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planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit 29cbe5a71212ff13e8d63e9ea57243fd0aeacbf9
author iuc
date Tue, 06 Dec 2022 10:40:53 +0000
parents f08181349fc4
children c5f7c311f1b0
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2:f08181349fc4 3:2bb38197ff75
1 <tool id="icescreen" name="ICEscreen" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.09"> 1 <tool id="icescreen" name="ICEscreen" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.09">
2 <description>detects and annotates ICEs (Integrative and Conjugative Elements) and IMEs (Integrative and Mobilizable Elements) in Firmicutes genomes.</description> 2 <description>detects and annotates ICEs (Integrative and Conjugative Elements) and IMEs (Integrative and Mobilizable Elements) in Firmicutes genomes.</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">1.0.4</token> 4 <token name="@TOOL_VERSION@">1.1.0</token>
5 <token name="@VERSION_SUFFIX@">0</token> 5 <token name="@VERSION_SUFFIX@">0</token>
6 </macros> 6 </macros>
7 <requirements> 7 <requirements>
8 <requirement type="package" version="@TOOL_VERSION@">icescreen</requirement> 8 <requirement type="package" version="@TOOL_VERSION@">icescreen</requirement>
9 <requirement type="package" version="3.0">zip</requirement> 9 <requirement type="package" version="3.0">zip</requirement>
43 && cd ./tmp_icescreen/ICEscreen_results/results/${gbname} && zip --quiet -r - -- . > '${outzip}' 43 && cd ./tmp_icescreen/ICEscreen_results/results/${gbname} && zip --quiet -r - -- . > '${outzip}'
44 #end if 44 #end if
45 ]]> 45 ]]>
46 </command> 46 </command>
47 <inputs> 47 <inputs>
48 <param name="genome" type="data" format="genbank" label="Input genomes to analyze in Genbank format" help=""/> 48 <param name="genome" type="data" format="genbank" label="Input genomes to analyze in Genbank format" help="Each Genbank file can only contain ONE record, multi-genbank files are not supported. Each Genbank file must include the ORIGIN nucleotide sequence at the end"/>
49 <section name="taxonomy" title="Taxonomy of the genomes to analyse" expanded="False"> 49 <section name="taxonomy" title="Taxonomy of the genomes to analyse" expanded="False">
50 <param name="mode" type="select" label="Firmicutes is the defaut parameter" help="Streptomyces is EXPERIMENTAL and is NOT recommended."> 50 <param name="mode" type="select" label="Firmicutes is the defaut parameter" help="Streptomyces is EXPERIMENTAL and is NOT recommended.">
51 <option value="firmicutes" selected="true">Firmicutes</option> 51 <option value="firmicutes" selected="true">Firmicutes</option>
52 <option value="streptomyces">Streptomyces</option> 52 <option value="streptomyces">Streptomyces</option>
53 </param> 53 </param>
87 <param name="genome" value="genbank/NC_004668_137848_164286.gb" ftype="genbank" /> 87 <param name="genome" value="genbank/NC_004668_137848_164286.gb" ftype="genbank" />
88 <output name="summary" file="NC_004668_137848_164286_detected_ME.summary" ftype="txt" /> 88 <output name="summary" file="NC_004668_137848_164286_detected_ME.summary" ftype="txt" />
89 <output name="detected_me" file="NC_004668_137848_164286_detected_ME.tsv" ftype="tabular" /> 89 <output name="detected_me" file="NC_004668_137848_164286_detected_ME.tsv" ftype="tabular" />
90 <output name="detected_sp" > 90 <output name="detected_sp" >
91 <assert_contents> 91 <assert_contents>
92 <has_text text="ICE IME Number" /> 92 <has_text text="ICE_IME_id" />
93 <has_text text="WP_002359295" /> 93 <has_text text="WP_002359295" />
94 <has_text text="VirB4" /> 94 <has_text text="VirB4" />
95 <has_n_columns n="47" /> 95 <has_n_columns n="54" />
96 <has_n_lines n="5" /> 96 <has_n_lines n="5" />
97 </assert_contents> 97 </assert_contents>
98 </output> 98 </output>
99 </test> 99 </test>
100 <test expect_num_outputs="4"> 100 <test expect_num_outputs="4">
