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comparison cuffmerge_wrapper.xml @ 10:b6e3849293b1 draft

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author devteam
date Fri, 19 Dec 2014 11:59:06 -0500
parents 424d49834830
children 1707a530e598
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9:424d49834830 10:b6e3849293b1
1 <tool id="cuffmerge" name="Cuffmerge" version="0.0.6"> 1 <tool id="cuffmerge" name="Cuffmerge" version="@VERSION@.0">
2 <!-- Wrapper supports Cuffmerge versions 1.3 and newer -->
3 <description>merge together several Cufflinks assemblies</description> 2 <description>merge together several Cufflinks assemblies</description>
4 <requirements> 3 <expand macro="requirements" />
5 <requirement type="package" version="2.1.1">cufflinks</requirement> 4 <expand macro="stdio" />
6 </requirements> 5 <macros>
6 <import>cuff_macros.xml</import>
7 </macros>
7 <command interpreter="python"> 8 <command interpreter="python">
8 cuffmerge_wrapper.py 9 cuffmerge_wrapper.py
9
10 --num-threads="\${GALAXY_SLOTS:-4}" 10 --num-threads="\${GALAXY_SLOTS:-4}"
11 11
12 ## Use annotation reference? 12 ## Use annotation reference?
13 #if $annotation.use_ref_annotation == "Yes": 13 #if $annotation.use_ref_annotation == "Yes":
14 -g "${annotation.reference_annotation}" 14 -g "${annotation.reference_annotation}"
15 #end if 15 #end if
16 16
17 ## Use sequence data? 17 ## Use sequence data?
18 #if $seq_data.use_seq_data == "Yes": 18 #if $seq_data.use_seq_data == "Yes":
19 -s 19 -s
20 #if $seq_data.seq_source.index_source == "history": 20 #if $seq_data.seq_source.index_source == "history":
21 --ref_file="${seq_data.seq_source.ref_file}" 21 --ref_file="${seq_data.seq_source.ref_file}"
22 #else: 22 #else:
23 --index="${seq_data.seq_source.index.fields.path}" 23 --index="${seq_data.seq_source.index.fields.path}"
24 #end if 24 #end if
25 #end if 25 #end if
26 26
27 --min-isoform-fraction="${min_isoform_fraction}"
28
27 ## Outputs. 29 ## Outputs.
28 --merged-transcripts="${merged_transcripts}" 30 --merged-transcripts="${merged_transcripts}"
29 31
30 ## Inputs. 32 @CUFFLINKS_GTF_INPUTS@
31 "${first_input}"
32 #for $input_file in $input_files:
33 "${input_file.additional_input}"
34 #end for
35
36 </command> 33 </command>
37 <inputs> 34 <inputs>
38 <param format="gtf" name="first_input" type="data" label="GTF file produced by Cufflinks" help=""/> 35 <expand macro="cufflinks_gtf_inputs" />
39 <repeat name="input_files" title="Additional GTF Input Files">
40 <param format="gtf" name="additional_input" type="data" label="GTF file produced by Cufflinks" help=""/>
41 </repeat>
42 <conditional name="annotation"> 36 <conditional name="annotation">
43 <param name="use_ref_annotation" type="select" label="Use Reference Annotation"> 37 <param name="use_ref_annotation" type="select" label="Use Reference Annotation">
44 <option value="No">No</option> 38 <option value="No">No</option>
45 <option value="Yes">Yes</option> 39 <option value="Yes">Yes</option>
46 </param> 40 </param>
63 <option value="history">History</option> 57 <option value="history">History</option>
64 </param> 58 </param>
65 <when value="cached"> 59 <when value="cached">
66 <param name="index" type="select" label="Using reference genome"> 60 <param name="index" type="select" label="Using reference genome">
67 <options from_data_table="fasta_indexes"> 61 <options from_data_table="fasta_indexes">
68 <filter type="data_meta" ref="first_input" key="dbkey" column="1" /> 62 <filter type="data_meta" ref="inputs" key="dbkey" column="1" />
69 <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" /> 63 <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" />
70 </options> 64 </options>
71 </param> 65 </param>
72 </when> 66 </when>
73 <when value="history"> 67 <when value="history">
74 <param name="ref_file" type="data" format="fasta" label="Using reference file" /> 68 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
75 </when> 69 </when>
76 </conditional> 70 </conditional>
77 </when> 71 </when>
78 </conditional> 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" />
79 </inputs> 74 </inputs>
80 75
81 <outputs> 76 <outputs>
82 <data format="gtf" name="merged_transcripts" label="${tool.name} on ${on_string}: merged transcripts"/> 77 <data format="gtf" name="merged_transcripts" label="${tool.name} on ${on_string}: merged transcripts"/>
83 </outputs> 78 </outputs>
85 <tests> 80 <tests>
86 <!-- 81 <!--
87 cuffmerge -g cuffcompare_in3.gtf cuffcompare_in1.gtf cuffcompare_in2.gtf 82 cuffmerge -g cuffcompare_in3.gtf cuffcompare_in1.gtf cuffcompare_in2.gtf
88 --> 83 -->
89 <test> 84 <test>
90 <param name="first_input" value="cuffcompare_in1.gtf" ftype="gtf"/> 85 <param name="inputs" value="cuffcompare_in1.gtf,cuffcompare_in2.gtf" ftype="gtf"/>
91 <param name="additional_input" value="cuffcompare_in2.gtf" ftype="gtf"/>
92 <param name="use_ref_annotation" value="Yes"/> 86 <param name="use_ref_annotation" value="Yes"/>
93 <param name="reference_annotation" value="cuffcompare_in3.gtf" ftype="gtf"/> 87 <param name="reference_annotation" value="cuffcompare_in3.gtf" ftype="gtf"/>
88 <param name="min_isoform_fraction" value="0.08" />
94 <param name="use_seq_data" value="No"/> 89 <param name="use_seq_data" value="No"/>
95 <!-- oId assignment differ/are non-deterministic --> 90 <!-- oId assignment differ/are non-deterministic -->
96 <output name="merged_transcripts" file="cuffmerge_out1.gtf" lines_diff="50"/> 91 <output name="merged_transcripts" file="cuffmerge_out1.gtf" lines_diff="50"/>
97 </test> 92 </test>
98 </tests> 93 </tests>
99 94
100 <help> 95 <help>
101 **Cuffmerge Overview** 96 **Cuffmerge Overview**
102 97
103 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 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
104 99
105 .. _Cufflinks: http://cufflinks.cbcb.umd.edu/ 100 .. _Cufflinks: http://cole-trapnell-lab.github.io/cufflinks/
106 101
107 ------ 102 ------
108 103
109 **Know what you are doing** 104 **Know what you are doing**
110 105
111 .. class:: warningmark 106 .. class:: warningmark
112 107
113 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. 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.
114 109
115 .. __: http://cufflinks.cbcb.umd.edu/manual.html#cuffmerge 110 .. __: http://cole-trapnell-lab.github.io/cufflinks/cuffmerge/
116 111
117 ------ 112 ------
118 113
119 **Input format** 114 **Input format**
120 115
128 123
129 Cuffmerge produces the following output files: 124 Cuffmerge produces the following output files:
130 125
131 Merged transcripts file: 126 Merged transcripts file:
132 127
133 Cuffmerge produces a GTF file that contains an assembly that merges together the input assemblies. </help> 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>
134 </tool> 133 </tool>