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comparison trinotate.xml @ 0:499d87c45612 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5
author iuc
date Tue, 15 Nov 2016 09:17:29 -0500
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children 9e61bc67866f
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-1:000000000000 0:499d87c45612
1 <tool id="trinotate" name="Trinotate" version="3.0.1.0">
2 <requirements>
3 <requirement type="package" version="3.0.1">trinotate</requirement>
4 <requirement type="package" version="1.18">gnu-wget</requirement>
5 </requirements>
6 <stdio>
7 <exit_code range="1:" />
8 </stdio>
9 <version_command>
10 <![CDATA[
11 Trinotate version 3.0.1
12 ]]>
13 </version_command>
14 <command><![CDATA[
15
16 #if str($cond_download.select_download) == "yes":
17 wget --no-verbose 'https://data.broadinstitute.org/Trinity/Trinotate_v3_RESOURCES/Trinotate_v3.sqlite.gz' -O Trinotate.sqlite.gz &&
18 gunzip Trinotate.sqlite.gz &&
19 #else:
20 ln -s '$cond_download.trinotate_sqlite_in' Trinotate.sqlite
21 #end if
22
23 Trinotate Trinotate.sqlite init --gene_trans_map '$gene_trans_map' --transcript_fasta $trinity --transdecoder_pep '$transdecoder' &&
24 #if $blastp:
25 Trinotate Trinotate.sqlite LOAD_swissprot_blastp '$blastp' &&
26 #end if
27 #if $blastx:
28 Trinotate Trinotate.sqlite LOAD_swissprot_blastx '$blastx' &&
29 #end if
30 #if $hmmscan:
31 Trinotate Trinotate.sqlite LOAD_pfam '$hmmscan' &&
32 #end if
33 #if $tmhmm:
34 Trinotate Trinotate.sqlite LOAD_tmhmm '$tmhmm' &&
35 #end if
36 #if $signalp:
37 Trinotate Trinotate.sqlite LOAD_signalp '$signalp' &&
38 #end if
39
40 Trinotate Trinotate.sqlite report -E $report_option.E --pfam_cutoff $report_option.pfam_cutoff $report_option.incl_pep $report_option.incl_trans > '$trinotate_out';
41
42 ]]></command>
43 <inputs>
44 <param name="trinity" type="data" format="fasta" optional="false" label="Transcripts" help="Trinity output: Assembled Transcripts" />
45 <param name="transdecoder" type="data" format="fasta" optional="false" label="Peptides" help="Transdecoder output: transdecoder_pep" />
46 <param name="gene_trans_map" type="data" format="tabular" optional="false" label="Genes to transcripts map" help="Genes to transcripts map output. Containing correspondance between gene ids and transcript ids based on the name of transcripts assembled by Trinity" />
47 <param name="blastp" type="data" format="tabular" optional="true" label="BLASTP: Peptides vs Uniprot.SwissProt" help="[optional] NCBI BLAST+ blastp output. Output format: Tabular (standard 12 columns)" />
48 <param name="blastx" type="data" format="tabular" optional="true" label="BLASTX: Transcripts vs Uniprot.SwissProt" help="[optional] NCBI BLAST+ blastx output. Output format: Tabular (standard 12 columns)" />
49 <param name="hmmscan" type="data" format="txt" optional="true" label="HMMER hmmscan: Peptides vs PFAM" help="[optional] HMMER hmmscan output: Table of per-domain hits. Output format: Table of per-domain hits (--domtblout)" />
50 <param name="tmhmm" type="data" format="tabular" optional="true" label="TMHMM on Peptides" help="[optional]"/>
51 <param name="signalp" type="data" format="tabular" optional="true" label="SignalP on Peptides" help="[optional]" />
52
53 <conditional name="cond_download">
54 <param name="select_download" type="select" label="Let Galaxy downloading the Trinotate Pre-generated Resource SQLite database">
55 <option value="yes" selected="True">Yes</option>
56 <option value="no">No, I will provide it</option>
57 </param>
58 <when value="no">
59 <param name="trinotate_sqlite_in" type="data" format="sqlite" optional="false" label="Trinotate Pre-generated Resource SQLite database" help="https://data.broadinstitute.org/Trinity/Trinotate_v3_RESOURCES/Trinotate_v3.sqlite.gz" />
60 </when>
61 <when value="yes" />
62 </conditional>
63
64 <section name="report_option" title="Report options" expanded="False">
