Mercurial > repos > devteam > cufflinks
comparison cufflinks_wrapper.xml @ 2:da11bfc10e81
Update to the new data table specification.
| author | Dave Bouvier <dave@bx.psu.edu> |
|---|---|
| date | Wed, 04 Dec 2013 13:24:49 -0500 |
| parents | b50aacc8ae49 |
| children | 9aab29e159a7 |
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| 1:b01956f26c36 | 2:da11bfc10e81 |
|---|---|
| 1 <tool id="cufflinks" name="Cufflinks" version="0.0.6"> | 1 <tool id="cufflinks" name="Cufflinks" version="0.0.7"> |
| 2 <!-- Wrapper supports Cufflinks versions v1.3.0 and newer --> | 2 <!-- Wrapper supports Cufflinks versions v1.3.0 and newer --> |
| 3 <description>transcript assembly and FPKM (RPKM) estimates for RNA-Seq data</description> | 3 <description>transcript assembly and FPKM (RPKM) estimates for RNA-Seq data</description> |
| 4 <requirements> | 4 <requirements> |
| 5 <requirement type="package" version="2.1.1">cufflinks</requirement> | 5 <requirement type="package" version="2.1.1">cufflinks</requirement> |
| 6 </requirements> | 6 </requirements> |
| 28 -N | 28 -N |
| 29 #end if | 29 #end if |
| 30 | 30 |
| 31 ## Bias correction? | 31 ## Bias correction? |
| 32 #if $bias_correction.do_bias_correction == "Yes": | 32 #if $bias_correction.do_bias_correction == "Yes": |
| 33 -b | 33 -b |
| 34 #if $bias_correction.seq_source.index_source == "history": | 34 #if $bias_correction.seq_source.index_source == "history": |
| 35 --ref_file=$bias_correction.seq_source.ref_file | 35 --ref_file=$bias_correction.seq_source.ref_file |
| 36 #else: | 36 #else: |
| 37 --ref_file="None" | 37 --index=${bias_correction.seq_source.index.fields.path} |
| 38 #end if | 38 #end if |
| 39 --dbkey=${input.metadata.dbkey} | |
| 40 --index_dir=${GALAXY_DATA_INDEX_DIR} | |
| 41 #end if | 39 #end if |
| 42 | 40 |
| 43 ## Multi-read correct? | 41 ## Multi-read correct? |
| 44 #if str($multiread_correct) == "Yes": | 42 #if str($multiread_correct) == "Yes": |
| 45 -u | 43 -u |
| 66 <option value="Use reference annotation guide">Use reference annotation as guide</option> | 64 <option value="Use reference annotation guide">Use reference annotation as guide</option> |
| 67 </param> | 65 </param> |
| 68 <when value="No"></when> | 66 <when value="No"></when> |
| 69 <when value="Use reference annotation"> | 67 <when value="Use reference annotation"> |
| 70 <param format="gff3,gtf" name="reference_annotation_file" type="data" label="Reference Annotation" help="Gene annotation dataset in GTF or GFF3 format."/> | 68 <param format="gff3,gtf" name="reference_annotation_file" type="data" label="Reference Annotation" help="Gene annotation dataset in GTF or GFF3 format."/> |
| 71 </when> | 69 </when> |
| 72 <when value="Use reference annotation guide"> | 70 <when value="Use reference annotation guide"> |
| 73 <param format="gff3,gtf" name="reference_annotation_guide_file" type="data" label="Reference Annotation" help="Gene annotation dataset in GTF or GFF3 format."/> | 71 <param format="gff3,gtf" name="reference_annotation_guide_file" type="data" label="Reference Annotation" help="Gene annotation dataset in GTF or GFF3 format."/> |
| 74 </when> | 72 </when> |
| 75 </conditional> | 73 </conditional> |
| 76 <conditional name="bias_correction"> | 74 <conditional name="bias_correction"> |
| 77 <param name="do_bias_correction" type="select" label="Perform Bias Correction" help="Bias detection and correction can significantly improve accuracy of transcript abundance estimates."> | 75 <param name="do_bias_correction" type="select" label="Perform Bias Correction" help="Bias detection and correction can significantly improve accuracy of transcript abundance estimates."> |
| 78 <option value="No" selected="true">No</option> | 76 <option value="No" selected="true">No</option> |
| 79 <option value="Yes">Yes</option> | 77 <option value="Yes">Yes</option> |
| 80 </param> | 78 </param> |
| 81 <when value="Yes"> | 79 <when value="Yes"> |
| 82 <conditional name="seq_source"> | 80 <conditional name="seq_source"> |
| 83 <param name="index_source" type="select" label="Reference sequence data"> | 81 <param name="index_source" type="select" label="Reference sequence data"> |
| 84 <option value="cached" selected="true">Locally cached</option> | 82 <option value="cached" selected="true">Locally cached</option> |
| 85 <option value="history">History</option> | 83 <option value="history">History</option> |
| 86 </param> | 84 </param> |
| 87 <when value="cached"></when> | 85 <when value="cached"> |
| 86 <param name="index" type="select" label="Using reference genome"> | |
| 87 <options from_data_table="fasta_indexes"> | |
| 88 <filter type="data_meta" ref="input" key="dbkey" column="1" /> | |
| 89 <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" /> | |
| 90 </options> | |
| 91 </param> | |
| 92 </when> | |
| 88 <when value="history"> | 93 <when value="history"> |
| 89 <param name="ref_file" type="data" format="fasta" label="Using reference file" /> | 94 <param name="ref_file" type="data" format="fasta" label="Using reference file" /> |
| 90 </when> | 95 </when> |
| 91 </conditional> | 96 </conditional> |
| 92 </when> | 97 </when> |