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annotate icescreen.xml @ 6:85c9849b429e draft

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planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit ebbb4da7c0c0176df539f9baa7c9323d9ff5f201
author iuc
date Tue, 31 Oct 2023 16:31:33 +0000
parents 28e82853c217
children d45c95f382d3
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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>
5
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4 <token name="@TOOL_VERSION@">1.2.0</token>
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85c9849b429e planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit ebbb4da7c0c0176df539f9baa7c9323d9ff5f201
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5 <token name="@VERSION_SUFFIX@">1</token>
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6 </macros>
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85c9849b429e planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit ebbb4da7c0c0176df539f9baa7c9323d9ff5f201
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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/${gbname}.gb
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22 && icescreen
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23 --galaxy
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24 --gbdir ./tmp_icescreen/source_genbank
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25 --outdir ./tmp_icescreen
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26 --mode '${taxonomy.mode}'
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27 --jobs "\${GALAXY_SLOTS:-4}" > ./tmp_icescreen/ICEscreen_log.txt 2>&1
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28
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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>
4
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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."/>
0
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52 <section name="taxonomy" title="Taxonomy of the genomes to analyse" expanded="False">
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53 <param name="mode" type="select" label="Firmicutes is the defaut parameter" help="Streptomyces is EXPERIMENTAL and is NOT recommended.">
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54 <option value="firmicutes" selected="true">Firmicutes</option>
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55 <option value="streptomyces">Streptomyces</option>
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56 </param>
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57 </section>
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58 <section name="additional_output" title="Additional output files" expanded="False">
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59 <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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60 <option value="output_annotation_genbank">Genome annotation in genbank format</option>
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61 <option value="output_annotation_gff">Genome annotation in gff format</option>
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62 <option value="output_annotation_embl">Genome annotation in embl format</option>
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63 <option value="output_zip_all_files">Zip of all final and intermediate results</option>
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64 <option value="output_log">ICEscreen log</option>
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65 </param>
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66 </section>
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67 </inputs>
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68 <outputs>
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69 <data format="tabular" name="detected_sp" label="${tool.name} on ${on_string}: Signature Proteins table" />
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70 <data format="tabular" name="detected_me" label="${tool.name} on ${on_string}: ICEs/IMEs table" />
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71 <data format="txt" name="summary" label="${tool.name} on ${on_string}: results summary" />
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72 <data format="genbank" name="gbout" label="${tool.name} on ${on_string}: annotated genbank" >
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73 <filter>additional_output['optional_files'] and "output_annotation_genbank" in additional_output['optional_files']</filter>
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74 </data>
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75 <data format="gff3" name="gffout" label="${tool.name} on ${on_string}: annotated GFF3" >
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76 <filter>additional_output['optional_files'] and "output_annotation_gff" in additional_output['optional_files']</filter>
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77 </data>
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78 <data format="embl" name="emblout" label="${tool.name} on ${on_string}: annotated EMBL" >
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79 <filter>additional_output['optional_files'] and "output_annotation_embl" in additional_output['optional_files']</filter>
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80 </data>
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81 <data format="zip" name="outzip" label="${tool.name} on ${on_string}: all results zipped">
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82 <filter>additional_output['optional_files'] and "output_zip_all_files" in additional_output['optional_files']</filter>
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83 </data>
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84 <data format="txt" name="log" label="${tool.name} on ${on_string}: log file" >
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85 <filter>additional_output['optional_files'] and "output_log" in additional_output['optional_files']</filter>
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86 </data>
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87 </outputs>
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88 <tests>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
89 <test expect_num_outputs="3">
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
90 <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
91 <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
92 <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
93 <output name="detected_sp" >
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
94 <assert_contents>
3
2bb38197ff75 planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit 29cbe5a71212ff13e8d63e9ea57243fd0aeacbf9
iuc
parents: 2
diff changeset
95 <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
96 <has_text text="WP_002359295" />
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
97 <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
98 <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
99 <has_n_lines n="5" />
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
100 </assert_contents>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
101 </output>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
102 </test>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
103 <test expect_num_outputs="4">
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
104 <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
105 <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
106 <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
107 </test>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
108 <test expect_num_outputs="4">
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
109 <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
110 <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
111 <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
112 </test>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
113 <test expect_num_outputs="4">
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
114 <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
115 <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
116 <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
117 </test>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
118 <test expect_num_outputs="4">
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
119 <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
120 <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
121 <output name="outzip" >
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
122 <assert_contents>
3
2bb38197ff75 planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit 29cbe5a71212ff13e8d63e9ea57243fd0aeacbf9
iuc
parents: 2
diff changeset
123 <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