65 <param argument="-E" type="float" value="1e-5" label="Maximum E-value for reporting best blast hit and associated annotations." />
66 <param argument="--pfam_cutoff" type="select" label="PFAM cutoff">
67 <option value="DNC">DNC : domain noise cutoff</option>
68 <option value="DGC">DGC : domain gathering cutoff</option>
69 <option value="DTC">DTC : domain trusted cutoff</option>
70 <option value="SNC">SNC : sequence noise cutoff</option>
71 <option value="SGC">SGC : sequence gathering cutoff</option>
72 <option value="STC">STC : sequence trusted cutoff</option>
73 </param>
74 <param argument="--incl_pep" type="boolean" truevalue="--incl_pep" falsevalue="" checked="false" label="Add the protein sequence data in the tab delimited report" />
75 <param argument="--incl_trans" type="boolean" truevalue="--incl_trans" falsevalue="" checked="false" label="Add the transcript sequence data in the tab delimited report" />
76 </section>
77 <param name="keep_sqlite" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Keep the sqlite database file: Trinotate.sqlite" help="Can be used for visualization purpose" />
78 </inputs>
79 <outputs>
80 <data name="trinotate_out" format="tabular" label="Trinotate output" >
81 <actions>
82 <action name="column_names" type="metadata" default="gene_id,transcript_id,sprot_Top_BLASTX_hit,RNAMMER,prot_id,prot_coords,sprot_Top_BLASTP_hit,custom_pombe_pep_BLASTX,custom_pombe_pep_BLASTP,Pfam,SignalP,TmHMM,eggnog,Kegg,gene_ontology_blast,gene_ontology_pfam,transcript,peptide" />
83 </actions>
84 </data>
85 <data name="trinotate_sqlite" format="sqlite" from_work_dir="Trinotate.sqlite" label="Trinotate sqlite database" >
86 <filter>keep_sqlite</filter>
87 </data>
88 </outputs>
89 <tests>
90 <test>
91 <param name="trinity" ftype="fasta" value="Trinity.fasta" />
92 <param name="transdecoder" ftype="fasta" value="Trinity.fasta.transdecoder.pep" />
93 <param name="gene_trans_map" ftype="tabular" value="Trinity.fasta.gene_to_trans_map" />
94 <param name="blastp" ftype="tabular" value="swissprot.blastp.outfmt6" />
95 <param name="blastx" ftype="tabular" value="swissprot.blastx.outfmt6" />
96 <param name="hmmscan" ftype="txt" value="TrinotatePFAM.out" />
97 <param name="tmhmm" ftype="tabular" value="tmhmm.out" />
98 <param name="signalp" ftype="tabular" value="signalp.out" />
99 <output name="trinotate_out" file="trinotate_annotation_report.xls" />
100 </test>
101 <test>
102 <param name="trinity" ftype="fasta" value="Trinity.fasta" />
103 <param name="transdecoder" ftype="fasta" value="Trinity.fasta.transdecoder.pep" />
104 <param name="gene_trans_map" ftype="tabular" value="Trinity.fasta.gene_to_trans_map" />
105 <param name="blastp" ftype="tabular" value="swissprot.blastp.outfmt6" />
106 <param name="blastx" ftype="tabular" value="swissprot.blastx.outfmt6" />
107 <param name="hmmscan" ftype="txt" value="TrinotatePFAM.out" />
108 <section name="report_option">
109 <param name="incl_pep" value="true" />
110 <param name="incl_trans" value="true" />
111 </section>
112 <param name="keep_sqlite" value="true" />
113 <output name="trinotate_out" file="trinotate_annotation_report_minus_tmhmm_signalp.xls" />
114 </test>
115 </tests>
116 <help><![CDATA[
117 .. class:: infomark
118
119 **What it does**
120
121 Trinotate_ is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. Trinotate makes use of a number of different well referenced methods for functional annotation including homology search to known sequence data (BLAST+/SwissProt), protein domain identification (HMMER/PFAM), protein signal peptide and transmembrane domain prediction (signalP/tmHMM), and leveraging various annotation databases (eggNOG/GO/Kegg databases). All functional annotation data derived from the analysis of transcripts is integrated into a SQLite database which allows fast efficient searching for terms with specific qualities related to a desired scientific hypothesis or a means to create a whole annotation report for a transcriptome.
