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planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit f759554562ce175fd1510d6878881154f5e1a331
author iuc
date Fri, 09 Feb 2024 21:26:42 +0000
parents d45c95f382d3
children
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1 <tool id="icescreen" name="ICEscreen" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.09">
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2 <description>detects and annotates ICEs (Integrative and Conjugative Elements) and IMEs (Integrative and Mobilizable Elements) in Bacillota genomes.</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">1.3.1</token>
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5 <token name="@VERSION_SUFFIX@">0</token>
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6 </macros>
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7 <xrefs>
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8 <xref type="bio.tools">icescreen</xref>
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9 </xrefs>
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10 <requirements>
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11 <requirement type="package" version="@TOOL_VERSION@">icescreen</requirement>
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12 <requirement type="package" version="3.0">zip</requirement>
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13 </requirements>
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14 <version_command><![CDATA[
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15 icescreen --version
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16 ]]>
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17 </version_command>
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18 <command detect_errors="aggressive"><![CDATA[
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19 #set $gbname = 'galaxy_genbank'
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20 mkdir -p ./tmp_icescreen/source_genbank
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21 && ln -s '${genome}' ./tmp_icescreen/source_genbank/${gbname}.gb
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22 && icescreen
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23 --galaxy
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24 --gbdir ./tmp_icescreen/source_genbank
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25 --outdir ./tmp_icescreen
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26 --phylum '${taxonomy.phylum}'
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27 --jobs "\${GALAXY_SLOTS:-4}" > ./tmp_icescreen/ICEscreen_log.txt 2>&1
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29 && cat ./tmp_icescreen/ICEscreen_results/results/${gbname}/icescreen_detection_ME/${gbname}_detected_ME.summary > '${summary}'
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30 && cat ./tmp_icescreen/ICEscreen_results/results/${gbname}/icescreen_detection_ME/${gbname}_detected_SP_withMEIds.tsv > '${detected_sp}'
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31 && cat ./tmp_icescreen/ICEscreen_results/results/${gbname}/icescreen_detection_ME/${gbname}_detected_ME.tsv > '${detected_me}'
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32
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33 #if "output_annotation_genbank" in $additional_output.optional_files:
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34 && mv ./tmp_icescreen/ICEscreen_results/results/${gbname}/visualization_files/${gbname}_icescreen.gb '${gbout}'
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35 #end if
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36 #if "output_annotation_gff" in $additional_output.optional_files:
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37 && mv ./tmp_icescreen/ICEscreen_results/results/${gbname}/visualization_files/${gbname}_icescreen.gff '${gffout}'
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38 #end if
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39 #if "output_annotation_embl" in $additional_output.optional_files:
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40 && mv ./tmp_icescreen/ICEscreen_results/results/${gbname}/visualization_files/${gbname}_icescreen.embl '${emblout}'
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41 #end if
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42 #if "output_log" in $additional_output.optional_files:
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43 && mv ./tmp_icescreen/ICEscreen_log.txt '${log}'
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44 #end if
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45 #if "output_zip_all_files" in $additional_output.optional_files:
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46 && cd ./tmp_icescreen/ICEscreen_results/results/${gbname} && zip --quiet -r - -- . > '${outzip}'
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47 #end if
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48 ]]>
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49 </command>
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50 <inputs>
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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."/>
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52 <section name="taxonomy" title="Phylum of the genomes to analyse" expanded="True">
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53 <param name="phylum" type="select" label="Bacillota is the defaut parameter">
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54 <option value="bacillota" selected="true">Bacillota</option>
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55 </param>
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56 </section>
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57 <section name="additional_output" title="Additional output files" expanded="False">
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58 <param name="optional_files" type="select" label="Make the following optional files available in the Galaxy history" multiple="true" optional="true" display="checkboxes" >
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59 <option value="output_annotation_genbank">Genome annotation in genbank format</option>
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60 <option value="output_annotation_gff">Genome annotation in gff format</option>
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61 <option value="output_annotation_embl">Genome annotation in embl format</option>
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62 <option value="output_zip_all_files">Zip of all final and intermediate results</option>
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63 <option value="output_log">ICEscreen log</option>
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64 </param>
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65 </section>
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66 </inputs>
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67 <outputs>
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68 <data format="tabular" name="detected_sp" label="${tool.name} on ${on_string}: Signature Proteins table" />
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69 <data format="tabular" name="detected_me" label="${tool.name} on ${on_string}: ICEs/IMEs table" />
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70 <data format="txt" name="summary" label="${tool.name} on ${on_string}: results summary" />
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71 <data format="genbank" name="gbout" label="${tool.name} on ${on_string}: annotated genbank" >
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72 <filter>additional_output['optional_files'] and "output_annotation_genbank" in additional_output['optional_files']</filter>
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73 </data>
