comparison rsem-bwt2.xml @ 3:26ead8419b63 draft

planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 36c2780df597aa4b14ae9c620457f7460166aaa5

2:9fa602bc29ec

        #elif $run_rsem.input.fasta.matepair=="paired":
          --paired-end
          $run_rsem.input.fasta.fasta1
          $run_rsem.input.fasta.fasta2
        #end if
      #elif $run_rsem.input.format=="sam"
        #if $run_rsem.input.matepair=="paired":
          --paired-end
        #end if
        #if $run_rsem.input.rsem_sam.is_of_type('sam'):
          --sam
        #elif $run_rsem.input.rsem_sam.is_of_type('bam'):
          --bam
        #end if
        $run_rsem.input.rsem_sam
      #end if
      ## RSEM reference
      #if $run_rsem.reference.refSrc == 'history':
        ${run_rsem.reference.rsem_ref.extra_files_path}/${run_rsem.reference.rsem_ref.metadata.reference_name}
      #elif $run_rsem.reference.refSrc == 'self':

        </conditional>
        <conditional name="input">
          <param name="format" type="select" label="RSEM Input file type">
            <option value="fastq">FASTQ</option>
            <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>

                <param name="fasta1" type="data" format="fasta" label="Read 1 fasta file" />
                <param name="fasta2" type="data" format="fasta" label="Read 2 fasta file" />
              </when>
            </conditional>
            <expand macro="bowtie2_options"/>
          </when>
          <when value="sam">
              <!-- convert-sam-for-rsem /ref/mouse_125 input.sam -o input_for_rsem.sam -->
              <param name="matepair" type="select" label="Library Type">
                <option value="single">Single End Reads</option>
                <option value="paired">Paired End Reads</option>
              </param>
              <param name="rsem_sam" type="data" format="sam,bam" label="RSEM formatted SAM file" />
          </when>
        </conditional>
        <expand macro="rsem_options"/>
        <conditional name="rsem_outputs">
          <param name="result_bams" type="select" label="Create bam results files" 

3:26ead8419b63

        #elif $run_rsem.input.fasta.matepair=="paired":
          --paired-end
          $run_rsem.input.fasta.fasta1
          $run_rsem.input.fasta.fasta2
        #end if
      #end if
      ## RSEM reference
      #if $run_rsem.reference.refSrc == 'history':
        ${run_rsem.reference.rsem_ref.extra_files_path}/${run_rsem.reference.rsem_ref.metadata.reference_name}
      #elif $run_rsem.reference.refSrc == 'self':

        </conditional>
        <conditional name="input">
          <param name="format" type="select" label="RSEM Input file type">
            <option value="fastq">FASTQ</option>
            <option value="fasta">FASTA</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>

                <param name="fasta1" type="data" format="fasta" label="Read 1 fasta file" />
                <param name="fasta2" type="data" format="fasta" label="Read 2 fasta file" />
              </when>
            </conditional>
            <expand macro="bowtie2_options"/>
          </when>
        </conditional>
        <expand macro="rsem_options"/>
        <conditional name="rsem_outputs">
          <param name="result_bams" type="select" label="Create bam results files"