Mercurial > repos > iuc > fraggenescan
comparison fraggenescan.xml @ 0:1f0a3e4497d4 draft
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/fraggenescan/ commit 59ac8955ccb33e3fcd6649c61779bb3ae9ccb6d4
author | iuc |
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date | Wed, 06 Sep 2017 13:23:14 -0400 |
parents | |
children | 2dfb2fba4081 |
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1 <tool id="fraggenescan" name="FragGeneScan" version="@WRAPPER_VERSION@.0"> | |
2 <description>for finding (fragmented) genes in short reads</description> | |
3 <macros> | |
4 <token name="@WRAPPER_VERSION@">1.30</token> | |
5 </macros> | |
6 <requirements> | |
7 <requirement type="package" version="@WRAPPER_VERSION@">fraggenescan</requirement> | |
8 </requirements> | |
9 <version_command>@WRAPPER_VERSION@</version_command> | |
10 <command detect_errors="aggressive"><![CDATA[ | |
11 run_FragGeneScan.pl | |
12 -genome='$genome' | |
13 -out="output_file_name" | |
14 -complete='$complete' | |
15 -train='$train' | |
16 -thread=\${GALAXY_SLOTS:-4} | |
17 ]]></command> | |
18 <inputs> | |
19 <param argument="-genome" type="data" format="fasta" label="Input equence file"/> | |
20 <param argument="-complete" type="boolean" truevalue="1" falsevalue="0" label="Does the sequence file have complete genomic sequences?"/> | |
21 <param argument="-train" type="select" label="Model"> | |
22 <option value="454_5">454 pyrosequencing reads with about 0.5% error rate (454_5)</option> | |
23 <option value="454_10">454 pyrosequencing reads with about 1% error rate (454_10)</option> | |
24 <option value="454_30">454 pyrosequencing reads with about 3% error rate (454_30)</option> | |
25 <option value="complete">complete genomic sequences or short sequence reads without sequencing error (complete)</option> | |
26 <option value="gene">gene</option> | |
27 <option value="illumina_1">Illumina sequencing reads with about 0.01% error rate (illumina_1)</option> | |
28 <option value="illumina_5">Illumina sequencing reads with about 0.5% error rate (illumina_5)</option> | |
29 <option value="illumina_10">Illumina sequencing reads with about 1% error rate (illumina_10)</option> | |
30 <option value="noncoding">noncoding</option> | |
31 <option value="pwm">pwm</option> | |
32 <option value="rgene">rgene</option> | |
33 <option value="sanger_5">Sanger sequencing reads with about 0.5% error rate (sanger_5)</option> | |
34 <option value="sanger_10">Sanger sequencing reads with about 1% error rate (sanger_10)</option> | |
35 <option value="start">start</option> | |
36 <option value="start1">start1</option> | |
37 <option value="stop">stop</option> | |
38 <option value="stop1">stop1</option> | |
39 </param> | |
40 </inputs> | |
41 <outputs> | |
42 <data name="coord" format="tabular" from_work_dir="output_file_name.out" label="${tool.name} on ${on_string}: Coordinates of putative genes"/> | |
43 <data name="nt_seq" format="fasta" from_work_dir="output_file_name.ffn" label="${tool.name} on ${on_string}: Nucleotide equences of putative genes"/> | |
44 <data name="prot_seq" format="fasta" from_work_dir="output_file_name.faa" label="${tool.name} on ${on_string}: Protein equences of putative genes"/> | |
45 <data name="gff" format="gff" from_work_dir="output_file_name.gff" label="${tool.name} on ${on_string}"/> | |
46 </outputs> | |
47 <tests> | |
48 <test> | |
49 <param name="genome" value="contigs.fasta"/> | |
50 <param name="complete" value="False"/> | |
51 <param name="train" value="complete"/> | |
52 <output name="coord" ftype="tabular" value="contigs.out"/> | |
53 <output name="nt_seq" ftype="fasta" value="contigs.ffn"/> | |
54 <output name="prot_seq" ftype="fasta" value="contigs.faa"/> | |
55 <output name="gff" ftype="gff" value="contigs.gff"/> | |
56 </test> | |
57 <test> | |
58 <param name="genome" value="NC_000913.fasta"/> | |
59 <param name="complete" value="True"/> | |
60 <param name="train" value="complete"/> | |
61 <output name="coord" ftype="tabular" value="NC_000913.out"/> | |
62 <output name="nt_seq" ftype="fasta" value="NC_000913.ffn"/> | |
63 <output name="prot_seq" ftype="fasta" value="NC_000913.faa"/> | |
64 <output name="gff" ftype="gff" value="NC_000913.gff"/> | |
65 </test> | |
66 <test> | |
67 <param name="genome" value="NC_000913-454.fasta"/> | |
68 <param name="complete" value="False"/> | |
69 <param name="train" value="454_10"/> | |
70 <output name="coord" ftype="tabular" value="NC_000913-454.out"/> | |
71 <output name="nt_seq" ftype="fasta" value="NC_000913-454.ffn"/> | |
72 <output name="prot_seq" ftype="fasta" value="NC_000913-454.faa"/> | |
73 <output name="gff" ftype="gff" value="NC_000913-454.gff"/> | |
74 </test> | |
75 </tests> | |
76 <help><![CDATA[ | |
77 **What it does** | |
78 | |
79 FragGeneScan is an application for finding (fragmented) genes in short reads. | |
80 It can also be applied to predict prokaryotic genes in incomplete assemblies or complete genomes. | |
81 | |
82 ]]></help> | |
83 <citations> | |
84 <citation type="doi">10.1093/nar/gkq747</citation> | |
85 </citations> | |
86 </tool> |