <requirements>
         <requirement type="package" version="3.6">python</requirement>
-        <requirement type="package" version="3.4.1">r-base</requirement>
-        <requirement type="package" version="0.1.0">peakachu</requirement>
+        <requirement type="package" version="4.1.0">r-base</requirement>
+        <requirement type="package" version="0.2.0">peakachu</requirement>
     </requirements>
     <version_command>
     <![CDATA[
@@ -59,7 +59,7 @@
         #end if
        --norm_method $mode.norm_method.norm_method_selector
         #if str($mode.norm_method.norm_method_selector) == 'manual':
-            --size_factors $size_factors
+            --size_factors '${mode.norm_method.size_factors}'
         #end if
         --mad_multiplier $mad_multiplier
         --fc_cutoff $fc_cutoff
@@ -68,10 +68,10 @@
         &&
         if ls ./tmp_output/peak_tables/*.csv > /dev/null;
         then 
-            cat ./tmp_output/peak_tables/*.csv | head -n 1 > peaks.tsv &&
+            sed -n 1p ./tmp_output/peak_tables/*.csv > peaks.tsv &&
             tail -n +2 -q ./tmp_output/peak_tables/*.csv >> peaks.tsv &&
             mv peaks.tsv '$peak_tables' &&
-            cat ./tmp_output/peak_annotations/*.gff | awk '/peak/ {print $0}' > peak_annotations.gff &&
+            awk '/peak/ {print $0}' ./tmp_output/peak_annotations/*.gff > peak_annotations.gff &&
             mv peak_annotations.gff '$peak_annotations' &&
             mv ./tmp_output/plots/Initial*.png '$MA_plot';
         else 
@@ -113,7 +113,7 @@
                 <param argument="--min_block_overlap" label="Minimum Block Overlap" help="Minimum fraction of the width of blocks for merging." type="float" value="0.5"/>
                 <param argument="--min_max_block_expr" label="Minimum Block Expression" help="Minimum fraction of expression of blocks for merging." type="float" value="0.1"/>
                 <conditional name="norm_method">
-                    <param name="norm_method_selector" type="select" label="Normalisation Method.">
+                    <param name="norm_method_selector" type="select" label="Normalisation Method">
                         <option value="deseq" selected="True">DESeq2</option>
                         <option value="manual">Manual</option>
                         <option value="none">None</option>
@@ -137,7 +137,7 @@
                     <option value="deseq">DESeq2</option>
                 </param>
                 <conditional name="norm_method">
-                    <param name="norm_method_selector" type="select" label="Normalisation Method.">
+                    <param name="norm_method_selector" type="select" label="Normalisation Method">
                         <option value="tmm" selected="True">TMM</option>
                         <option value="deseq">DESeq2</option>
                         <option value="count">Count</option>
@@ -149,7 +149,7 @@
                     <when value="count"/>
                     <when value="none"/>
                     <when value="manual">
-                        <param argument="--size_factors" label="Size Factors" type="text" help="Size factors have to be seperated by SPACE">
+                        <param argument="--size_factors" label="Size Factors" type="text" help="Size factors have to be separated by SPACE">
                             <sanitizer>
                                 <valid initial="default"/>
                             </sanitizer>