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annotate icescreen.xml @ 5:6262a9977181 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/icescreen commit c45c31257dbfd6991c86cee56bb8961e4c5cbe47
author iuc
date Sun, 23 Feb 2025 16:52:24 +0000
parents 49bf81065a47
children
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1 <tool id="icescreen" name="ICEscreen" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.09">
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2 <description>annotates ICEs and IMEs in Bacillota genomes</description>
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3
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="xrefs"/>
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8 <expand macro="requirements"/>
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9
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10 <version_command><![CDATA[
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11 icescreen --version
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12 ]]>
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13 </version_command>
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14 <command detect_errors="aggressive"><![CDATA[
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15 #set $gbname = 'galaxy_genbank'
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16 mkdir -p ./tmp_icescreen/source_genbank
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17 && mkdir -p ./tmp_icescreen/icescreen_result
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18 && ln -s '${genome}' ./tmp_icescreen/source_genbank/${gbname}.gb
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19 && icescreen
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20 --galaxy
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21 --gbdir ./tmp_icescreen/source_genbank
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22 --outdir ./tmp_icescreen/icescreen_result
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23 --phylum '${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_result/ICEscreen_results/${gbname}/detected_mobile_elements/${gbname}_detected_ME.summary > '${summary}'
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27 && cat ./tmp_icescreen/icescreen_result/ICEscreen_results/${gbname}/detected_mobile_elements/${gbname}_detected_SP_withMEIds.tsv > '${detected_sp}'
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28 && cat ./tmp_icescreen/icescreen_result/ICEscreen_results/${gbname}/detected_mobile_elements/${gbname}_detected_ME.tsv > '${detected_me}'
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30 ]]>
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31 </command>
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32 <inputs>
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33 <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 nucleotide sequence."/>
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34 <section name="taxonomy" title="Phylum of the genomes to analyse" expanded="True">
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35 <param name="phylum" type="select" label="Bacillota is the defaut parameter">
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36 <option value="bacillota" selected="true">Bacillota</option>
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37 </param>
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38 </section>
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39 <section name="additional_output" title="Additional output files" expanded="False">
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40 <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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41 <option value="output_annotation_genbank" selected="false">Annotation in genbank format (full)</option>
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42 <option value="output_annotation_gff" selected="false">Annotation in gff format (ICEs and IMEs only)</option>
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43 <option value="output_annotation_embl" selected="false">Annotation in embl format (ICEs and IMEs only)</option>
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44 <option value="output_tar_gz_intermediate_files" selected="false">Archive of intermediate files</option>
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45 <option value="output_log" selected="false">Log file</option>
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46 <option value="output_param_conf" selected="false">Param conf file</option>
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47 </param>
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48 </section>
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49 </inputs>
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50 <outputs>
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51 <data format="tabular" name="detected_sp" label="${tool.name} on ${on_string}: Signature Proteins table" />
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52 <data format="tabular" name="detected_me" label="${tool.name} on ${on_string}: ICEs/IMEs table" />
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53 <data format="txt" name="summary" label="${tool.name} on ${on_string}: results summary" />
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54 <data format="genbank.gz" name="gbout" from_work_dir="./tmp_icescreen/icescreen_result/ICEscreen_results/galaxy_genbank/detected_mobile_elements/standard_genome_annotation_formats/galaxy_genbank_icescreen.gb.gz" label="${tool.name} on ${on_string}: genbank annotation (full)" >
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55 <filter>additional_output['optional_files'] and "output_annotation_genbank" in additional_output['optional_files']</filter>
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56 </data>
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57 <data format="gff3.gz" name="gffout" from_work_dir="./tmp_icescreen/icescreen_result/ICEscreen_results/galaxy_genbank/detected_mobile_elements/standard_genome_annotation_formats/galaxy_genbank_icescreen.gff.gz" label="${tool.name} on ${on_string}: GFF3 annotation (ICEs and IMEs only)" >
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58 <filter>additional_output['optional_files'] and "output_annotation_gff" in additional_output['optional_files']</filter>
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59 </data>
