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"planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
author iuc
date Tue, 04 Jan 2022 10:52:42 +0000
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-1:000000000000 0:7c77b2896ac2
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>
3 <macros>
4 <token name="@TOOL_VERSION@">1.0.1</token>
5 <token name="@VERSION_SUFFIX@">0</token>
6 </macros>
7 <requirements>
8 <requirement type="package" version="@TOOL_VERSION@">icescreen</requirement>
9 <requirement type="package" version="3.0">zip</requirement>
10 </requirements>
11 <version_command><![CDATA[
12 icescreen --version
13 ]]>
14 </version_command>
15 <command detect_errors="aggressive"><![CDATA[
16 #set $gbname = 'galaxy_genbank'
17 mkdir -p ./tmp_icescreen/source_genbank
18 && ln -s '${genome}' ./tmp_icescreen/source_genbank/${gbname}.gb
19 && icescreen
20 --galaxy
21 --gbdir ./tmp_icescreen/source_genbank
22 --outdir ./tmp_icescreen
23 --mode '${taxonomy.mode}'
24 --jobs "\${GALAXY_SLOTS:-4}" > ./tmp_icescreen/ICEscreen_log.txt 2>&1
25
26 && cat ./tmp_icescreen/ICEscreen_results/results/${gbname}/icescreen_detection_ME/${gbname}_detected_ME.summary > '${summary}'
27 && cat ./tmp_icescreen/ICEscreen_results/results/${gbname}/icescreen_detection_ME/${gbname}_detected_SP_withMEIds.tsv > '${detected_sp}'
28 && cat ./tmp_icescreen/ICEscreen_results/results/${gbname}/icescreen_detection_ME/${gbname}_detected_ME.tsv > '${detected_me}'
29
30 #if "output_annotation_genbank" in $additional_output.optional_files:
31 && mv ./tmp_icescreen/ICEscreen_results/results/${gbname}/visualization_files/${gbname}_icescreen.gb '${gbout}'
32 #end if
33 #if "output_annotation_gff" in $additional_output.optional_files:
34 && mv ./tmp_icescreen/ICEscreen_results/results/${gbname}/visualization_files/${gbname}_icescreen.gff '${gffout}'
35 #end if
36 #if "output_annotation_embl" in $additional_output.optional_files:
37 && mv ./tmp_icescreen/ICEscreen_results/results/${gbname}/visualization_files/${gbname}_icescreen.embl '${emblout}'
38 #end if
39 #if "output_log" in $additional_output.optional_files:
40 && mv ./tmp_icescreen/ICEscreen_log.txt '${log}'
41 #end if
42 #if "output_zip_all_files" in $additional_output.optional_files:
43 && cd ./tmp_icescreen/ICEscreen_results/results/${gbname} && zip --quiet -r - -- . > '${outzip}'
44 #end if
45 ]]>
46 </command>
47 <inputs>
48 <param name="genome" type="data" format="genbank" label="Input genomes to analyze in Genbank format" help=""/>
49 <section name="taxonomy" title="Taxonomy of the genomes to analyse" expanded="False">
50 <param name="mode" type="select" label="Firmicutes is the defaut parameter" help="Streptomyces is EXPERIMENTAL and is NOT recommended.">
51 <option value="firmicutes" selected="true">Firmicutes</option>
52 <option value="streptomyces">Streptomyces</option>
53 </param>
54 </section>
55 <section name="additional_output" title="Additional output files" expanded="False">
56 <param name="optional_files" type="select" label="Make the following optional files available in the Galaxy history" multiple="true" optional="true" display="checkboxes" >
57 <option value="output_annotation_genbank">Genome annotation in genbank format</option>
58 <option value="output_annotation_gff">Genome annotation in gff format</option>
59 <option value="output_annotation_embl">Genome annotation in embl format</option>
60 <option value="output_zip_all_files">Zip of all final and intermediate results</option>
61 <option value="output_log">ICEscreen log</option>
62 </param>
63 </section>
64 </inputs>
65 <outputs>
66 <data format="tabular" name="detected_sp" label="${tool.name} on ${on_string}: Signature Proteins table" />
67 <data format="tabular" name="detected_me" label="${tool.name} on ${on_string}: ICEs/IMEs table" />
68 <data format="txt" name="summary" label="${tool.name} on ${on_string}: results summary" />
69 <data format="genbank" name="gbout" label="${tool.name} on ${on_string}: annotated genbank" >
70 <filter>additional_output['optional_files'] and "output_annotation_genbank" in additional_output['optional_files']</filter>
71 </data>
72 <data format="gff3" name="gffout" label="${tool.name} on ${on_string}: annotated GFF3" >
73 <filter>additional_output['optional_files'] and "output_annotation_gff" in additional_output['optional_files']</filter>
74 </data>
75 <data format="embl" name="emblout" label="${tool.name} on ${on_string}: annotated EMBL" >
76 <filter>additional_output['optional_files'] and "output_annotation_embl" in additional_output['optional_files']</filter>
77 </data>
78 <data format="zip" name="outzip" label="${tool.name} on ${on_string}: all results zipped">
79 <filter>additional_output['optional_files'] and "output_zip_all_files" in additional_output['optional_files']</filter>
80 </data>
81 <data format="txt" name="log" label="${tool.name} on ${on_string}: log file" >
82 <filter>additional_output['optional_files'] and "output_log" in additional_output['optional_files']</filter>
83 </data>
84 </outputs>
85 <tests>
86 <test expect_num_outputs="3">
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" />
89 <output name="detected_me" file="NC_004668_137848_164286_detected_ME.tsv" ftype="tabular" />
