Mercurial > repos > vipints > rdiff
comparison rDiff/galaxy/rdiff.xml @ 0:0f80a5141704
version 0.3 uploaded
| author | vipints |
|---|---|
| date | Thu, 14 Feb 2013 23:38:36 -0500 |
| parents | |
| children | 233c30f91d66 |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:0f80a5141704 |
|---|---|
| 1 <tool id="rdiff-web" name="rDiff" version="0.3"> | |
| 2 <description>Determines differentially expressed transcripts from read alignments</description> | |
| 3 <command interpreter="bash"> | |
| 4 rdiff_run.sh $test_meth $anno_input $read_length $rdiff_out $rdiff_out.extra_files_path | |
| 5 #for $i in $replicate_groups | |
| 6 #for $j in $i.replicates | |
| 7 $j.bam_alignment? | |
| 8 #end for | |
| 9 : | |
| 10 #end for | |
| 11 >> $Log_File | |
| 12 </command> | |
| 13 <inputs> | |
| 14 | |
| 15 <!-- genome annotation in GFF format --> | |
| 16 <param format="gff3" name="anno_input" type="data" label="Genome annotation in GFF3 file" help="A tab delimited format for storing sequence features and annotations"/> | |
| 17 | |
| 18 <!-- RNA-seq samples and corresponding replicates --> | |
| 19 <repeat name="replicate_groups" title="Sample" min="2" max="2"> | |
| 20 <repeat name="replicates" title="Replicate"> | |
| 21 <param format="bam" name="bam_alignment" type="data" label="BAM alignment file" help="BAM is the binary version of the SAM format, a tab-delimited text file that contains sequence alignment data."/> | |
| 22 </repeat> | |
| 23 </repeat> | |
| 24 | |
| 25 | |
| 26 <param name="test_meth" type="select" label="rDiff testing method" help="Statistical test on differential transcript expression data." > | |
| 27 <option value="poisson">Poisson</option> | |
| 28 <option value="param">Parametric</option> | |
| 29 <option value="nonparam">Nonparametric</option> | |
| 30 </param> | |
| 31 <param name="read_length" type="text" value="75" help="default 75 nucleotide." label="Read length from sequencing experiment"/> | |
| 32 | |
| 33 </inputs> | |
| 34 | |
| 35 <outputs> | |
| 36 <data format="txt" name="rdiff_out" label="${tool.name} on ${on_string}: Differential Testing Result" /> | |
| 37 <data format="txt" name="Log_File" label="${tool.name} on ${on_string}: log"/> | |
| 38 </outputs> | |
| 39 | |
| 40 <help> | |
| 41 | |
| 42 .. class:: infomark | |
| 43 | |
| 44 **What it does** | |
| 45 | |
| 46 rDiff_ is a tool for differential expression testing of RNA-Seq data. | |
| 47 | |
| 48 .. _rDiff: http://bioweb.me/rdiff | |
| 49 | |
| 50 </help> | |
| 51 </tool> |