Mercurial > repos > devteam > cuffmerge

comparison cuffmerge_wrapper.xml @ 0:dbbd37e013aa

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded tool tarball.
author devteam
date Tue, 01 Oct 2013 12:57:24 -0400
parents
children 5b285b6e4ee3
comparison
equal deleted inserted replaced
-1:000000000000 0:dbbd37e013aa
1 <tool id="cuffmerge" name="Cuffmerge" version="0.0.5">
2 <!-- Wrapper supports Cuffmerge versions 1.3 and newer -->
3 <description>merge together several Cufflinks assemblies</description>
4 <requirements>
5 <requirement type="package" version="2.1.1">cufflinks</requirement>
6 </requirements>
7 <command interpreter="python">
8 cuffmerge_wrapper.py
9
10 --num-threads="4"
11
12 ## Use annotation reference?
13 #if $annotation.use_ref_annotation == "Yes":
14 -g $annotation.reference_annotation
15 #end if
16
17 ## Use sequence data?
18 #if $seq_data.use_seq_data == "Yes":
19 -s
20 #if $seq_data.seq_source.index_source == "history":
21 --ref_file=$seq_data.seq_source.ref_file
22 #else:
23 --ref_file="None"
24 #end if
25 --dbkey=${first_input.metadata.dbkey}
26 --index_dir=${GALAXY_DATA_INDEX_DIR}
27 #end if
28
29 ## Outputs.
30 --merged-transcripts=${merged_transcripts}
31
32 ## Inputs.
33 ${first_input}
34 #for $input_file in $input_files:
35 ${input_file.additional_input}
36 #end for
37
38 </command>
39 <inputs>
40 <param format="gtf" name="first_input" type="data" label="GTF file produced by Cufflinks" help=""/>
41 <repeat name="input_files" title="Additional GTF Input Files">
42 <param format="gtf" name="additional_input" type="data" label="GTF file produced by Cufflinks" help=""/>
43 </repeat>
44 <conditional name="annotation">
45 <param name="use_ref_annotation" type="select" label="Use Reference Annotation">
46 <option value="No">No</option>
47 <option value="Yes">Yes</option>
48 </param>
49 <when value="Yes">
50 <param format="gff3,gtf" name="reference_annotation" type="data" label="Reference Annotation" help="Requires an annotation file in GFF3 or GTF format."/>
51 </when>
52 <when value="No">
53 </when>
54 </conditional>
55 <conditional name="seq_data">
56 <param name="use_seq_data" type="select" label="Use Sequence Data" help="Use sequence data for some optional classification functions, including the addition of the p_id attribute required by Cuffdiff.">
57 <option value="No">No</option>
58 <option value="Yes">Yes</option>
59 </param>
60 <when value="No"></when>
61 <when value="Yes">
62 <conditional name="seq_source">
63 <param name="index_source" type="select" label="Choose the source for the reference list">
64 <option value="cached">Locally cached</option>
65 <option value="history">History</option>
66 </param>
67 <when value="cached"></when>
68 <when value="history">
69 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
70 </when>
71 </conditional>
72 </when>
73 </conditional>
74 </inputs>
75
76 <outputs>
77 <data format="gtf" name="merged_transcripts" label="${tool.name} on ${on_string}: merged transcripts"/>
78 </outputs>
79
80 <tests>
81 <!--
82 cuffmerge -g cuffcompare_in3.gtf cuffcompare_in1.gtf cuffcompare_in2.gtf
83 -->
84 <test>
85 <param name="first_input" value="cuffcompare_in1.gtf" ftype="gtf"/>
86 <param name="additional_input" value="cuffcompare_in2.gtf" ftype="gtf"/>
87 <param name="use_ref_annotation" value="Yes"/>
88 <param name="reference_annotation" value="cuffcompare_in3.gtf" ftype="gtf"/>
89 <param name="use_seq_data" value="No"/>
90 <!-- oId assignment differ/are non-deterministic -->
91 <output name="merged_transcripts" file="cuffmerge_out1.gtf" lines_diff="50"/>
92 </test>
93 </tests>
94
95 <help>
96 **Cuffmerge Overview**
97
98 Cuffmerge is part of Cufflinks_. Please cite: Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ, Salzberg SL, Wold B, Pachter L. Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms. Nature Biotechnology doi:10.1038/nbt.1621
99
100 .. _Cufflinks: http://cufflinks.cbcb.umd.edu/
101
102 ------
103
104 **Know what you are doing**
105
106 .. class:: warningmark
107
108 There is no such thing (yet) as an automated gearshift in expression analysis. It is all like stick-shift driving in San Francisco. In other words, running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to **understand** the parameters by carefully reading the `documentation`__ and experimenting. Fortunately, Galaxy makes experimenting easy.
109
110 .. __: http://cufflinks.cbcb.umd.edu/manual.html#cuffmerge
111
112 ------
113
114 **Input format**
115
116 Cuffmerge takes Cufflinks' GTF output as input, and optionally can take a "reference" annotation (such as from Ensembl_)
117
118 .. _Ensembl: http://www.ensembl.org
119
120 ------
121
122 **Outputs**
123
124 Cuffmerge produces the following output files:
125
126 Merged transcripts file:
127
128 Cuffmerge produces a GTF file that contains an assembly that merges together the input assemblies. </help>
129 </tool>