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