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

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

7:bea8435e1e79

<tool id="probecoverage" name="Probe Coverage" version="0.7.0">
  <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>
  <stdio>
      <exit_code range="1:" level="fatal" description="Tool exception" />
  </stdio>
  <command detect_errors="exit_code"><![CDATA[
      #for $file in $inputs
          samtools index '$file' &&
      #end for
      #if $method == 'pysam':
          python $__tool_directory__/multicov.py
      #else:
          bedtools multicov
      #end if
          -bams
              #for $file in $inputs
                  '$file'
              #end for
          -bed '$bed' > $coverage_dataframe &&
      Rscript '$__tool_directory__'/probecoverage.r
          --method '$method'
          --input '$coverage_dataframe' 

8:0adb846ca056

<tool id="probecoverage" name="Probe Coverage" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
  <description></description>
    <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 $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
      #else:
          bedtools multicov
      #end if
          -bams
              #for $i, $file in enumerate($inputs):
                  '${i}.bam'
              #end for
          -bed '$bed' > $coverage_dataframe &&
      Rscript '$__tool_directory__'/probecoverage.r
          --method '$method'
          --input '$coverage_dataframe'