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comparison fraggenescan.xml @ 0:1f0a3e4497d4 draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/fraggenescan/ commit 59ac8955ccb33e3fcd6649c61779bb3ae9ccb6d4
author iuc
date Wed, 06 Sep 2017 13:23:14 -0400
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children 2dfb2fba4081
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-1:000000000000 0:1f0a3e4497d4
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>