116 <param name="genome" value="genbank/NC_004668_137848_164286.gb" ftype="genbank" /> 116 <param name="genome" value="genbank/NC_004668_137848_164286.gb" ftype="genbank" />
117 <param name="optional_files" value="output_zip_all_files" /> 117 <param name="optional_files" value="output_zip_all_files" />
118 118
119 <output name="outzip" > 119 <output name="outzip" >
120 <assert_contents> 120 <assert_contents>
121 <has_archive_member path=".*/*_detected_SP_withMEIds.tsv"><has_text text="ICE IME Number" /></has_archive_member> 121 <has_archive_member path=".*/*_detected_SP_withMEIds.tsv"><has_text text="ICE_IME_id" /></has_archive_member>
122 </assert_contents> 122 </assert_contents>
123 </output> 123 </output>
124 </test> 124 </test>
125 <test expect_num_outputs="4"> 125 <test expect_num_outputs="4">
126 <param name="genome" value="genbank/NC_004668_137848_164286.gb" ftype="genbank" /> 126 <param name="genome" value="genbank/NC_004668_137848_164286.gb" ftype="genbank" />
158 </test> 158 </test>
159 </tests> 159 </tests>
160 <help><![CDATA[ 160 <help><![CDATA[
161 .. class:: warningmark 161 .. class:: warningmark
162 162
163 This tool requires *genbank* format. 163 ICEscreen requires input files in genbank format. Multigenbank files (i.e. gbff files featuring multiple genome records back to back) are supported. Each Genbank record must include the ORIGIN nucleotide sequence.
164 164
165 ----- 165 -----
166 166
167 **What it does** 167 **What it does**
168 168
169 ICEscreen is a bioinformatic pipeline for the detection and annotation of ICEs (Integrative and Conjugative Elements) and IMEs (Integrative and Mobilizable Elements) in Firmicutes genomes. The full documentation is available at https://icescreen.migale.inrae.fr. The forge of the project is accessible at https://forgemia.inra.fr/ices_imes_analysis/icescreen. 169 ICEscreen is a bioinformatic pipeline for the detection and annotation of ICEs (Integrative and Conjugative Elements) and IMEs (Integrative and Mobilizable Elements) in Firmicutes genomes. The full documentation is available at https://icescreen.migale.inrae.fr. The forge of the project is accessible at https://forgemia.inra.fr/ices_imes_analysis/icescreen.
170 170
171 **Main features of ICEscreen** 171 **Main features of ICEscreen**
172 172
173 - Detection of signature proteins (SPs) of ICEs/IMEs by using blastP on a curated resource. BlastP allows for an accurate assignment of hits to a given ICE/IME superfamily or family. The curated resource was derived from an analysis of over 120 ICEs and IMEs in Streptococcus genomes by the DINAMIC lab. 173 - Detection of signature proteins (SPs) of ICEs/IMEs by using blastP on a curated resource. BlastP allows for an accurate assignment of hits to a given ICE/IME superfamily or family. The curated resource was derived from an analysis of over 120 ICEs and IMEs in Streptococcus genomes by the DINAMIC lab.
174 - Detection of distant homologs of SPs by using HMM profiles of ICEs/IMEs protein families. The HMM profiles have been either imported from trusted resources or created and curated when needed. 174 - Detection of distant homologs of SPs by using HMM profiles of ICEs/IMEs protein families. The HMM profiles have been either imported from trusted resources or created and curated when needed.
175 - Detection of the ICE/IME structures: ICEScreen groups together SPs that belong to the same ICE/IME structures to the best of its ability. 175 - Detection of the ICE/IME structures: ICEScreen groups together SPs that belong to the same ICE/IME structures to the best of its ability.
176 - Delimitation of the elements at the gene or nucleotide level is not yet implemented and still needs manual curation. 176 - Delimitation of the elements at the gene or nucleotide level is not yet implemented and still needs manual curation.
177 177
178 **Output files** 178 **Output files**