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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 $test_meth $anno_input $read_length $rdiff_out $rdiff_out.extra_files_path
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5 #for $i in $replicate_groups
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6 #for $j in $i.replicates
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7 $j.bam_alignment?
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8 #end for
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9 :
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10 #end for
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11 >> $Log_File
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12 </command>
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13 <inputs>
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14
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15 <!-- genome annotation in GFF format -->
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16 <param format="gff3" name="anno_input" type="data" label="Genome annotation in GFF3 file" help="A tab delimited format for storing sequence features and annotations"/>
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17
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18 <!-- RNA-seq samples and corresponding replicates -->
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19 <repeat name="replicate_groups" title="Sample" min="2" max="2">
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20 <repeat name="replicates" title="Replicate">
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21 <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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22 </repeat>
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23 </repeat>
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24
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25
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26 <param name="test_meth" type="select" label="rDiff testing method" help="Statistical test on differential transcript expression data." >
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27 <option value="poisson">Poisson</option>
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28 <option value="param">Parametric</option>
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29 <option value="nonparam">Nonparametric</option>
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30 </param>
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31 <param name="read_length" type="text" value="75" help="default 75 nucleotide." label="Read length from sequencing experiment"/>
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32
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33 </inputs>
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34
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35 <outputs>
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36 <data format="txt" name="rdiff_out" label="${tool.name} on ${on_string}: Differential Testing Result" />
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37 <data format="txt" name="Log_File" label="${tool.name} on ${on_string}: log"/>
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38 </outputs>
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39
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40 <help>
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41
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42 .. class:: infomark
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43
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44 **What it does**
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45
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46 rDiff_ is a tool for differential expression testing of RNA-Seq data.
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47
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48 .. _rDiff: http://bioweb.me/rdiff
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49
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50 </help>
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51 </tool>
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