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74 <data format="gff3" name="gffout" label="${tool.name} on ${on_string}: annotated GFF3" >
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75 <filter>additional_output['optional_files'] and "output_annotation_gff" in additional_output['optional_files']</filter>
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76 </data>
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77 <data format="embl" name="emblout" label="${tool.name} on ${on_string}: annotated EMBL" >
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78 <filter>additional_output['optional_files'] and "output_annotation_embl" in additional_output['optional_files']</filter>
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79 </data>
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80 <data format="zip" name="outzip" label="${tool.name} on ${on_string}: all results zipped">
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81 <filter>additional_output['optional_files'] and "output_zip_all_files" in additional_output['optional_files']</filter>
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82 </data>
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83 <data format="txt" name="log" label="${tool.name} on ${on_string}: log file" >
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84 <filter>additional_output['optional_files'] and "output_log" in additional_output['optional_files']</filter>
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85 </data>
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86 </outputs>
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87 <tests>
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88 <test expect_num_outputs="3">
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
89 <param name="genome" value="genbank/NC_004668_137848_164286.gb" ftype="genbank" />
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
90 <output name="summary" file="NC_004668_137848_164286_detected_ME.summary" ftype="txt" />
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
91 <output name="detected_me" file="NC_004668_137848_164286_detected_ME.tsv" ftype="tabular" />
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
92 <output name="detected_sp" >
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
93 <assert_contents>
3
2bb38197ff75 planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit 29cbe5a71212ff13e8d63e9ea57243fd0aeacbf9
iuc
parents: 2
diff changeset
94 <has_text text="ICE_IME_id" />
0
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
95 <has_text text="WP_002359295" />
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
96 <has_text text="VirB4" />
3
2bb38197ff75 planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit 29cbe5a71212ff13e8d63e9ea57243fd0aeacbf9
iuc
parents: 2
diff changeset
97 <has_n_columns n="54" />
0
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
98 <has_n_lines n="5" />
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
99 </assert_contents>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
100 </output>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
101 </test>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
102 <test expect_num_outputs="4">
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
103 <param name="genome" value="genbank/NC_004668_137848_164286.gb" ftype="genbank" />
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
104 <param name="optional_files" value="output_annotation_genbank" />
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
105 <output name="gbout" file="NC_004668_137848_164286_icescreen.gb" ftype="genbank" />
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
106 </test>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
107 <test expect_num_outputs="4">
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
108 <param name="genome" value="genbank/NC_004668_137848_164286.gb" ftype="genbank" />
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
109 <param name="optional_files" value="output_annotation_gff" />
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
110 <output name="gffout" file="NC_004668_137848_164286_icescreen.gff" ftype="gff3" />
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
111 </test>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
112 <test expect_num_outputs="4">
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
113 <param name="genome" value="genbank/NC_004668_137848_164286.gb" ftype="genbank" />
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
114 <param name="optional_files" value="output_annotation_embl" />
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
115 <output name="emblout" file="NC_004668_137848_164286_icescreen.embl" ftype="embl" />
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
116 </test>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
117 <test expect_num_outputs="4">
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
118 <param name="genome" value="genbank/NC_004668_137848_164286.gb" ftype="genbank" />
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
119 <param name="optional_files" value="output_zip_all_files" />
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
120 <output name="outzip" >
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
121 <assert_contents>
3
2bb38197ff75 planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit 29cbe5a71212ff13e8d63e9ea57243fd0aeacbf9
iuc
parents: 2
diff changeset
122 <has_archive_member path=".*/*_detected_SP_withMEIds.tsv"><has_text text="ICE_IME_id" /></has_archive_member>
0
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
123 </assert_contents>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
124 </output>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
125 </test>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
126 <test expect_num_outputs="4">
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
127 <param name="genome" value="genbank/NC_004668_137848_164286.gb" ftype="genbank" />
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
128 <param name="optional_files" value="output_log" />
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
129 <output name="log" >
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
130 <assert_contents>
7
d45c95f382d3 planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit bc68b3c32a23a39507f54cb6b4453676174712d6
iuc
parents: 6
diff changeset
131 <has_text text="bacillota" />
0
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
132 <has_text text="Building DAG of jobs" />
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
133 <has_text text="Complete log" />
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
134 <not_has_text text="Error" />
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
135 </assert_contents>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
136 </output>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
137 </test>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
138 <test expect_num_outputs="4">
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
139 <param name="genome" value="genbank/NC_004668_137848_164286.gb" ftype="genbank" />
7
d45c95f382d3 planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit bc68b3c32a23a39507f54cb6b4453676174712d6
iuc
parents: 6
diff changeset
140 <param name="phylum" value="bacillota" />
0
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
141 <param name="optional_files" value="output_log" />
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
142 <output name="log" >
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
143 <assert_contents>
7
d45c95f382d3 planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit bc68b3c32a23a39507f54cb6b4453676174712d6
iuc
parents: 6
diff changeset
144 <has_text text="bacillota" />
0
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