122
123 .. _Trinotate: https://trinotate.github.io/
124
125 --------
126
127 **Suggested upstream Galaxy tools**
128
129 Transcripts
130
131 - Trinity: iuc/trinity_
132
133 .. _trinity: https://toolshed.g2.bx.psu.edu/repository?repository_id=faf6028922d9220a
134
135 Peptides
136
137 - TransDecoder: iuc/transdecoder_
138
139 .. _transdecoder: https://toolshed.g2.bx.psu.edu/repository?repository_id=7a2a8151a50f8099
140
141 Genes to transcripts map
142
143 - Generate gene to transcript map for Trinity assembly: iuc/trinity_gene_to_trans_map_
144
145 .. _trinity_gene_to_trans_map: https://toolshed.g2.bx.psu.edu/repository?repository_id=faf6028922d9220a
146
147 BLASTP: Peptides vs Uniprot.SwissProt
148
149 - NCBI BLAST+ blastp: devteam/ncbi_blast_plus_
150
151 .. _ncbi_blast_plus: https://toolshed.g2.bx.psu.edu/repository?repository_id=1d92ebdf7e8d466c
152
153 BLASTX: Transcripts vs Uniprot.SwissProt
154
155 - NCBI BLAST+ blastx: devteam/ncbi_blast_plus_
156
157 .. _ncbi_blast_plus: https://toolshed.g2.bx.psu.edu/repository?repository_id=1d92ebdf7e8d466c
158
159 HMMER hmmscan: Peptides vs PFAM
160
161 - HMMER hmmscan: iuc/hmmer_hmmscan_
162
163 .. _hmmer_hmmscan: https://toolshed.g2.bx.psu.edu/repository?repository_id=a2cc4683090b1800
164
165 TMHMM on Peptides
166
167 - TMHMM 2.0: peterjc/tmhmm_and_signalp_
168
169 .. _tmhmm_and_signalp: https://toolshed.g2.bx.psu.edu/repository?repository_id=292389a45f1a238a
170
171 SignalP on Peptides
172
173 - SignalP 3.0: peterjc/tmhmm_and_signalp_
174
175 .. _tmhmm_and_signalp: https://toolshed.g2.bx.psu.edu/repository?repository_id=292389a45f1a238a
176
177
178 Trinotate Pre-generated Resource SQLite database
179
180 - You can provide the SQLite database yourself, if Galaxy have trouble to download it : https://data.broadinstitute.org/Trinity/Trinotate_v3_RESOURCES/Trinotate_v3.sqlite.gz
181
182 --------
183
184 **Output**
185
186 The output has the following column headers:
187
188
189 ====== =======================
190 Column Description
191 ------ -----------------------
192 0 #gene_id
193 1 transcript_id
194 2 sprot_Top_BLASTX_hit
195 3 RNAMMER
196 4 prot_id
197 5 prot_coords
198 6 sprot_Top_BLASTP_hit
199 7 custom_pombe_pep_BLASTX
200 8 custom_pombe_pep_BLASTP
201 9 Pfam
202 10 SignalP
203 11 TmHMM
204 12 eggnog
205 13 Kegg
206 14 gene_ontology_blast
207 15 gene_ontology_pfam
208 16 transcript
209 17 peptide
210 ====== =======================
211
212 ]]></help>
213 <citations>
214 <citation type="doi">10.1038/nbt.1883</citation>
215 </citations>
216 </tool>