diff probecoverage.xml @ 8:0adb846ca056 draft default tip

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage commit 668f7e9be66ae301f840b395d72ddcc311da7aa2

--- a/probecoverage.xml	Thu Jun 03 23:59:31 2021 +0000
+++ b/probecoverage.xml	Tue Feb 20 08:34:16 2024 +0000
@@ -1,19 +1,25 @@
-<tool id="probecoverage" name="Probe Coverage" version="0.7.0">
+<tool id="probecoverage" name="Probe Coverage" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
   <description></description>
-  <requirements>
-        <requirement type="package" version="1.10=h9402c20_2">samtools</requirement>
-        <requirement type="package" version="2.29.2=hc088bd4_0">bedtools</requirement>
-        <requirement type="package" version="1.6.4=r36h6115d3f_0">r-optparse</requirement>
-        <requirement type="package" version="3.2.1=r36h6115d3f_0">r-ggplot2</requirement>
-        <requirement type="package" version="1.17.3=py37h95a1406_0">numpy</requirement>
-        <requirement type="package" version="0.16.0.1">pysam</requirement>
-  </requirements>
+    <macros>
+        <token name="@TOOL_VERSION@">0.22.0</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@PROFILE@">23.0</token>
+    </macros>
+   <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">pysam</requirement>
+        <requirement type="package" version="2.31.1">bedtools</requirement>
+        <requirement type="package" version="1.7.4">r-optparse</requirement>
+        <requirement type="package" version="3.4.4">r-ggplot2</requirement>
+        <requirement type="package" version="1.4.4">r-reshape2</requirement>
+        <requirement type="package" version="1.26.4">numpy</requirement>
+    </requirements>
   <stdio>
       <exit_code range="1:" level="fatal" description="Tool exception" />
   </stdio>
   <command detect_errors="exit_code"><![CDATA[
-      #for $file in $inputs
-          samtools index '$file' &&
+      #for $i, $file in enumerate($inputs):
+          ln -f -s '$file' ${i}.bam &&
+          ln -f -s '$file.metadata.bam_index' ${i}.bam.bai &&
       #end for
       #if $method == 'pysam':
           python $__tool_directory__/multicov.py
@@ -21,8 +27,8 @@
           bedtools multicov
       #end if
           -bams
-              #for $file in $inputs
-                  '$file'
+              #for $i, $file in enumerate($inputs):
+                  '${i}.bam'
               #end for
           -bed '$bed' > $coverage_dataframe &&
       Rscript '$__tool_directory__'/probecoverage.r