comparison spotyping.xml @ 2:efa2be6db310 draft default tip

planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 059ddaa55a5e4bdac5aaba74fe489e9268731390

1:f82981245fbe

<tool id="spotyping" name="SpoTyping" version="@TOOL_VERSION@+galaxy1" profile="17.01">
  <description>fast and accurate in silico Mycobacterium spoligotyping from sequence reads</description>

  <macros>
    <import>spotyping_macros.xml</import>
  </macros>

  <requirements>
    <requirement type="package" version="@TOOL_VERSION@">spotyping</requirement>
  </requirements>

  <command detect_errors="exit_code"><![CDATA[
    #set $input_file='input.' + $input.extension
    ln -s '${input}' $input_file &&
    SpoTyping.py
    $advanced.noQuery
    $advanced.seq

      <output name="output_txt">
        <assert_contents>
          <has_text text="1111111111111111101111111111111100001111111" />
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="2">
      <param name="input" value="input.fastq.gz" ftype="fastq.gz" />
      <param name="noQuery" value="" />
      <output name="output_txt">

2:efa2be6db310

<tool id="spotyping" name="SpoTyping" version="@TOOL_VERSION@+galaxy2" profile="17.01">
  <description>fast and accurate in silico Mycobacterium spoligotyping from sequence reads</description>

  <macros>
    <import>spotyping_macros.xml</import>
  </macros>

  <requirements>
    <requirement type="package" version="@TOOL_VERSION@">spotyping</requirement>
  </requirements>

  <command detect_errors="aggressive"><![CDATA[
    #set $input_file='input.' + $input.extension
    ln -s '${input}' $input_file &&
    SpoTyping.py
    $advanced.noQuery
    $advanced.seq

      <output name="output_txt">
        <assert_contents>
          <has_text text="1111111111111111101111111111111100001111111" />
        </assert_contents>
      </output>
    </test>
    <test expect_failure="true">
      <param name="input" value="input.fastq.gz" ftype="fastq.gz" />
      <param name="seq" value="--seq" />
      <assert_stderr>
        <has_text text="BLAST options error" />
      </assert_stderr>
    </test>
    <test expect_num_outputs="2">
      <param name="input" value="input.fastq.gz" ftype="fastq.gz" />
      <param name="noQuery" value="" />
      <output name="output_txt">