124 </assert_contents>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
125 </output>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
126 </test>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
127 <test expect_num_outputs="4">
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
128 <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
129 <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
130 <output name="log" >
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
131 <assert_contents>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
132 <has_text text="firmicutes" />
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
133 <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
134 <has_text text="Complete log" />
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
135 <not_has_text text="Error" />
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
136 </assert_contents>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
137 </output>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
138 </test>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
139 <test expect_num_outputs="4">
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
140 <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
141 <param name="mode" value="streptomyces" />
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
142 <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
143 <output name="log" >
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
144 <assert_contents>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
145 <has_text text="streptomyces" />
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
146 <not_has_text text="Error" />
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
147 </assert_contents>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
148 </output>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
149 </test>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
150 <test expect_num_outputs="5">
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
151 <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
152 <param name="mode" value="firmicutes" />
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
153 <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
154 <output name="log" >
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
155 <assert_contents>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
156 <has_text text="firmicutes" />
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
157 <not_has_text text="Error" />
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
158 </assert_contents>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
159 </output>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
160 </test>
4
c5f7c311f1b0 planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit a9bc15365abc70c0367d732b790763d8fa53b220
iuc
parents: 3
diff changeset
161 <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
162 <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
163 <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
164 <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
165 <output name="detected_sp" >
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 <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
168 <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
169 <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
170 </assert_contents>
c5f7c311f1b0 planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit a9bc15365abc70c0367d732b790763d8fa53b220
iuc
parents: 3
diff changeset
171 </output>
c5f7c311f1b0 planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit a9bc15365abc70c0367d732b790763d8fa53b220
iuc
parents: 3
diff changeset
172 </test>
0
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
173 </tests>
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
174 <help><![CDATA[
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
175 .. class:: warningmark
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
176
3
2bb38197ff75 planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit 29cbe5a71212ff13e8d63e9ea57243fd0aeacbf9
iuc
parents: 2
diff changeset
177 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
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
7c77b2896ac2 "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
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181 **What it does**
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182
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183 ICEscreen is a bioinformatic pipeline for the detection and annotation of ICEs (Integrative and Conjugative Elements) and IMEs (Integrative and Mobilizable Elements) in Firmicutes genomes. The full documentation is available at https://icescreen.migale.inrae.fr. The forge of the project is accessible at https://forgemia.inra.fr/ices_imes_analysis/icescreen.
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184
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185 **Main features of ICEscreen**
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186
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187 - Detection of signature proteins (SPs) of ICEs/IMEs by using blastP on a curated resource. BlastP allows for an accurate assignment of hits to a given ICE/IME superfamily or family. The curated resource was derived from an analysis of over 120 ICEs and IMEs in Streptococcus genomes by the DINAMIC lab.
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188 - Detection of distant homologs of SPs by using HMM profiles of ICEs/IMEs protein families. The HMM profiles have been either imported from trusted resources or created and curated when needed.
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189 - 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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190 - Delimitation of the elements at the gene or nucleotide level is not yet implemented and still needs manual curation.
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191
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192 **Output files**
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193
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194 There are 3 main output results files generated by ICEscreen:
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195
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196 - Detected Signature Proteins table (`*_detected_SP_withMEIds.csv`): list of the signature proteins detected by the tool and their possible assignment to an ICE or IME element. It is a comma separated table of 48 columns with a one line header. Each line represents a signature protein detected by ICEscreen.
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197 - Detected ICEs/IMEs table (`*_detected_ME.tsv`): list of the ICEs and IMEs elements detected by the tool, including information about the signature proteins they contain. It is a tab separated table of 21 columns, the header is at line #3. Information in this file is similar to the output file _withICEIMEIds.csv (option -m) but centered around a list of ICE / IME structures instead of a list of SPs.
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198 - 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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199
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200 Other optional and additional output files generated by ICEscreen:
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201
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202 - Annotated Genbank, EMBL, and GFF3 files: tose files contains the annotations of the original Genbank file in addition to annotations added by ICEscreen such as ICEscreen signature proteins and mobile elements.
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203 - 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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204 - 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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205
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206 ]]>
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207
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208 </help>
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209 <citations>
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210 <citation type="bibtex">@UNPUBLISHED{Kim07aninterior-point,
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211 author = {Julie Lao and Thomas Lacroix and Gérard Guédon and Charles Coluzzi and Nathalie Leblond-Bourget and Hélène Chiapello},
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212 title = {"See our latest publication at https://icescreen.migale.inrae.fr."}
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213 }
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214 </citation>
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215 </citations>
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216 </tool>