Mercurial > repos > iuc > icescreen

comparison icescreen.xml @ 4:c5f7c311f1b0 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit a9bc15365abc70c0367d732b790763d8fa53b220
author iuc
date Tue, 28 Feb 2023 14:10:38 +0000
parents 2bb38197ff75
children 28e82853c217
comparison
equal deleted inserted replaced
3:2bb38197ff75 4:c5f7c311f1b0
1 <tool id="icescreen" name="ICEscreen" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.09"> 1 <tool id="icescreen" name="ICEscreen" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.09">
2 <description>detects and annotates ICEs (Integrative and Conjugative Elements) and IMEs (Integrative and Mobilizable Elements) in Firmicutes genomes.</description> 2 <description>detects and annotates ICEs (Integrative and Conjugative Elements) and IMEs (Integrative and Mobilizable Elements) in Firmicutes genomes.</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">1.1.0</token> 4 <token name="@TOOL_VERSION@">1.1.1</token>
5 <token name="@VERSION_SUFFIX@">0</token> 5 <token name="@VERSION_SUFFIX@">0</token>
6 </macros> 6 </macros>
7 <requirements> 7 <requirements>
8 <requirement type="package" version="@TOOL_VERSION@">icescreen</requirement> 8 <requirement type="package" version="@TOOL_VERSION@">icescreen</requirement>
9 <requirement type="package" version="3.0">zip</requirement> 9 <requirement type="package" version="3.0">zip</requirement>
43 && cd ./tmp_icescreen/ICEscreen_results/results/${gbname} && zip --quiet -r - -- . > '${outzip}' 43 && cd ./tmp_icescreen/ICEscreen_results/results/${gbname} && zip --quiet -r - -- . > '${outzip}'
44 #end if 44 #end if
45 ]]> 45 ]]>
46 </command> 46 </command>
47 <inputs> 47 <inputs>
48 <param name="genome" type="data" format="genbank" label="Input genomes to analyze in Genbank format" help="Each Genbank file can only contain ONE record, multi-genbank files are not supported. Each Genbank file must include the ORIGIN nucleotide sequence at the end"/> 48 <param name="genome" type="data" format="genbank" label="Input genomes to analyze in Genbank format" help="Multi-genbank files (i.e. gbff) are supported. Each record must include the ORIGIN nucleotide sequence at the end."/>
49 <section name="taxonomy" title="Taxonomy of the genomes to analyse" expanded="False"> 49 <section name="taxonomy" title="Taxonomy of the genomes to analyse" expanded="False">
50 <param name="mode" type="select" label="Firmicutes is the defaut parameter" help="Streptomyces is EXPERIMENTAL and is NOT recommended."> 50 <param name="mode" type="select" label="Firmicutes is the defaut parameter" help="Streptomyces is EXPERIMENTAL and is NOT recommended.">
51 <option value="firmicutes" selected="true">Firmicutes</option> 51 <option value="firmicutes" selected="true">Firmicutes</option>
52 <option value="streptomyces">Streptomyces</option> 52 <option value="streptomyces">Streptomyces</option>
53 </param> 53 </param>
113 <output name="emblout" file="NC_004668_137848_164286_icescreen.embl" ftype="embl" /> 113 <output name="emblout" file="NC_004668_137848_164286_icescreen.embl" ftype="embl" />
114 </test> 114 </test>
115 <test expect_num_outputs="4"> 115 <test expect_num_outputs="4">
116 <param name="genome" value="genbank/NC_004668_137848_164286.gb" ftype="genbank" /> 116 <param name="genome" value="genbank/NC_004668_137848_164286.gb" ftype="genbank" />
117 <param name="optional_files" value="output_zip_all_files" /> 117 <param name="optional_files" value="output_zip_all_files" />
118
119 <output name="outzip" > 118 <output name="outzip" >
120 <assert_contents> 119 <assert_contents>
121 <has_archive_member path=".*/*_detected_SP_withMEIds.tsv"><has_text text="ICE_IME_id" /></has_archive_member> 120 <has_archive_member path=".*/*_detected_SP_withMEIds.tsv"><has_text text="ICE_IME_id" /></has_archive_member>
122 </assert_contents> 121 </assert_contents>
123 </output> 122 </output>
151 <param name="optional_files" value="output_zip_all_files,output_log" /> 150 <param name="optional_files" value="output_zip_all_files,output_log" />
152 <output name="log" > 151 <output name="log" >
153 <assert_contents> 152 <assert_contents>
154 <has_text text="firmicutes" /> 153 <has_text text="firmicutes" />
155 <not_has_text text="Error" /> 154 <not_has_text text="Error" />
155 </assert_contents>
156 </output>
157 </test>
158 <test expect_num_outputs="3">
159 <param name="genome" value="genbank/NC_013798_298468_322494_NC_020450_643089_661957.gb" ftype="genbank" />
160 <output name="summary" file="NC_013798_298468_322494_NC_020450_643089_661957_detected_ME.summary" ftype="txt" />
161 <output name="detected_me" file="NC_013798_298468_322494_NC_020450_643089_661957_detected_ME.tsv" ftype="tabular" />
162 <output name="detected_sp" >
163 <assert_contents>
164 <has_text text="ICE_IME_id" />
165 <has_text text="WP_044555479.1" />
166 <has_text text="WP_015426013.1" />
156 </assert_contents> 167 </assert_contents>
157 </output> 168 </output>
158 </test> 169 </test>
159 </tests> 170 </tests>
160 <help><![CDATA[ 171 <help><![CDATA[