Mercurial > repos > anmoljh > align_and_estimate_abundance

changeset 1:16aaa05e7d67 draft

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Uploaded
author anmoljh
date Thu, 27 Aug 2015 12:35:23 -0400
parents 972c930ed278
children 96a9a03f8948
files align_and_estimate_abundance.xml
diffstat 1 files changed, 83 insertions(+), 0 deletions(-) [+]
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line diff
--- 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
@@ -61,3 +61,86 @@
 
 </command>
 
+<inputs>
+
+<!-- Required -->
+	<param name="transcripts" type="data" format="fasta" label="Transcripts [ in fasta format ]" help="--transcripts &lt; string &gt; ; 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>
+