| Previous changeset 0:972c930ed278 (2015-08-27) Next changeset 2:96a9a03f8948 (2015-08-27) |
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align_and_estimate_abundance.xml |
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| diff -r 972c930ed278 -r 16aaa05e7d67 align_and_estimate_abundance.xml --- a/align_and_estimate_abundance.xml Thu Aug 27 12:23:47 2015 -0400 +++ b/align_and_estimate_abundance.xml Thu Aug 27 12:35:23 2015 -0400 |
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| @@ -61,3 +61,86 @@ </command> +<inputs> + +<!-- Required --> + <param name="transcripts" type="data" format="fasta" label="Transcripts [ in fasta format ]" help="--transcripts < string > ; transcript fasta file"/> + + <param name="est_method" type="select" display="radio" label="Choose abundance estimation method" help=""> + <option value="RSEM" selected="True">RSEM</option> + <option value="eXpress">eXpress</option> + </param> + + <param name="aln_method" type="select" display="radio" label="Choose alignment method" help=""> + <option value="bowtie" selected="True">bowtie</option> + <option value="bowtie2">bowtie2</option> + </param> + +<conditional name="reads"> + <param name="paired_or_single" type="select" label="Paired or Single-end reads?"> + <option value="paired">Paired</option> + <option value="single">Single</option> + </param> + + + <when value="paired"> + <param format="fasta,fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/> + <param format="fasta,fastq" name="right_input" type="data" label="Right/Reverse strand reads" help=""/> + + <param name="seqtype" type="select" label="--seqType" help=""> + <option value='fq' selected='true'>fastq</option> + <option value='fa'>fasta</option> + </param> + + <conditional name='optional'> + <param name='use_options' type='select' label='Use Optional parameters?'> + <option value='no'>NO</option> + <option value='yes'>YES</option> + </param> + <when value='no'/> + <when value='yes'> + <param name="library_type" type="select" label="Strand-specific Library Type"> + <option value="None">None</option> + <option value="FR">FR</option> + <option value="RF">RF</option> + </param> + + + + </when> + </conditional> + </when> + <when value="single"> + <param format="fasta,fastq" name="input" type="data" label="Single-end reads" help=""/> + <param name="seqtype" type="select" label="--seqType" help=""> + <option value='fq' selected='true'>fastq</option> + <option value='fa'>fasta</option> + </param> + + <conditional name='optional'> + <param name='use_options' type='select' label='Use Optional parameters?'> + <option value='no'>NO</option> + <option value='yes'>YES</option> + </param> + <when value='no'/> + <when value='yes'> + <param name="library_type" type="select" label="Strand-specific Library Type"> + <option value="None">None</option> + <option value="F">F</option> + <option value="R">R</option> + </param> + </when> + </conditional> + </when> +</conditional> + +</inputs> + +<outputs> + <data format="txt" name="align_and_estimate_abundance_log" label="${tool.name} on ${on_string}: log" /> + <data format="bam" name="bowtie_bam" label="${tool.name} on ${on_string}: bam" from_work_dir="bowtie.bam" /> + <data format="tabular" name="rsem_isoforms" label="${tool.name} on ${on_string}: isoforms" from_work_dir="RSEM.isoforms.results"/> + <data format="tabular" name="rsem_genes" label="${tool.name} on ${on_string}: genes" from_work_dir="RSEM.genes.results"/> +</outputs> +</tool> + |