90 <output name="detected_sp" >
91 <assert_contents>
92 <has_text text="ICE IME Number" />
93 <has_text text="WP_002359295" />
94 <has_text text="VirB4" />
95 <has_n_columns n="47" />
96 <has_n_lines n="5" />
97 </assert_contents>
98 </output>
99 </test>
100 <test expect_num_outputs="4">
101 <param name="genome" value="genbank/NC_004668_137848_164286.gb" ftype="genbank" />
102 <param name="optional_files" value="output_annotation_genbank" />
103 <output name="gbout" file="NC_004668_137848_164286_icescreen.gb" ftype="genbank" />
104 </test>
105 <test expect_num_outputs="4">
106 <param name="genome" value="genbank/NC_004668_137848_164286.gb" ftype="genbank" />
107 <param name="optional_files" value="output_annotation_gff" />
108 <output name="gffout" file="NC_004668_137848_164286_icescreen.gff" ftype="gff3" />
109 </test>
110 <test expect_num_outputs="4">
111 <param name="genome" value="genbank/NC_004668_137848_164286.gb" ftype="genbank" />
112 <param name="optional_files" value="output_annotation_embl" />
113 <output name="emblout" file="NC_004668_137848_164286_icescreen.embl" ftype="embl" />
114 </test>
115 <test expect_num_outputs="4">
116 <param name="genome" value="genbank/NC_004668_137848_164286.gb" ftype="genbank" />
117 <param name="optional_files" value="output_zip_all_files" />
118
119 <output name="outzip" >
120 <assert_contents>
121 <has_archive_member path=".*/*_detected_SP_withMEIds.tsv"><has_text text="ICE IME Number" /></has_archive_member>
122 </assert_contents>
123 </output>
124 </test>
125 <test expect_num_outputs="4">
126 <param name="genome" value="genbank/NC_004668_137848_164286.gb" ftype="genbank" />
127 <param name="optional_files" value="output_log" />
128 <output name="log" >
129 <assert_contents>
130 <has_text text="firmicutes" />
131 <has_text text="Building DAG of jobs" />
132 <has_text text="Complete log" />
133 <not_has_text text="Error" />
134 </assert_contents>
135 </output>
136 </test>
137 <test expect_num_outputs="4">
138 <param name="genome" value="genbank/NC_004668_137848_164286.gb" ftype="genbank" />
139 <param name="mode" value="streptomyces" />
140 <param name="optional_files" value="output_log" />
141 <output name="log" >
142 <assert_contents>
143 <has_text text="streptomyces" />
144 <not_has_text text="Error" />
145 </assert_contents>
146 </output>
147 </test>
148 <test expect_num_outputs="5">
149 <param name="genome" value="genbank/NC_004668_137848_164286.gb" ftype="genbank" />
150 <param name="mode" value="firmicutes" />
151 <param name="optional_files" value="output_zip_all_files,output_log" />
152 <output name="log" >
153 <assert_contents>
154 <has_text text="firmicutes" />
155 <not_has_text text="Error" />
156 </assert_contents>
157 </output>
158 </test>
159 </tests>
160 <help><![CDATA[
161 .. class:: warningmark
162
163 This tool requires *genbank* format.
164
165 -----
166
167 **What it does**
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.
170
171 **Main features of ICEscreen**
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.
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.
176 - Delimitation of the elements at the gene or nucleotide level is not yet implemented and still needs manual curation.
177
178 **Output files**
179
180 There are 3 main output results files generated by ICEscreen:
181
182 - Detected Signature Proteins table (`*_detected_SP_withMEIds.csv`): list of the signature proteins detected by the tool and their possible assignment to an ICE or IME element. It is a comma separated table of 48 columns with a one line header. Each line represents a signature protein detected by ICEscreen.
183 - Detected ICEs/IMEs table (`*_detected_ME.tsv`): list of the ICEs and IMEs elements detected by the tool, including information about the signature proteins they contain. It is a tab separated table of 21 columns, the header is at line #3. Information in this file is similar to the output file _withICEIMEIds.csv (option -m) but centered around a list of ICE / IME structures instead of a list of SPs.
184 - Results summary (`*_detected_ME.summary`): this file summarizes the main parameters and statistics regarding the ICE / IME structures and the SPs.
185
186 Other optional and additional output files generated by ICEscreen:
187
188 - Annotated Genbank, EMBL, and GFF3 files: tose files contains the annotations of the original Genbank file in addition to annotations added by ICEscreen such as ICEscreen signature proteins and mobile elements.
189 - All results zipped file: You can download this file locally and unzip it to have the complete output folder generated by the tool, including intermediate processing files. See https://icescreen.migale.inrae.fr for details.
190 - Log file (`*_detected_ME.log`): this file contains the detailed internal details used by ICEscreen to generate the results and logs of each step of the ICEscreen tool pipeline.
191
192 ]]>
193
194 </help>
195 <citations>
196 <citation type="bibtex">@UNPUBLISHED{Kim07aninterior-point,
197 author = {Julie Lao and Thomas Lacroix and Gérard Guédon and Charles Coluzzi and Nathalie Leblond-Bourget and Hélène Chiapello},
198 title = {"See our latest publication at https://icescreen.migale.inrae.fr."}
199 }
200 </citation>
201 </citations>
202 </tool>