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comparison icescreen.xml @ 3:0d38ba6112be draft

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planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit a9bc15365abc70c0367d732b790763d8fa53b220
author iuc
date Tue, 28 Feb 2023 14:10:26 +0000
parents 411d99e24c62
children 49bf81065a47
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2:411d99e24c62 3:0d38ba6112be
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@">1.1.1</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="Multi-genbank files (i.e. gbff) are supported. Each record 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">
113 <output name="emblout" file="NC_004668_137848_164286_icescreen.embl" ftype="embl" /> 113 <output name="emblout" file="NC_004668_137848_164286_icescreen.embl" ftype="embl" />
114 </test> 114 </test>
115 <test expect_num_outputs="4"> 115 <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
119 <output name="outzip" > 118 <output name="outzip" >
120 <assert_contents> 119 <assert_contents>
121 <has_archive_member path=".*/*_detected_SP_withMEIds.tsv"><has_text text="ICE IME Number" /></has_archive_member> 120 <has_archive_member path=".*/*_detected_SP_withMEIds.tsv"><has_text text="ICE_IME_id" /></has_archive_member>
122 </assert_contents> 121 </assert_contents>
123 </output> 122 </output>
124 </test> 123 </test>
125 <test expect_num_outputs="4"> 124 <test expect_num_outputs="4">
126 <param name="genome" value="genbank/NC_004668_137848_164286.gb" ftype="genbank" /> 125 <param name="genome" value="genbank/NC_004668_137848_164286.gb" ftype="genbank" />
154 <has_text text="firmicutes" /> 153 <has_text text="firmicutes" />
155 <not_has_text text="Error" /> 154 <not_has_text text="Error" />
156 </assert_contents> 155 </assert_contents>
157 </output> 156 </output>
158 </test> 157 </test>
158 <test expect_num_outputs="3">
159 <param name="genome" value="genbank/NC_013798_298468_322494_NC_020450_643089_661957.gb" ftype="genbank" />
160 <output name="summary" file="NC_013798_298468_322494_NC_020450_643089_661957_detected_ME.summary" ftype="txt" />
161 <output name="detected_me" file="NC_013798_298468_322494_NC_020450_643089_661957_detected_ME.tsv" ftype="tabular" />
162 <output name="detected_sp" >
163 <assert_contents>
164 <has_text text="ICE_IME_id" />
165 <has_text text="WP_044555479.1" />
166 <has_text text="WP_015426013.1" />
167 </assert_contents>
168 </output>
169 </test>
159 </tests> 170 </tests>
160 <help><![CDATA[ 171 <help><![CDATA[
161 .. class:: warningmark 172 .. class:: warningmark
162 173
163 This tool requires *genbank* format. 174 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.
164 175
165 ----- 176 -----
166 177
167 **What it does** 178 **What it does**
168 179
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. 180 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.
170 181
171 **Main features of ICEscreen** 182 **Main features of ICEscreen**
172 183
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. 184 - 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. 185 - 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. 186 - 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. 187 - Delimitation of the elements at the gene or nucleotide level is not yet implemented and still needs manual curation.
177 188
178 **Output files** 189 **Output files**