Mercurial > repos > devteam > cuffmerge
comparison cuffmerge_wrapper.xml @ 10:b6e3849293b1 draft
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author | devteam |
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date | Fri, 19 Dec 2014 11:59:06 -0500 |
parents | 424d49834830 |
children | 1707a530e598 |
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9:424d49834830 | 10:b6e3849293b1 |
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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> |