comparison revertR2orientationInBam.xml @ 1:21ddefab2e4f draft default tip

planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam commit 49a42d0e75d6ae7faa3ce399524157c35546fbaa

0:05aa21d39189

<tool id="revertR2orientationInBam" name="revertR2orientationInBam" version="0.0.1" profile="16.04">
  <description> Revert the mapped orientation of R2 mates in a bam.</description>
  <requirements>
    <requirement type="package" version="1.9">samtools</requirement>
  </requirements>
  <stdio>
    <!-- Anything other than zero is an error -->
    <exit_code range="1:" />
    <exit_code range=":-1" />

    <regex match="Error:" />
    <regex match="Exception:" />
  </stdio>
  <command>
<![CDATA[
        bash $__tool_directory__/revertR2orientationInBam.sh $input $output
]]>
  </command>
  <inputs>
    <!-- note unsorted bam includes all derived bam types (inlcuding bam which is sorted) -->
    <param name="input" type="data" format="sam,bam" label="Select a sam or bam file."/>

  </outputs>

  <tests>
    <test>
      <param name="input" value="input.sam"/>
      <output name="output" file="output.bam" ftype="bam"/>
    </test>
  </tests>  
  <help>
<![CDATA[
    This tool is very useful when you have paired-end stranded RNA-seq.

1:21ddefab2e4f

<tool id="revertR2orientationInBam" name="revertR2orientationInBam" version="0.0.2" profile="16.04">
  <description> Revert the mapped orientation of R2 mates in a bam.</description>
  <requirements>
    <requirement type="package" version="1.16.1">samtools</requirement>
    <requirement type="package" version="5.1.0">gawk</requirement>
  </requirements>
  <stdio>
    <!-- Anything other than zero is an error -->
    <exit_code range="1:" />
    <exit_code range=":-1" />

    <regex match="Error:" />
    <regex match="Exception:" />
  </stdio>
  <command>
<![CDATA[
        set -o pipefail;
        bash $__tool_directory__/revertR2orientationInBam.sh '$input' '$output'
]]>
  </command>
  <inputs>
    <!-- note unsorted bam includes all derived bam types (inlcuding bam which is sorted) -->
    <param name="input" type="data" format="sam,bam" label="Select a sam or bam file."/>

  </outputs>

  <tests>
    <test>
      <param name="input" value="input.sam"/>
      <output name="output" file="output.bam" ftype="bam" lines_diff="2"/>
    </test>
  </tests>  
  <help>
<![CDATA[
    This tool is very useful when you have paired-end stranded RNA-seq.