comparison rsem_calculate_expression.xml @ 2:f6b8155ab12a

Add test cases

1:1ff2fc8da328

  </macros>

  <inputs>
    <param name="sample" type="text" value="rsem_sample" label="Sample name" />
    <conditional name="reference">
      <param name="refSrc" type="select" label="RSEM Reference">
        <option value="cached">Locally cached</option>
        <option value="history">From your history</option>
      </param>
      <when value="cached">
        <param name="index" type="select" label="Select RSEM reference" help="Select from a list of pre-indexed references. If you don't see anything consult the wrapper's documentation on how to create or download a reference">

        <option value="fasta">FASTA</option>
        <option value="sam">SAM/BAM</option>
      </param>
      <when value="fastq">
        <param name="fastq_select" size="15" type="select" label="FASTQ type" >
          <option value="--phred33-quals">phred33 qualities (default for sanger)</option>
          <option value="--solexa-quals">solexa qualities</option>
          <option value="--phred64-quals">phred64 qualities</option>
        </param>
        <conditional name="fastq">
          <param name="matepair" type="select" label="Library type">

  </inputs>
  <stdio>
    <exit_code range="1:"  level="fatal" description="Error Running RSEM" />
  </stdio>
  <outputs>
    <data format="tabular" name="output" label="${sample}.gene_abundances" from_work_dir="rsem_output.genes.results"/>
    <data format="tabular" name="isoforms" label="${sample}.isoform_abundances" from_work_dir="rsem_output.isoforms.results"/>
    <data format="bam" name="transcript_bam" label="${sample}.transcript.bam" from_work_dir="rsem_output.transcript.bam" >
      <filter>rsem_outputs['result_bams'] != "none"</filter>
    </data>
    <data format="bam" name="transcript__sorted_bam" label="${sample}.transcript.bam" from_work_dir="rsem_output.transcript.sorted.bam" >
      <filter>rsem_outputs['result_bams'] != "none"</filter>
    </data>
    <data format="bam" name="genome_bam" label="${sample}.genome.bam" from_work_dir="rsem_output.genome.bam">
      <filter>rsem_outputs['result_bams'] == "both"</filter>
    </data>
    <data format="bam" name="genome_sorted_bam" label="${sample}.genome.bam" from_work_dir="rsem_output.genome.sorted.bam">
      <filter>rsem_outputs['result_bams'] == "both"</filter>
    </data>
    <data format="txt" name="log" label="${sample}.rsem_log"/>
  </outputs>
  <help>
  

RSEM HOME PAGE - http://deweylab.biostat.wisc.edu/rsem/

2:f6b8155ab12a

  </macros>

  <inputs>
    <param name="sample" type="text" value="rsem_sample" label="Sample name" />
    <conditional name="reference">
      <param name="refSrc" type="select" label="RSEM Reference Source">
        <option value="cached">Locally cached</option>
        <option value="history">From your history</option>
      </param>
      <when value="cached">
        <param name="index" type="select" label="Select RSEM reference" help="Select from a list of pre-indexed references. If you don't see anything consult the wrapper's documentation on how to create or download a reference">

        <option value="fasta">FASTA</option>
        <option value="sam">SAM/BAM</option>
      </param>
      <when value="fastq">
        <param name="fastq_select" size="15" type="select" label="FASTQ type" >
          <option value="--phred33-quals" selected="true">phred33 qualities (default for sanger)</option>
          <option value="--solexa-quals">solexa qualities</option>
          <option value="--phred64-quals">phred64 qualities</option>
        </param>
        <conditional name="fastq">
          <param name="matepair" type="select" label="Library type">

  </inputs>
  <stdio>
    <exit_code range="1:"  level="fatal" description="Error Running RSEM" />
  </stdio>
  <outputs>
    <data format="tabular" name="gene_abundances" label="${sample}.gene_abundances" from_work_dir="rsem_output.genes.results"/>
    <data format="tabular" name="isoform_abundances" label="${sample}.isoform_abundances" from_work_dir="rsem_output.isoforms.results"/>
    <data format="bam" name="transcript_bam" label="${sample}.transcript.bam" from_work_dir="rsem_output.transcript.bam" >
      <filter>rsem_outputs['result_bams'] != "none"</filter>
    </data>
    <data format="bam" name="transcript_sorted_bam" label="${sample}.transcript.bam" from_work_dir="rsem_output.transcript.sorted.bam" >
      <filter>rsem_outputs['result_bams'] != "none"</filter>
    </data>
    <data format="bam" name="genome_bam" label="${sample}.genome.bam" from_work_dir="rsem_output.genome.bam">
      <filter>rsem_outputs['result_bams'] == "both"</filter>
    </data>
    <data format="bam" name="genome_sorted_bam" label="${sample}.genome.sorted.bam" from_work_dir="rsem_output.genome.sorted.bam">
      <filter>rsem_outputs['result_bams'] == "both"</filter>
    </data>
    <data format="txt" name="log" label="${sample}.rsem_log"/>
  </outputs>
  <tests>
    <test>
      <param name="sample" value="rsem_sample"/>
      <param name="refSrc" value="history"/>
      <param name="rsem_ref" value="RSEM_ref_reference.zip" ftype="rsem_ref"/>
      <param name="format" value="fastq"/>
      <param name="matepair" value="single"/>
      <param name="singlefastq" value="test.fastq" ftype="fastqsanger"/>
      <param name="result_bams" value="none"/>
      <output name="gene_abundances"> 
        <assert_contents>
          <has_text text="ENST00000423562,ENST00000438504,ENST00000488147,ENST00000538476,ENST00000541675" />
        </assert_contents>
      </output>
      <output name="isoform_abundances"> 
        <assert_contents>
          <has_text text="ENST00000332831" />
        </assert_contents>
      </output>
      <output name="log"> 
        <assert_contents>
          <has_text text="Expression Results are written" />
        </assert_contents>
      </output>
    </test>
  </tests>
  <help>
  

RSEM HOME PAGE - http://deweylab.biostat.wisc.edu/rsem/