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annotate icescreen.xml @ 1:19a3d3dffe83 draft

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"planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit ca3989312611d8b90805aa60dec6769a0c428d41"
author iuc
date Mon, 31 Jan 2022 21:03:18 +0000
parents 7c77b2896ac2
children f08181349fc4
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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 Firmicutes genomes.</description>
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3 <macros>
1
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4 <token name="@TOOL_VERSION@">1.0.3</token>
0
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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/${gbname}.gb
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19 && icescreen
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20 --galaxy
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21 --gbdir ./tmp_icescreen/source_genbank
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22 --outdir ./tmp_icescreen
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23 --mode '${taxonomy.mode}'
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24 --jobs "\${GALAXY_SLOTS:-4}" > ./tmp_icescreen/ICEscreen_log.txt 2>&1
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25
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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=""/>
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49 <section name="taxonomy" title="Taxonomy of the genomes to analyse" expanded="False">
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50 <param name="mode" type="select" label="Firmicutes is the defaut parameter" help="Streptomyces is EXPERIMENTAL and is NOT recommended.">
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51 <option value="firmicutes" selected="true">Firmicutes</option>
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52 <option value="streptomyces">Streptomyces</option>
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53 </param>
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54 </section>
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55 <section name="additional_output" title="Additional output files" expanded="False">
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56 <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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57 <option value="output_annotation_genbank">Genome annotation in genbank format</option>
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58 <option value="output_annotation_gff">Genome annotation in gff format</option>
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59 <option value="output_annotation_embl">Genome annotation in embl format</option>
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60 <option value="output_zip_all_files">Zip of all final and intermediate results</option>
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61 <option value="output_log">ICEscreen log</option>
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62 </param>
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63 </section>
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64 </inputs>
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65 <outputs>
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66 <data format="tabular" name="detected_sp" label="${tool.name} on ${on_string}: Signature Proteins table" />
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67 <data format="tabular" name="detected_me" label="${tool.name} on ${on_string}: ICEs/IMEs table" />
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68 <data format="txt" name="summary" label="${tool.name} on ${on_string}: results summary" />
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69 <data format="genbank" name="gbout" label="${tool.name} on ${on_string}: annotated genbank" >
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70 <filter>additional_output['optional_files'] and "output_annotation_genbank" in additional_output['optional_files']</filter>
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71 </data>
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72 <data format="gff3" name="gffout" label="${tool.name} on ${on_string}: annotated GFF3" >
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73 <filter>additional_output['optional_files'] and "output_annotation_gff" in additional_output['optional_files']</filter>
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74 </data>
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75 <data format="embl" name="emblout" label="${tool.name} on ${on_string}: annotated EMBL" >
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76 <filter>additional_output['optional_files'] and "output_annotation_embl" in additional_output['optional_files']</filter>
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77 </data>
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78 <data format="zip" name="outzip" label="${tool.name} on ${on_string}: all results zipped">
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79 <filter>additional_output['optional_files'] and "output_zip_all_files" in additional_output['optional_files']</filter>
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80 </data>
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81 <data format="txt" name="log" label="${tool.name} on ${on_string}: log file" >
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82 <filter>additional_output['optional_files'] and "output_log" in additional_output['optional_files']</filter>
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83 </data>
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84 </outputs>
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85 <tests>
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86 <test expect_num_outputs="3">
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87 <param name="genome" value="genbank/NC_004668_137848_164286.gb" ftype="genbank" />
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88 <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
89 <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
90 <output name="detected_sp" >
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
91 <assert_contents>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
92 <has_text text="ICE IME Number" />
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
93 <has_text text="WP_002359295" />
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
94 <has_text text="VirB4" />
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
95 <has_n_columns n="47" />
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
96 <has_n_lines n="5" />
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
97 </assert_contents>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
98 </output>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
99 </test>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
100 <test expect_num_outputs="4">
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
101 <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
102 <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
103 <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
104 </test>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
105 <test expect_num_outputs="4">
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
106 <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:
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107 <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
108 <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
109 </test>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
110 <test expect_num_outputs="4">
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
111 <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
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112 <param name="optional_files" value="output_annotation_embl" />
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
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parents:
diff changeset
113 <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
114 </test>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
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115 <test expect_num_outputs="4">
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
116 <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
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diff changeset
117 <param name="optional_files" value="output_zip_all_files" />
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
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parents:
diff changeset
118
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
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119 <output name="outzip" >
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 <has_archive_member path=".*/*_detected_SP_withMEIds.tsv"><has_text text="ICE IME Number" /></has_archive_member>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
122 </assert_contents>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
123 </output>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
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124 </test>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
125 <test expect_num_outputs="4">
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
126 <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
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diff changeset
127 <param name="optional_files" value="output_log" />
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
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128 <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
129 <assert_contents>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
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parents:
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130 <has_text text="firmicutes" />
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
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parents:
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131 <has_text text="Building DAG of jobs" />
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
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132 <has_text text="Complete log" />
