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comparison glimmer_wo_icm.xml @ 3:75cedbd8cf1b draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit a80e3e4aa3a40970af507bf9119cf7f1c2ffb336
author iuc
date Mon, 16 Dec 2024 14:42:00 +0000
parents 73c58e2debd0
children
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2:73c58e2debd0 3:75cedbd8cf1b
1 <tool id="glimmer_not_knowledge_based" name="Glimmer3" version="@WRAPPER_VERSION@"> 1 <tool id="glimmer_not_knowledge_based" name="Glimmer3" version="@WRAPPER_VERSION@" profile="@PROFILE_VERSION@">
2 <description>Predict ORFs in prokaryotic genomes (not knowlegde-based)</description> 2 <description>Predict ORFs in prokaryotic genomes (not knowlegde-based)</description>
3 <expand macro="bio_tools"/>
4 <macros> 3 <macros>
5 <import>macros.xml</import> 4 <import>macros.xml</import>
6 </macros> 5 </macros>
6 <expand macro="bio_tools"/>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 <command><![CDATA[ 8 <command><![CDATA[
9 python '$__tool_directory__/glimmer_wo_icm.py' 9 python '$__tool_directory__/glimmer_wo_icm.py'
10 '$input' 10 '$input'
11 #if $report: 11 #if $report:
29 <param name="overlap" type="integer" value="0" label="Set maximum overlap length. Overlaps this short or shorter are ignored." /> 29 <param name="overlap" type="integer" value="0" label="Set maximum overlap length. Overlaps this short or shorter are ignored." />
30 <param name="gene_length" type="integer" value="110" label="Set minimum gene length." /> 30 <param name="gene_length" type="integer" value="110" label="Set minimum gene length." />
31 <param name="threshold" type="integer" value="30" label="Set threshold score for calling as gene. If the in-frame score >= N, then the region is given a number and considered a potential gene." /> 31 <param name="threshold" type="integer" value="30" label="Set threshold score for calling as gene. If the in-frame score >= N, then the region is given a number and considered a potential gene." />
32 <param name="linear" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Assume linear rather than circular genome, i.e., no wraparound" /> 32 <param name="linear" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Assume linear rather than circular genome, i.e., no wraparound" />
33 33
34 <param name="detailed_report" type="boolean" truevalue="" falsevalue="" checked="false" label="Output a detailed gene prediction report as separate file" /> 34 <param name="detailed_report" type="boolean" checked="false" label="Output a detailed gene prediction report as separate file" />
35 <param name="report" type="boolean" truevalue="" falsevalue="" checked="false" label="Report the classic glimmer table output" /> 35 <param name="report" type="boolean" checked="false" label="Report the classic glimmer table output" />
36 </inputs> 36 </inputs>
37 <outputs> 37 <outputs>
38 <data name="genes_output" format="fasta" label="Glimmer3 on ${on_string} (Gene Prediction FASTA)" /> 38 <data name="genes_output" format="fasta" label="Glimmer3 on ${on_string} (Gene Prediction FASTA)" />
39 <data name="prediction" format="txt" label="Glimmer3 on ${on_string} (Gene Prediction table)"> 39 <data name="prediction" format="txt" label="Glimmer3 on ${on_string} (Gene Prediction table)">
40 <filter>report == True</filter> 40 <filter>report</filter>
41 </data> 41 </data>
42 <data name="detailed" format="txt" label="Glimmer3 on ${on_string} (detailed report)"> 42 <data name="detailed" format="txt" label="Glimmer3 on ${on_string} (detailed report)">
43 <filter>detailed_report == True</filter> 43 <filter>detailed_report</filter>
44 </data> 44 </data>
45 </outputs> 45 </outputs>
46 <tests> 46 <tests>
47 <test> 47 <test expect_num_outputs="1">
48 <param name="input" value="streptomyces_Tue6071_plasmid_genomic.fasta" /> 48 <param name="input" value="streptomyces_Tue6071_plasmid_genomic.fasta" />
49 <param name="overlap" value="0" /> 49 <param name="overlap" value="0" />
50 <param name="gene_length" value="110" /> 50 <param name="gene_length" value="110" />
51 <param name="threshold" value="30" /> 51 <param name="threshold" value="30" />
52 <param name="linear" value="true" /> 52 <param name="linear" value="true" />
53 <param name="detailed_report" value="" /> 53 <param name="detailed_report" value="" />
54 <param name="report" value="" /> 54 <param name="report" value="" />
55 <output name="genes_output" file="glimmer_wo_icm_trans-table-11_plasmid_genomic.fasta" ftype="fasta" />
56 </test>
57 <test expect_num_outputs="3">
58 <param name="input" value="streptomyces_Tue6071_plasmid_genomic.fasta" />
59 <param name="overlap" value="0" />
60 <param name="gene_length" value="110" />
61 <param name="threshold" value="30" />
62 <param name="linear" value="true" />
63 <param name="detailed_report" value="true" />
64 <param name="report" value="true" />
55 <output name="genes_output" file="glimmer_wo_icm_trans-table-11_plasmid_genomic.fasta" ftype="fasta" /> 65 <output name="genes_output" file="glimmer_wo_icm_trans-table-11_plasmid_genomic.fasta" ftype="fasta" />
56 </test> 66 </test>
57 </tests> 67 </tests>
58 <help> 68 <help>
59 <![CDATA[ 69 <![CDATA[