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comparison rDiff/galaxy/rdiff.xml @ 2:233c30f91d66

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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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0:0f80a5141704 2:233c30f91d66
1 <tool id="rdiff-web" name="rDiff" version="0.3"> 1 <tool id="rdiff-web" name="rDiff" version="0.3">
2 <description>Determines differentially expressed transcripts from read alignments</description> 2 <description>Determines differentially expressed transcripts from read alignments</description>
3 <command interpreter="bash"> 3 <command interpreter="bash">
4 rdiff_run.sh $test_meth $anno_input $read_length $rdiff_out $rdiff_out.extra_files_path 4 rdiff_run.sh
5 #for $i in $replicate_groups 5 $test_meth
6 #for $j in $i.replicates 6 $anno_input
7 $j.bam_alignment? 7 $read_length
8 #end for 8 $rdiff_out $rdiff_out.extra_files_path
9 : 9 ##
10 #end for 10 ## replicate groups
11 ##
12 #for $i in $replicate_groups
13 #for $j in $i.replicates
14 $j.bam_alignment?
15 #end for
16 :
17 #end for
18
11 >> $Log_File 19 >> $Log_File
12 </command> 20 </command>
13 <inputs> 21 <inputs>
14 22
15 <!-- genome annotation in GFF format --> 23 <!-- 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"/> 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)"/>
17 25
18 <!-- RNA-seq samples and corresponding replicates --> 26 <!-- RNA-seq samples and corresponding replicates -->
19 <repeat name="replicate_groups" title="Sample" min="2" max="2"> 27 <repeat name="replicate_groups" title="Sample" min="2" max="2">
20 <repeat name="replicates" title="Replicate"> 28 <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."/> 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."/>
22 </repeat> 30 </repeat>
23 </repeat> 31 </repeat>
24 32
25 33 <!-- rDiff test method -->
26 <param name="test_meth" type="select" label="rDiff testing method" help="Statistical test on differential transcript expression data." > 34 <param name="test_meth" type="select" label="rDiff testing method" help="Statistical test on differential transcript expression data." >
27 <option value="poisson">Poisson</option> 35 <option value="poisson">Poisson</option>
28 <option value="param">Parametric</option> 36 <option value="param">Parametric</option>
29 <option value="nonparam">Nonparametric</option> 37 <option value="nonparam">Nonparametric</option>
30 </param> 38 </param>
39
40 <!-- read length uesd in the experiment-->
31 <param name="read_length" type="text" value="75" help="default 75 nucleotide." label="Read length from sequencing experiment"/> 41 <param name="read_length" type="text" value="75" help="default 75 nucleotide." label="Read length from sequencing experiment"/>
32 42
33 </inputs> 43 </inputs>
34 44
35 <outputs> 45 <outputs>
36 <data format="txt" name="rdiff_out" label="${tool.name} on ${on_string}: Differential Testing Result" /> 46 <data format="txt" name="rdiff_out" label="${tool.name} on ${on_string}: Differential Expression" />
37 <data format="txt" name="Log_File" label="${tool.name} on ${on_string}: log"/> 47 <data format="txt" name="Log_File" label="${tool.name} on ${on_string}: Log"/>
38 </outputs> 48 </outputs>
39 49
40 <help> 50 <help>
41 51
42 .. class:: infomark 52 .. class:: infomark