Mercurial > repos > iuc > icescreen
comparison icescreen.xml @ 7:d45c95f382d3 draft
planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit bc68b3c32a23a39507f54cb6b4453676174712d6
author | iuc |
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date | Fri, 26 Jan 2024 13:38:40 +0000 |
parents | 85c9849b429e |
children | 130a217f8d3f |
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6:85c9849b429e | 7:d45c95f382d3 |
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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. |