Mercurial > repos > vipints > rdiff
annotate rDiff/galaxy/rdiff.xml @ 3:29a698dc5c7e default tip
Merge multiple heads.
| author | Dave Bouvier <dave@bx.psu.edu> |
|---|---|
| date | Mon, 27 Jan 2014 14:15:36 -0500 |
| parents | 233c30f91d66 |
| children |
| rev | line source |
|---|---|
| 0 | 1 <tool id="rdiff-web" name="rDiff" version="0.3"> |
| 2 <description>Determines differentially expressed transcripts from read alignments</description> | |
| 3 <command interpreter="bash"> | |
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233c30f91d66
updated python based GFF parsing module which will handle GTF/GFF/GFF3 file types
vipints <vipin@cbio.mskcc.org>
parents:
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4 rdiff_run.sh |
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233c30f91d66
updated python based GFF parsing module which will handle GTF/GFF/GFF3 file types
vipints <vipin@cbio.mskcc.org>
parents:
0
diff
changeset
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5 $test_meth |
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233c30f91d66
updated python based GFF parsing module which will handle GTF/GFF/GFF3 file types
vipints <vipin@cbio.mskcc.org>
parents:
0
diff
changeset
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6 $anno_input |
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233c30f91d66
updated python based GFF parsing module which will handle GTF/GFF/GFF3 file types
vipints <vipin@cbio.mskcc.org>
parents:
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diff
changeset
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7 $read_length |
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233c30f91d66
updated python based GFF parsing module which will handle GTF/GFF/GFF3 file types
vipints <vipin@cbio.mskcc.org>
parents:
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8 $rdiff_out $rdiff_out.extra_files_path |
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233c30f91d66
updated python based GFF parsing module which will handle GTF/GFF/GFF3 file types
vipints <vipin@cbio.mskcc.org>
parents:
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9 ## |
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233c30f91d66
updated python based GFF parsing module which will handle GTF/GFF/GFF3 file types
vipints <vipin@cbio.mskcc.org>
parents:
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10 ## replicate groups |
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233c30f91d66
updated python based GFF parsing module which will handle GTF/GFF/GFF3 file types
vipints <vipin@cbio.mskcc.org>
parents:
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changeset
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11 ## |
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233c30f91d66
updated python based GFF parsing module which will handle GTF/GFF/GFF3 file types
vipints <vipin@cbio.mskcc.org>
parents:
0
diff
changeset
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12 #for $i in $replicate_groups |
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233c30f91d66
updated python based GFF parsing module which will handle GTF/GFF/GFF3 file types
vipints <vipin@cbio.mskcc.org>
parents:
0
diff
changeset
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13 #for $j in $i.replicates |
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233c30f91d66
updated python based GFF parsing module which will handle GTF/GFF/GFF3 file types
vipints <vipin@cbio.mskcc.org>
parents:
0
diff
changeset
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14 $j.bam_alignment? |
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233c30f91d66
updated python based GFF parsing module which will handle GTF/GFF/GFF3 file types
vipints <vipin@cbio.mskcc.org>
parents:
0
diff
changeset
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15 #end for |
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233c30f91d66
updated python based GFF parsing module which will handle GTF/GFF/GFF3 file types
vipints <vipin@cbio.mskcc.org>
parents:
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16 : |
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233c30f91d66
updated python based GFF parsing module which will handle GTF/GFF/GFF3 file types
vipints <vipin@cbio.mskcc.org>
parents:
0
diff
changeset
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17 #end for |
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233c30f91d66
updated python based GFF parsing module which will handle GTF/GFF/GFF3 file types
vipints <vipin@cbio.mskcc.org>
parents:
0
diff
changeset
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18 |
| 0 | 19 >> $Log_File |
| 20 </command> | |
| 21 <inputs> | |
| 22 | |
| 23 <!-- genome annotation in GFF format --> | |
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233c30f91d66
updated python based GFF parsing module which will handle GTF/GFF/GFF3 file types
vipints <vipin@cbio.mskcc.org>
parents:
0
diff
changeset
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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)"/> |
| 0 | 25 |
| 26 <!-- RNA-seq samples and corresponding replicates --> | |
| 27 <repeat name="replicate_groups" title="Sample" min="2" max="2"> | |
| 28 <repeat name="replicates" title="Replicate"> | |
| 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."/> | |
| 30 </repeat> | |
| 31 </repeat> | |
| 32 | |
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233c30f91d66
updated python based GFF parsing module which will handle GTF/GFF/GFF3 file types
vipints <vipin@cbio.mskcc.org>
parents:
0
diff
changeset
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33 <!-- rDiff test method --> |
| 0 | 34 <param name="test_meth" type="select" label="rDiff testing method" help="Statistical test on differential transcript expression data." > |
| 35 <option value="poisson">Poisson</option> | |
| 36 <option value="param">Parametric</option> | |
| 37 <option value="nonparam">Nonparametric</option> | |
| 38 </param> | |
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233c30f91d66
updated python based GFF parsing module which will handle GTF/GFF/GFF3 file types
vipints <vipin@cbio.mskcc.org>
parents:
0
diff
changeset
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39 |
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233c30f91d66
updated python based GFF parsing module which will handle GTF/GFF/GFF3 file types
vipints <vipin@cbio.mskcc.org>
parents:
0
diff
changeset
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40 <!-- read length uesd in the experiment--> |
| 0 | 41 <param name="read_length" type="text" value="75" help="default 75 nucleotide." label="Read length from sequencing experiment"/> |
| 42 | |
| 43 </inputs> | |
| 44 | |
| 45 <outputs> | |
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233c30f91d66
updated python based GFF parsing module which will handle GTF/GFF/GFF3 file types
vipints <vipin@cbio.mskcc.org>
parents:
0
diff
changeset
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46 <data format="txt" name="rdiff_out" label="${tool.name} on ${on_string}: Differential Expression" /> |
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233c30f91d66
updated python based GFF parsing module which will handle GTF/GFF/GFF3 file types
vipints <vipin@cbio.mskcc.org>
parents:
0
diff
changeset
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47 <data format="txt" name="Log_File" label="${tool.name} on ${on_string}: Log"/> |
| 0 | 48 </outputs> |
| 49 | |
| 50 <help> | |
| 51 | |
| 52 .. class:: infomark | |
| 53 | |
| 54 **What it does** | |
| 55 | |
| 56 rDiff_ is a tool for differential expression testing of RNA-Seq data. | |
| 57 | |
| 58 .. _rDiff: http://bioweb.me/rdiff | |
| 59 | |
| 60 </help> | |
| 61 </tool> |