145 <not_has_text text="Error" />
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
146 </assert_contents>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
147 </output>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
148 </test>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
149 <test expect_num_outputs="5">
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
150 <param name="genome" value="genbank/NC_004668_137848_164286.gb" ftype="genbank" />
7
d45c95f382d3 planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit bc68b3c32a23a39507f54cb6b4453676174712d6
iuc
parents: 6
diff changeset
151 <param name="phylum" value="bacillota" />
0
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
152 <param name="optional_files" value="output_zip_all_files,output_log" />
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
153 <output name="log" >
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
154 <assert_contents>
7
d45c95f382d3 planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit bc68b3c32a23a39507f54cb6b4453676174712d6
iuc
parents: 6
diff changeset
155 <has_text text="bacillota" />
0
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
156 <not_has_text text="Error" />
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
157 </assert_contents>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
158 </output>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
159 </test>
4
c5f7c311f1b0 planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit a9bc15365abc70c0367d732b790763d8fa53b220
iuc
parents: 3
diff changeset
160 <test expect_num_outputs="3">
c5f7c311f1b0 planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit a9bc15365abc70c0367d732b790763d8fa53b220
iuc
parents: 3
diff changeset
161 <param name="genome" value="genbank/NC_013798_298468_322494_NC_020450_643089_661957.gb" ftype="genbank" />
c5f7c311f1b0 planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit a9bc15365abc70c0367d732b790763d8fa53b220
iuc
parents: 3
diff changeset
162 <output name="summary" file="NC_013798_298468_322494_NC_020450_643089_661957_detected_ME.summary" ftype="txt" />
c5f7c311f1b0 planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit a9bc15365abc70c0367d732b790763d8fa53b220
iuc
parents: 3
diff changeset
163 <output name="detected_me" file="NC_013798_298468_322494_NC_020450_643089_661957_detected_ME.tsv" ftype="tabular" />
c5f7c311f1b0 planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit a9bc15365abc70c0367d732b790763d8fa53b220
iuc
parents: 3
diff changeset
164 <output name="detected_sp" >
c5f7c311f1b0 planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit a9bc15365abc70c0367d732b790763d8fa53b220
iuc
parents: 3
diff changeset
165 <assert_contents>
c5f7c311f1b0 planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit a9bc15365abc70c0367d732b790763d8fa53b220
iuc
parents: 3
diff changeset
166 <has_text text="ICE_IME_id" />
c5f7c311f1b0 planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit a9bc15365abc70c0367d732b790763d8fa53b220
iuc
parents: 3
diff changeset
167 <has_text text="WP_044555479.1" />
c5f7c311f1b0 planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit a9bc15365abc70c0367d732b790763d8fa53b220
iuc
parents: 3
diff changeset
168 <has_text text="WP_015426013.1" />
c5f7c311f1b0 planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit a9bc15365abc70c0367d732b790763d8fa53b220
iuc
parents: 3
diff changeset
169 </assert_contents>
c5f7c311f1b0 planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit a9bc15365abc70c0367d732b790763d8fa53b220
iuc
parents: 3
diff changeset
170 </output>
c5f7c311f1b0 planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit a9bc15365abc70c0367d732b790763d8fa53b220
iuc
parents: 3
diff changeset
171 </test>
0
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
172 </tests>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
173 <help><![CDATA[
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
174 .. class:: warningmark
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
175
3
2bb38197ff75 planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit 29cbe5a71212ff13e8d63e9ea57243fd0aeacbf9
iuc
parents: 2
diff changeset
176 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.
0
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
177
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
178 -----
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
179
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
180 **What it does**
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
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181
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182 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.
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183
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184 **Main features of ICEscreen**
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185
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186 - 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.
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187 - 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.
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188 - Detection of the ICE/IME structures: ICEScreen groups together SPs that belong to the same ICE/IME structures to the best of its ability.
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189 - Delimitation of the elements at the gene or nucleotide level is not yet implemented and still needs manual curation.
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190
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191 **Output files**
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192
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193 There are 3 main output results files generated by ICEscreen:
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194
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195 - 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.
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196 - 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.
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197 - Results summary (`*_detected_ME.summary`): this file summarizes the main parameters and statistics regarding the ICE / IME structures and the SPs.
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198
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199 Other optional and additional output files generated by ICEscreen:
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200
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201 - 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.
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202 - 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.
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203 - 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.
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204
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205 ]]>
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206
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207 </help>
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208 <citations>
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209 <citation type="bibtex">@UNPUBLISHED{Kim07aninterior-point,
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210 author = {Julie Lao and Thomas Lacroix and Gérard Guédon and Charles Coluzzi and Nathalie Leblond-Bourget and Hélène Chiapello},
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211 title = {"See our latest publication at https://icescreen.migale.inrae.fr."}
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212 }
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213 </citation>
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214 </citations>
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215 </tool>