Mercurial > repos > iracooke > proteogenomics_msms_to_gff_workflow
comparison proteogenomics_workflow.ga @ 4:2129f34e534c draft default tip
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author | iracooke |
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date | Wed, 19 Mar 2014 00:14:32 -0400 |
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3:380d3f2e1a58 | 4:2129f34e534c |
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1 { | |
2 "a_galaxy_workflow": "true", | |
3 "annotation": "Creates a protein database from a 6-frame translation of a genome, and from predicted transcripts, then searches msms data using this database and maps peptides back to the genome", | |
4 "format-version": "0.1", | |
5 "name": "Proteogenomics Map Peptides to GFF", | |
6 "steps": { | |
7 "0": { | |
8 "annotation": "MSMSData", | |
9 "id": 0, | |
10 "input_connections": {}, | |
11 "inputs": [ | |
12 { | |
13 "description": "MSMSData", | |
14 "name": "MSMS Data" | |
15 } | |
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27 "type": "data_input", | |
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35 { | |
36 "description": "", | |
37 "name": "Genome" | |
38 } | |
39 ], | |
40 "name": "Input dataset", | |
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45 }, | |
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52 }, | |
53 "2": { | |
54 "annotation": "", | |
55 "id": 2, | |
56 "input_connections": {}, | |
57 "inputs": [ | |
58 { | |
59 "description": "", | |
60 "name": "Predicted Genes" | |
61 } | |
62 ], | |
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70 "tool_id": null, | |
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76 "3": { | |
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80 "type|input": { | |
81 "id": 0, | |
82 "output_name": "output" | |
83 } | |
84 }, | |
85 "inputs": [], | |
86 "name": "msconvert3", | |
87 "outputs": [ | |
88 { | |
89 "name": "output", | |
90 "type": "mzml" | |
91 } | |
92 ], | |
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96 }, | |
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105 "4": { | |
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107 "id": 4, | |
108 "input_connections": { | |
109 "fasta_file": { | |
110 "id": 1, | |
111 "output_name": "output" | |
112 } | |
113 }, | |
114 "inputs": [], | |
115 "name": "Generate 6-frame translation", | |
116 "outputs": [ | |
117 { | |
118 "name": "output", | |
119 "type": "fasta" | |
120 } | |
121 ], | |
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133 }, | |
134 "5": { | |
135 "annotation": "", | |
136 "id": 5, | |
137 "input_connections": { | |
138 "gff_file": { | |
139 "id": 2, | |
140 "output_name": "output" | |
141 } | |
142 }, | |
143 "inputs": [], | |
144 "name": "Extract proteins from gff3", | |
145 "outputs": [ | |
146 { | |
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148 "type": "fasta" | |
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150 ], | |
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159 "tool_version": "1.0.1", | |
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162 }, | |
163 "6": { | |
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171 "queries_0|input2": { | |
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173 "output_name": "output" | |
174 } | |
175 }, | |
176 "inputs": [], | |
177 "name": "Concatenate datasets", | |
178 "outputs": [ | |
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180 "name": "out_file1", | |
181 "type": "input" | |
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206 "name": "Generate protein decoy sequences", | |
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210 "type": "fasta" | |
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235 "output_name": "output" | |
236 } | |
237 }, | |
238 "inputs": [], | |
239 "name": "MSGF+ MSMS Search", | |
240 "outputs": [ | |
241 { | |
242 "name": "output", | |
243 "type": "mzid" | |
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