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comparison icescreen.xml @ 7:d45c95f382d3 draft

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planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit bc68b3c32a23a39507f54cb6b4453676174712d6
author iuc
date Fri, 26 Jan 2024 13:38:40 +0000
parents 85c9849b429e
children 130a217f8d3f
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6:85c9849b429e 7:d45c95f382d3
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 Bacillota genomes.</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">1.2.0</token> 4 <token name="@TOOL_VERSION@">1.3.1</token>
5 <token name="@VERSION_SUFFIX@">1</token> 5 <token name="@VERSION_SUFFIX@">0</token>
6 </macros> 6 </macros>
7 <xrefs>
8 <xref type="bio.tools">ICEscreen</xref>
9 </xrefs>
10 <requirements> 7 <requirements>
11 <requirement type="package" version="@TOOL_VERSION@">icescreen</requirement> 8 <requirement type="package" version="@TOOL_VERSION@">icescreen</requirement>
12 <requirement type="package" version="3.0">zip</requirement> 9 <requirement type="package" version="3.0">zip</requirement>
13 </requirements> 10 </requirements>
14 <version_command><![CDATA[ 11 <version_command><![CDATA[
21 && ln -s '${genome}' ./tmp_icescreen/source_genbank/${gbname}.gb 18 && ln -s '${genome}' ./tmp_icescreen/source_genbank/${gbname}.gb
22 && icescreen 19 && icescreen
23 --galaxy 20 --galaxy
24 --gbdir ./tmp_icescreen/source_genbank 21 --gbdir ./tmp_icescreen/source_genbank
25 --outdir ./tmp_icescreen 22 --outdir ./tmp_icescreen
26 --mode '${taxonomy.mode}' 23 --phylum '${taxonomy.phylum}'
27 --jobs "\${GALAXY_SLOTS:-4}" > ./tmp_icescreen/ICEscreen_log.txt 2>&1 24 --jobs "\${GALAXY_SLOTS:-4}" > ./tmp_icescreen/ICEscreen_log.txt 2>&1
28 25
29 && cat ./tmp_icescreen/ICEscreen_results/results/${gbname}/icescreen_detection_ME/${gbname}_detected_ME.summary > '${summary}' 26 && cat ./tmp_icescreen/ICEscreen_results/results/${gbname}/icescreen_detection_ME/${gbname}_detected_ME.summary > '${summary}'
30 && cat ./tmp_icescreen/ICEscreen_results/results/${gbname}/icescreen_detection_ME/${gbname}_detected_SP_withMEIds.tsv > '${detected_sp}' 27 && cat ./tmp_icescreen/ICEscreen_results/results/${gbname}/icescreen_detection_ME/${gbname}_detected_SP_withMEIds.tsv > '${detected_sp}'
31 && cat ./tmp_icescreen/ICEscreen_results/results/${gbname}/icescreen_detection_ME/${gbname}_detected_ME.tsv > '${detected_me}' 28 && cat ./tmp_icescreen/ICEscreen_results/results/${gbname}/icescreen_detection_ME/${gbname}_detected_ME.tsv > '${detected_me}'
47 #end if 44 #end if
48 ]]> 45 ]]>
49 </command> 46 </command>
50 <inputs> 47 <inputs>
51 <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."/> 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."/>
52 <section name="taxonomy" title="Taxonomy of the genomes to analyse" expanded="False"> 49 <section name="taxonomy" title="Phylum of the genomes to analyse" expanded="True">
53 <param name="mode" type="select" label="Firmicutes is the defaut parameter" help="Streptomyces is EXPERIMENTAL and is NOT recommended."> 50 <param name="phylum" type="select" label="Bacillota is the defaut parameter">
54 <option value="firmicutes" selected="true">Firmicutes</option> 51 <option value="bacillota" selected="true">Bacillota</option>
55 <option value="streptomyces">Streptomyces</option>
56 </param> 52 </param>
57 </section> 53 </section>
58 <section name="additional_output" title="Additional output files" expanded="False"> 54 <section name="additional_output" title="Additional output files" expanded="False">
59 <param name="optional_files" type="select" label="Make the following optional files available in the Galaxy history" multiple="true" optional="true" display="checkboxes" > 55 <param name="optional_files" type="select" label="Make the following optional files available in the Galaxy history" multiple="true" optional="true" display="checkboxes" >
60 <option value="output_annotation_genbank">Genome annotation in genbank format</option> 56 <option value="output_annotation_genbank">Genome annotation in genbank format</option>
127 <test expect_num_outputs="4"> 123 <test expect_num_outputs="4">
128 <param name="genome" value="genbank/NC_004668_137848_164286.gb" ftype="genbank" /> 124 <param name="genome" value="genbank/NC_004668_137848_164286.gb" ftype="genbank" />
