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comparison trinotate.xml @ 2:6fd16fad465d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit 4aa8226ad3031636041eaa6f29a7fb4721dcdc43
author iuc
date Mon, 06 Aug 2018 06:52:04 -0400
parents 9e61bc67866f
children 4383070d29ed
comparison
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1:9e61bc67866f 2:6fd16fad465d
1 <tool id="trinotate" name="Trinotate" version="3.0.1.0"> 1 <tool id="trinotate" name="Trinotate" version="3.1.1">
2 <requirements> 2 <requirements>
3 <requirement type="package" version="3.0.1">trinotate</requirement> 3 <requirement type="package" version="3.1.1">trinotate</requirement>
4 <requirement type="package" version="1.18">gnu-wget</requirement> 4 <requirement type="package" version="1.18">gnu-wget</requirement>
5 </requirements> 5 </requirements>
6 <stdio> 6 <stdio>
7 <exit_code range="1:" /> 7 <exit_code range="1:" />
8 </stdio> 8 </stdio>
9 <version_command> 9 <version_command>
10 <![CDATA[ 10 <![CDATA[
11 Trinotate version 3.0.1 11 Trinotate version 3.1.1
12 ]]> 12 ]]>
13 </version_command> 13 </version_command>
14 <command><![CDATA[ 14 <command><![CDATA[
15 15
16 #if str($cond_download.select_download) == "yes": 16 #if str($cond_download.select_download) == "yes":
17 wget --no-verbose 'https://data.broadinstitute.org/Trinity/__deprecated_trinotate_resources/Trinotate_v3_RESOURCES/Trinotate_v3.sqlite.gz' -O Trinotate.sqlite.gz && 17 Build_Trinotate_Boilerplate_SQLite_db.pl Trinotate &&
18 gunzip Trinotate.sqlite.gz &&
19 #else: 18 #else:
20 ln -s '$cond_download.trinotate_sqlite_in' Trinotate.sqlite 19 ln -s '$cond_download.trinotate_sqlite_in' Trinotate.sqlite &&
21 #end if 20 #end if
22 21
23 Trinotate Trinotate.sqlite init --gene_trans_map '$gene_trans_map' --transcript_fasta $trinity --transdecoder_pep '$transdecoder' && 22 Trinotate Trinotate.sqlite init --gene_trans_map '$gene_trans_map' --transcript_fasta $trinity --transdecoder_pep '$transdecoder' &&
24 #if $blastp: 23 #if $blastp:
25 Trinotate Trinotate.sqlite LOAD_swissprot_blastp '$blastp' && 24 Trinotate Trinotate.sqlite LOAD_swissprot_blastp '$blastp' &&
35 #end if 34 #end if
36 #if $signalp: 35 #if $signalp:
37 Trinotate Trinotate.sqlite LOAD_signalp '$signalp' && 36 Trinotate Trinotate.sqlite LOAD_signalp '$signalp' &&
38 #end if 37 #end if
39 38
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'; 39 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 40
42 ]]></command> 41 ]]></command>
43 <inputs> 42 <inputs>
44 <param name="trinity" type="data" format="fasta" optional="false" label="Transcripts" help="Trinity output: Assembled Transcripts" /> 43 <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" /> 44 <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" /> 45 <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)" /> 46 <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)" /> 47 <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)" /> 48 <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]"/> 49 <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]" /> 50 <param name="signalp" type="data" format="tabular" optional="true" label="SignalP on Peptides" help="[optional]" />
52 51
53 <conditional name="cond_download"> 52 <conditional name="cond_download">
54 <param name="select_download" type="select" label="Let Galaxy downloading the Trinotate Pre-generated Resource SQLite database"> 53 <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> 54 <option value="yes" selected="True">Yes</option>
56 <option value="no">No, I will provide it</option> 55 <option value="no">No, I will provide it</option>
58 <when value="no"> 57 <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/__deprecated_trinotate_resources/Trinotate_v3_RESOURCES/Trinotate_v3.sqlite.gz" /> 58 <param name="trinotate_sqlite_in" type="data" format="sqlite" optional="false" label="Trinotate Pre-generated Resource SQLite database" help="https://data.broadinstitute.org/Trinity/__deprecated_trinotate_resources/Trinotate_v3_RESOURCES/Trinotate_v3.sqlite.gz" />
60 </when> 59 </when>
61 <when value="yes" /> 60 <when value="yes" />
62 </conditional> 61 </conditional>
63 62
64 <section name="report_option" title="Report options" expanded="False"> 63 <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." /> 64 <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"> 65 <param argument="--pfam_cutoff" type="select" label="PFAM cutoff">
67 <option value="DNC">DNC : domain noise cutoff</option> 66 <option value="DNC">DNC : domain noise cutoff</option>
68 <option value="DGC">DGC : domain gathering cutoff</option> 67 <option value="DGC">DGC : domain gathering cutoff</option>
95 <param name="blastx" ftype="tabular" value="swissprot.blastx.outfmt6" /> 94 <param name="blastx" ftype="tabular" value="swissprot.blastx.outfmt6" />
96 <param name="hmmscan" ftype="txt" value="TrinotatePFAM.out" /> 95 <param name="hmmscan" ftype="txt" value="TrinotatePFAM.out" />
97 <param name="tmhmm" ftype="tabular" value="tmhmm.out" /> 96 <param name="tmhmm" ftype="tabular" value="tmhmm.out" />
98 <param name="signalp" ftype="tabular" value="signalp.out" /> 97 <param name="signalp" ftype="tabular" value="signalp.out" />
99 <output name="trinotate_out" file="trinotate_annotation_report.xls" /> 98 <output name="trinotate_out" file="trinotate_annotation_report.xls" />
99 <output name="trinotate_out" file="trinotate_annotation_report.xls" />
100 </test> 100 </test>
101 <test> 101 <test>
102 <param name="trinity" ftype="fasta" value="Trinity.fasta" /> 102 <param name="trinity" ftype="fasta" value="Trinity.fasta" />
103 <param name="transdecoder" ftype="fasta" value="Trinity.fasta.transdecoder.pep" /> 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" /> 104 <param name="gene_trans_map" ftype="tabular" value="Trinity.fasta.gene_to_trans_map" />
171 SignalP on Peptides 171 SignalP on Peptides
172 172
173 - SignalP 3.0: peterjc/tmhmm_and_signalp_ 173 - SignalP 3.0: peterjc/tmhmm_and_signalp_
174 174
175 .. _tmhmm_and_signalp: https://toolshed.g2.bx.psu.edu/repository?repository_id=292389a45f1a238a 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/__deprecated_trinotate_resources/Trinotate_v3_RESOURCES/Trinotate_v3.sqlite.gz
181 176
182 -------- 177 --------
183 178
184 **Output** 179 **Output**
185 180