comparison cufflinks_wrapper.xml @ 4:398329a94c99

Merge heads.
author Dave Bouvier <dave@bx.psu.edu>
date Wed, 08 Jan 2014 09:13:56 -0500
parents da11bfc10e81
children 9aab29e159a7
comparison
equal deleted inserted replaced
3:7498f5a8fe06 4:398329a94c99
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>