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
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diff changeset
133 <not_has_text text="Error" />
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
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134 </assert_contents>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
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diff changeset
135 </output>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
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diff changeset
136 </test>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
137 <test expect_num_outputs="4">
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
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diff changeset
138 <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
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diff changeset
139 <param name="mode" value="streptomyces" />
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
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diff changeset
140 <param name="optional_files" value="output_log" />
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
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diff changeset
141 <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
142 <assert_contents>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
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143 <has_text text="streptomyces" />
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
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144 <not_has_text text="Error" />
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
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145 </assert_contents>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
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146 </output>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
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147 </test>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
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148 <test expect_num_outputs="5">
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
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diff changeset
149 <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
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150 <param name="mode" value="firmicutes" />
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
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151 <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"
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152 <output name="log" >
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
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153 <assert_contents>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
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154 <has_text text="firmicutes" />
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
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155 <not_has_text text="Error" />
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
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parents:
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156 </assert_contents>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
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157 </output>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
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158 </test>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
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159 </tests>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
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160 <help><![CDATA[
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
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161 .. class:: warningmark
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
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162
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
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163 This tool requires *genbank* format.
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
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164
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
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165 -----
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
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166
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
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167 **What it does**
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
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168
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
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169 ICEscreen is a bioinformatic pipeline for the detection and annotation of ICEs (Integrative and Conjugative Elements) and IMEs (Integrative and Mobilizable Elements) in Firmicutes genomes. The full documentation is available at https://icescreen.migale.inrae.fr. The forge of the project is accessible at https://forgemia.inra.fr/ices_imes_analysis/icescreen.
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
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170
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
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171 **Main features of ICEscreen**
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
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172
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
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173 - Detection of signature proteins (SPs) of ICEs/IMEs by using blastP on a curated resource. BlastP allows for an accurate assignment of hits to a given ICE/IME superfamily or family. The curated resource was derived from an analysis of over 120 ICEs and IMEs in Streptococcus genomes by the DINAMIC lab.
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
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174 - Detection of distant homologs of SPs by using HMM profiles of ICEs/IMEs protein families. The HMM profiles have been either imported from trusted resources or created and curated when needed.
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
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175 - Detection of the ICE/IME structures: ICEScreen groups together SPs that belong to the same ICE/IME structures to the best of its ability.
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
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176 - Delimitation of the elements at the gene or nucleotide level is not yet implemented and still needs manual curation.
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
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177
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
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178 **Output files**
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
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179
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
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180 There are 3 main output results files generated by ICEscreen:
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
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181
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
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182 - Detected Signature Proteins table (`*_detected_SP_withMEIds.csv`): list of the signature proteins detected by the tool and their possible assignment to an ICE or IME element. It is a comma separated table of 48 columns with a one line header. Each line represents a signature protein detected by ICEscreen.
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183 - Detected ICEs/IMEs table (`*_detected_ME.tsv`): list of the ICEs and IMEs elements detected by the tool, including information about the signature proteins they contain. It is a tab separated table of 21 columns, the header is at line #3. Information in this file is similar to the output file _withICEIMEIds.csv (option -m) but centered around a list of ICE / IME structures instead of a list of SPs.
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184 - 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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185
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186 Other optional and additional output files generated by ICEscreen:
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187
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188 - Annotated Genbank, EMBL, and GFF3 files: tose files contains the annotations of the original Genbank file in addition to annotations added by ICEscreen such as ICEscreen signature proteins and mobile elements.
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189 - All results zipped file: You can download this file locally and unzip it to have the complete output folder generated by the tool, including intermediate processing files. See https://icescreen.migale.inrae.fr for details.
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190 - Log file (`*_detected_ME.log`): this file contains the detailed internal details used by ICEscreen to generate the results and logs of each step of the ICEscreen tool pipeline.
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191
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192 ]]>
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193
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194 </help>
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195 <citations>
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196 <citation type="bibtex">@UNPUBLISHED{Kim07aninterior-point,
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197 author = {Julie Lao and Thomas Lacroix and Gérard Guédon and Charles Coluzzi and Nathalie Leblond-Bourget and Hélène Chiapello},
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198 title = {"See our latest publication at https://icescreen.migale.inrae.fr."}
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199 }
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200 </citation>
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201 </citations>
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202 </tool>