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60 <data format="embl.gz" name="emblout" from_work_dir="./tmp_icescreen/icescreen_result/ICEscreen_results/galaxy_genbank/detected_mobile_elements/standard_genome_annotation_formats/galaxy_genbank_icescreen.embl.gz" label="${tool.name} on ${on_string}: EMBL annotation (ICEs and IMEs only)" >
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61 <filter>additional_output['optional_files'] and "output_annotation_embl" in additional_output['optional_files']</filter>
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62 </data>
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63 <data format="tar.gz" name="intermediate_tar_gz" from_work_dir="./tmp_icescreen/icescreen_result/ICEscreen_results/galaxy_genbank/tmp_intermediate_files.tar.gz" label="${tool.name} on ${on_string}: intermediate files archive">
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64 <filter>additional_output['optional_files'] and "output_tar_gz_intermediate_files" in additional_output['optional_files']</filter>
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65 </data>
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66 <data format="txt" name="log" from_work_dir="./tmp_icescreen/ICEscreen_log.txt" label="${tool.name} on ${on_string}: log file" >
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67 <filter>additional_output['optional_files'] and "output_log" in additional_output['optional_files']</filter>
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68 </data>
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69 <data format="gz" name="param_conf" from_work_dir="./tmp_icescreen/icescreen_result/ICEscreen_results/galaxy_genbank/param.conf.gz" label="${tool.name} on ${on_string}: param conf file" >
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70 <filter>additional_output['optional_files'] and "output_param_conf" in additional_output['optional_files']</filter>
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71 </data>
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72 </outputs>
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73 <tests>
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74 <test expect_num_outputs="3">
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75 <param name="genome" value="genbank/NC_004668_137848_164286.gb" ftype="genbank" />
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76 <output name="summary" file="NC_004668_137848_164286_detected_ME.summary" ftype="txt" />
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77 <output name="detected_me" file="NC_004668_137848_164286_detected_ME.tsv" ftype="tabular" />
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78 <output name="detected_sp" >
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79 <assert_contents>
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80 <has_text text="ICE_IME_id" />
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81 <has_text text="WP_002359295" />
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82 <has_text text="VirB4" />
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83 <has_n_columns n="54" />
0
d72ff95846ca "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
84 <has_n_lines n="5" />
d72ff95846ca "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
85 </assert_contents>
d72ff95846ca "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
86 </output>
d72ff95846ca "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
87 </test>
d72ff95846ca "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
88 <test expect_num_outputs="4">
d72ff95846ca "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
89 <param name="genome" value="genbank/NC_004668_137848_164286.gb" ftype="genbank" />
d72ff95846ca "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
90 <param name="optional_files" value="output_annotation_genbank" />
5
6262a9977181 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/icescreen commit c45c31257dbfd6991c86cee56bb8961e4c5cbe47
iuc
parents: 4
diff changeset
91 <output name="gbout" ftype="genbank.gz">
6262a9977181 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/icescreen commit c45c31257dbfd6991c86cee56bb8961e4c5cbe47
iuc
parents: 4
diff changeset
92 <assert_contents>
6262a9977181 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/icescreen commit c45c31257dbfd6991c86cee56bb8961e4c5cbe47
iuc
parents: 4
diff changeset
93 <has_size value="19794" delta="100"/>
6262a9977181 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/icescreen commit c45c31257dbfd6991c86cee56bb8961e4c5cbe47
iuc
parents: 4
diff changeset
94 </assert_contents>
6262a9977181 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/icescreen commit c45c31257dbfd6991c86cee56bb8961e4c5cbe47
iuc
parents: 4
diff changeset
95 </output>
0
d72ff95846ca "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
96 </test>
d72ff95846ca "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
97 <test expect_num_outputs="4">
d72ff95846ca "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
98 <param name="genome" value="genbank/NC_004668_137848_164286.gb" ftype="genbank" />
d72ff95846ca "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
99 <param name="optional_files" value="output_annotation_gff" />
5
6262a9977181 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/icescreen commit c45c31257dbfd6991c86cee56bb8961e4c5cbe47
iuc
parents: 4
diff changeset
100 <output name="gffout" ftype="gff3.gz">
6262a9977181 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/icescreen commit c45c31257dbfd6991c86cee56bb8961e4c5cbe47
iuc
parents: 4
diff changeset
101 <assert_contents>
6262a9977181 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/icescreen commit c45c31257dbfd6991c86cee56bb8961e4c5cbe47
iuc
parents: 4
diff changeset
102 <has_size value="794" delta="100"/>
6262a9977181 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/icescreen commit c45c31257dbfd6991c86cee56bb8961e4c5cbe47
iuc
parents: 4
diff changeset
103 </assert_contents>
6262a9977181 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/icescreen commit c45c31257dbfd6991c86cee56bb8961e4c5cbe47
iuc
parents: 4
diff changeset
104 </output>
0
d72ff95846ca "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
105 </test>
d72ff95846ca "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
106 <test expect_num_outputs="4">
d72ff95846ca "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
107 <param name="genome" value="genbank/NC_004668_137848_164286.gb" ftype="genbank" />
d72ff95846ca "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
108 <param name="optional_files" value="output_annotation_embl" />
5
6262a9977181 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/icescreen commit c45c31257dbfd6991c86cee56bb8961e4c5cbe47