129 <param name="optional_files" value="output_log" /> 125 <param name="optional_files" value="output_log" />
130 <output name="log" > 126 <output name="log" >
131 <assert_contents> 127 <assert_contents>
132 <has_text text="firmicutes" /> 128 <has_text text="bacillota" />
133 <has_text text="Building DAG of jobs" /> 129 <has_text text="Building DAG of jobs" />
134 <has_text text="Complete log" /> 130 <has_text text="Complete log" />
135 <not_has_text text="Error" /> 131 <not_has_text text="Error" />
136 </assert_contents> 132 </assert_contents>
137 </output> 133 </output>
138 </test> 134 </test>
139 <test expect_num_outputs="4"> 135 <test expect_num_outputs="4">
140 <param name="genome" value="genbank/NC_004668_137848_164286.gb" ftype="genbank" /> 136 <param name="genome" value="genbank/NC_004668_137848_164286.gb" ftype="genbank" />
141 <param name="mode" value="streptomyces" /> 137 <param name="phylum" value="bacillota" />
142 <param name="optional_files" value="output_log" /> 138 <param name="optional_files" value="output_log" />
143 <output name="log" > 139 <output name="log" >
144 <assert_contents> 140 <assert_contents>
145 <has_text text="streptomyces" /> 141 <has_text text="bacillota" />
146 <not_has_text text="Error" /> 142 <not_has_text text="Error" />
147 </assert_contents> 143 </assert_contents>
148 </output> 144 </output>
149 </test> 145 </test>
150 <test expect_num_outputs="5"> 146 <test expect_num_outputs="5">
151 <param name="genome" value="genbank/NC_004668_137848_164286.gb" ftype="genbank" /> 147 <param name="genome" value="genbank/NC_004668_137848_164286.gb" ftype="genbank" />
152 <param name="mode" value="firmicutes" /> 148 <param name="phylum" value="bacillota" />
153 <param name="optional_files" value="output_zip_all_files,output_log" /> 149 <param name="optional_files" value="output_zip_all_files,output_log" />
154 <output name="log" > 150 <output name="log" >
155 <assert_contents> 151 <assert_contents>
156 <has_text text="firmicutes" /> 152 <has_text text="bacillota" />
157 <not_has_text text="Error" /> 153 <not_has_text text="Error" />
158 </assert_contents> 154 </assert_contents>
159 </output> 155 </output>
160 </test> 156 </test>
161 <test expect_num_outputs="3"> 157 <test expect_num_outputs="3">
178 174
179 ----- 175 -----
180 176
181 **What it does** 177 **What it does**
182 178
183 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. 179 ICEscreen is a bioinformatic pipeline for the detection and annotation of ICEs (Integrative and Conjugative Elements) and IMEs (Integrative and Mobilizable Elements) in Bacillota 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.
184 180
185 **Main features of ICEscreen** 181 **Main features of ICEscreen**
186 182
187 - 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. 183 - 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.
188 - 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. 184 - 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.
191 187
192 **Output files** 188 **Output files**
193 189
194 There are 3 main output results files generated by ICEscreen: 190 There are 3 main output results files generated by ICEscreen:
195 191
196 - 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. 192 - 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. Each line represents a signature protein detected by ICEscreen.
197 - 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. 193 - 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. Information in this file is complementary to the _withICEIMEIds.csv file above with each line representing an ICE / IME structures instead of a signature protein.
198 - Results summary (`*_detected_ME.summary`): this file summarizes the main parameters and statistics regarding the ICE / IME structures and the SPs. 194 - Results summary (`*_detected_ME.summary`): this file summarizes the main parameters and statistics regarding the ICE / IME structures and the SPs.
199 195
200 Other optional and additional output files generated by ICEscreen: 196 Other optional and additional output files generated by ICEscreen:
201 197
202 - 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. 198 - 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.