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updated python based GFF parsing module which will handle GTF/GFF/GFF3 file types
author vipints <vipin@cbio.mskcc.org>
date Tue, 08 Oct 2013 07:15:44 -0400
parents 0f80a5141704
children
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1 <tool id="rdiff-web" name="rDiff" version="0.3">
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2 <description>Determines differentially expressed transcripts from read alignments</description>
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3 <command interpreter="bash">
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4 rdiff_run.sh
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5 $test_meth
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6 $anno_input
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7 $read_length
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8 $rdiff_out $rdiff_out.extra_files_path
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9 ##
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10 ## replicate groups
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11 ##
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12 #for $i in $replicate_groups
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13 #for $j in $i.replicates
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14 $j.bam_alignment?
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15 #end for
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16 :
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17 #end for
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18
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19 >> $Log_File
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20 </command>
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21 <inputs>
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22
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23 <!-- genome annotation in GFF format -->
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24 <param format="gff,gtf,gff3" name="anno_input" type="data" label="Genome annotation file" help="A tab delimited format for storing sequence features and annotations(GFF/GTF/GFF3)"/>
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25
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26 <!-- RNA-seq samples and corresponding replicates -->
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27 <repeat name="replicate_groups" title="Sample" min="2" max="2">
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28 <repeat name="replicates" title="Replicate">
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29 <param format="bam" name="bam_alignment" type="data" label="BAM alignment file" help="BAM is the binary version of the SAM format, a tab-delimited text file that contains sequence alignment data."/>
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30 </repeat>
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31 </repeat>
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32
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33 <!-- rDiff test method -->
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34 <param name="test_meth" type="select" label="rDiff testing method" help="Statistical test on differential transcript expression data." >
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35 <option value="poisson">Poisson</option>
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36 <option value="param">Parametric</option>
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37 <option value="nonparam">Nonparametric</option>
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38 </param>
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40 <!-- read length uesd in the experiment-->
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41 <param name="read_length" type="text" value="75" help="default 75 nucleotide." label="Read length from sequencing experiment"/>
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42
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43 </inputs>
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44
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45 <outputs>
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46 <data format="txt" name="rdiff_out" label="${tool.name} on ${on_string}: Differential Expression" />
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47 <data format="txt" name="Log_File" label="${tool.name} on ${on_string}: Log"/>
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48 </outputs>
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49
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50 <help>
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51
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52 .. class:: infomark
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53
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54 **What it does**
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55
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56 rDiff_ is a tool for differential expression testing of RNA-Seq data.
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57
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58 .. _rDiff: http://bioweb.me/rdiff
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59
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60 </help>
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61 </tool>