iuc
parents: 4
diff changeset
109 <output name="emblout" ftype="embl.gz">
6262a9977181 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/icescreen commit c45c31257dbfd6991c86cee56bb8961e4c5cbe47
iuc
parents: 4
diff changeset
110 <assert_contents>
6262a9977181 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/icescreen commit c45c31257dbfd6991c86cee56bb8961e4c5cbe47
iuc
parents: 4
diff changeset
111 <has_size value="1002" delta="100"/>
6262a9977181 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/icescreen commit c45c31257dbfd6991c86cee56bb8961e4c5cbe47
iuc
parents: 4
diff changeset
112 </assert_contents>
6262a9977181 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/icescreen commit c45c31257dbfd6991c86cee56bb8961e4c5cbe47
iuc
parents: 4
diff changeset
113 </output>
0
d72ff95846ca "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
114 </test>
d72ff95846ca "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
115 <test expect_num_outputs="4">
d72ff95846ca "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" />
5
6262a9977181 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/icescreen commit c45c31257dbfd6991c86cee56bb8961e4c5cbe47
iuc
parents: 4
diff changeset
117 <param name="optional_files" value="output_tar_gz_intermediate_files" />
6262a9977181 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/icescreen commit c45c31257dbfd6991c86cee56bb8961e4c5cbe47
iuc
parents: 4
diff changeset
118 <output name="intermediate_tar_gz" >
0
d72ff95846ca "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
119 <assert_contents>
5
6262a9977181 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/icescreen commit c45c31257dbfd6991c86cee56bb8961e4c5cbe47
iuc
parents: 4
diff changeset
120 <has_archive_member path=".*/*_detected_SP.tsv"><has_text text="Is_hit_blast" /></has_archive_member>
0
d72ff95846ca "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
121 </assert_contents>
d72ff95846ca "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
122 </output>
d72ff95846ca "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
123 </test>
d72ff95846ca "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
124 <test expect_num_outputs="4">
d72ff95846ca "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
125 <param name="genome" value="genbank/NC_004668_137848_164286.gb" ftype="genbank" />
d72ff95846ca "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
126 <param name="optional_files" value="output_log" />
d72ff95846ca "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
127 <output name="log" >
d72ff95846ca "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
128 <assert_contents>
5
6262a9977181 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/icescreen commit c45c31257dbfd6991c86cee56bb8961e4c5cbe47
iuc
parents: 4
diff changeset
129 <has_text text="bacillota" />
0
d72ff95846ca "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
130 <has_text text="Building DAG of jobs" />
d72ff95846ca "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
131 <has_text text="Complete log" />
d72ff95846ca "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
132 <not_has_text text="Error" />
d72ff95846ca "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
133 </assert_contents>
d72ff95846ca "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
134 </output>
d72ff95846ca "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
135 </test>
d72ff95846ca "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
136 <test expect_num_outputs="4">
d72ff95846ca "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
137 <param name="genome" value="genbank/NC_004668_137848_164286.gb" ftype="genbank" />
5
6262a9977181 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/icescreen commit c45c31257dbfd6991c86cee56bb8961e4c5cbe47
iuc
parents: 4
diff changeset
138 <param name="phylum" value="bacillota" />
0
d72ff95846ca "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
139 <param name="optional_files" value="output_log" />
d72ff95846ca "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
140 <output name="log" >
d72ff95846ca "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
141 <assert_contents>
5
6262a9977181 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/icescreen commit c45c31257dbfd6991c86cee56bb8961e4c5cbe47
iuc
parents: 4
diff changeset
142 <has_text text="bacillota" />
0
d72ff95846ca "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
143 <not_has_text text="Error" />
d72ff95846ca "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
144 </assert_contents>
d72ff95846ca "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
145 </output>
d72ff95846ca "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
146 </test>
5
6262a9977181 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/icescreen commit c45c31257dbfd6991c86cee56bb8961e4c5cbe47
iuc
parents: 4
diff changeset
147 <test expect_num_outputs="6">
0
d72ff95846ca "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
148 <param name="genome" value="genbank/NC_004668_137848_164286.gb" ftype="genbank" />
5
6262a9977181 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/icescreen commit c45c31257dbfd6991c86cee56bb8961e4c5cbe47
iuc
parents: 4
diff changeset
149 <param name="phylum" value="bacillota" />
6262a9977181 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/icescreen commit c45c31257dbfd6991c86cee56bb8961e4c5cbe47
iuc
parents: 4
diff changeset
150 <param name="optional_files" value="output_tar_gz_intermediate_files,output_log,output_param_conf" />
0
d72ff95846ca "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
151 <output name="log" >
d72ff95846ca "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
152 <assert_contents>
5
6262a9977181 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/icescreen commit c45c31257dbfd6991c86cee56bb8961e4c5cbe47
iuc
parents: 4
diff changeset
153 <has_text text="bacillota" />
0
d72ff95846ca "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
154 <not_has_text text="Error" />
d72ff95846ca "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
155 </assert_contents>
d72ff95846ca "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
156 </output>
d72ff95846ca "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
157 </test>
3
0d38ba6112be planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit a9bc15365abc70c0367d732b790763d8fa53b220
iuc
parents: 2
diff changeset
158 <test expect_num_outputs="3">
0d38ba6112be planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit a9bc15365abc70c0367d732b790763d8fa53b220
iuc
parents: 2
diff changeset
