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comparison cuffmerge_wrapper.xml @ 0:e556721b9872 draft

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author devteam
date Wed, 26 Nov 2014 13:58:56 -0500
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1 <tool id="cuffmerge" name="Cuffmerge" version="@VERSION@.0">
2 <description>merge together several Cufflinks assemblies</description>
3 <expand macro="requirements" />
4 <expand macro="stdio" />
5 <macros>
6 <import>cuff_macros.xml</import>
7 </macros>
8 <command interpreter="python">
9 cuffmerge_wrapper.py
10 --num-threads="\${GALAXY_SLOTS:-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 --index="${seq_data.seq_source.index.fields.path}"
24 #end if
25 #end if
26
27 --min-isoform-fraction="${min_isoform_fraction}"
28
29 ## Outputs.
30 --merged-transcripts="${merged_transcripts}"
31
32 @CUFFLINKS_GTF_INPUTS@
33 </command>
34 <inputs>
35 <expand macro="cufflinks_gtf_inputs" />
36 <conditional name="annotation">
37 <param name="use_ref_annotation" type="select" label="Use Reference Annotation">
38 <option value="No">No</option>
39 <option value="Yes">Yes</option>
40 </param>
41 <when value="Yes">
42 <param format="gff3,gtf" name="reference_annotation" type="data" label="Reference Annotation" help="Requires an annotation file in GFF3 or GTF format."/>
43 </when>
44 <when value="No">
45 </when>
46 </conditional>
47 <conditional name="seq_data">
48 <param name="use_seq_data" type="select" label="Use Sequence Data" help="Use sequence data for some optional classification functions, including the addition of the p_id attribute required by Cuffdiff.">
49 <option value="No">No</option>
50 <option value="Yes">Yes</option>
51 </param>
52 <when value="No"></when>
53 <when value="Yes">
54 <conditional name="seq_source">
55 <param name="index_source" type="select" label="Choose the source for the reference list">
56 <option value="cached">Locally cached</option>
57 <option value="history">History</option>
58 </param>
59 <when value="cached">
60 <param name="index" type="select" label="Using reference genome">
61 <options from_data_table="fasta_indexes">
62 <filter type="data_meta" ref="inputs" key="dbkey" column="1" />
63 <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" />
64 </options>
65 </param>
66 </when>
67 <when value="history">
68 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
69 </when>
70 </conditional>
71 </when>
72 </conditional>
73 <param name="min_isoform_fraction" type="float" min="0" max="1" value="0.05" label="Minimum isoform fraction" help="Discard isoforms with abundance below this value" />
74 </inputs>
75
76 <outputs>
77 <data format="gtf" name="merged_transcripts" label="${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="inputs" value="cuffcompare_in1.gtf,cuffcompare_in2.gtf" ftype="gtf"/>
86 <param name="use_ref_annotation" value="Yes"/>
87 <param name="reference_annotation" value="cuffcompare_in3.gtf" ftype="gtf"/>
88 <param name="min_isoform_fraction" value="0.08" />
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.
129 </help>
130 <citations>
131 <citation type="doi">10.1038/nbt.1621</citation>
132 </citations>
133 </tool>