159 <param name="genome" value="genbank/NC_013798_298468_322494_NC_020450_643089_661957.gb" ftype="genbank" />
0d38ba6112be planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit a9bc15365abc70c0367d732b790763d8fa53b220
iuc
parents: 2
diff changeset
160 <output name="summary" file="NC_013798_298468_322494_NC_020450_643089_661957_detected_ME.summary" ftype="txt" />
0d38ba6112be planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit a9bc15365abc70c0367d732b790763d8fa53b220
iuc
parents: 2
diff changeset
161 <output name="detected_me" file="NC_013798_298468_322494_NC_020450_643089_661957_detected_ME.tsv" ftype="tabular" />
0d38ba6112be planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit a9bc15365abc70c0367d732b790763d8fa53b220
iuc
parents: 2
diff changeset
162 <output name="detected_sp" >
0d38ba6112be planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit a9bc15365abc70c0367d732b790763d8fa53b220
iuc
parents: 2
diff changeset
163 <assert_contents>
0d38ba6112be planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit a9bc15365abc70c0367d732b790763d8fa53b220
iuc
parents: 2
diff changeset
164 <has_text text="ICE_IME_id" />
0d38ba6112be planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit a9bc15365abc70c0367d732b790763d8fa53b220
iuc
parents: 2
diff changeset
165 <has_text text="WP_044555479.1" />
0d38ba6112be planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit a9bc15365abc70c0367d732b790763d8fa53b220
iuc
parents: 2
diff changeset
166 <has_text text="WP_015426013.1" />
0d38ba6112be planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit a9bc15365abc70c0367d732b790763d8fa53b220
iuc
parents: 2
diff changeset
167 </assert_contents>
0d38ba6112be planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit a9bc15365abc70c0367d732b790763d8fa53b220
iuc
parents: 2
diff changeset
168 </output>
0d38ba6112be planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit a9bc15365abc70c0367d732b790763d8fa53b220
iuc
parents: 2
diff changeset
169 </test>
0
d72ff95846ca "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
170 </tests>
d72ff95846ca "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
171 <help><![CDATA[
d72ff95846ca "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
172 .. class:: warningmark
d72ff95846ca "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
173
5
6262a9977181 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/icescreen commit c45c31257dbfd6991c86cee56bb8961e4c5cbe47
iuc
parents: 4
diff changeset
174 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 nucleotide sequence.
0
d72ff95846ca "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
175
d72ff95846ca "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
176 -----
d72ff95846ca "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
iuc
parents:
diff changeset
177
d72ff95846ca "planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit e77a58fd03abe136aca7b79db16be4644520bb64"
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178 **What it does**
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179
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180 ICEscreen is a bioinformatic pipeline for the detection and annotation of ICEs (Integrative and Conjugative Elements) and IMEs (Integrative and Mobilizable Elements) in Bacillota genomes. The full documentation is available at https://icescreen.migale.inrae.fr. The forge of the project is accessible at https://forgemia.inra.fr/ices_imes_analysis/icescreen.
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181
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182 **Main features of ICEscreen**
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183
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184 - 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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185 - 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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186 - 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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187 - Delimitation of the elements at the gene or nucleotide level is not yet implemented and still needs manual curation.
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188
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189 **Output files**
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190
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191 There are 3 main output results files generated by ICEscreen:
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192
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193 - 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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194 - 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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195 - 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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196
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197 Other optional and additional output files generated by ICEscreen:
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198
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199 - Genbank annotation file (full): annotations of the original Genbank file as well as annotations of ICEscreen on ICEs, IMEs, and the detected signature proteins.
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200 - EMBL and GFF3 annotation files (ICEs and IMEs only): annotations of ICEscreen on ICEs, IMEs, and the detected signature proteins.
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201 - Intermediate files (tar.gz): You can download this file locally and uncompress it to have the intermediate files generated by the tool. See https://icescreen.migale.inrae.fr for details.
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202 - Log file (`*_detected_ME.log`): this file contains the log of each step of the ICEscreen pipeline.
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203 - Param conf file (`param.conf.gz`): this file contains the configuration parameters related to the ICEscreen run.
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204
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205 ]]>
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206
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207 </help>
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208
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209 <expand macro="citation"/>
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210
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211 </tool>