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comparison domestication.xml @ 10:c52967fb95da draft default tip

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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
author tduigou
date Tue, 27 May 2025 08:08:21 +0000
parents 450ed9dca5d5
children
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9:450ed9dca5d5 10:c52967fb95da
28 --allow_edits '$adv.allow_edits' 28 --allow_edits '$adv.allow_edits'
29 --output_dom 'output_zip.zip' 29 --output_dom 'output_zip.zip'
30 --output_gb_dom 'outdir_gb' 30 --output_gb_dom 'outdir_gb'
31 --output_methprot 'metoutdir_gb' 31 --output_methprot 'metoutdir_gb'
32 --methylation_protection '$methylation_protection' && 32 --methylation_protection '$methylation_protection' &&
33 cp 'output_zip.zip' '$output_zip' 33 cp 'output_zip.zip' '$domesticated_zip'
34 ]]></command> 34 ]]></command>
35 <inputs> 35 <inputs>
36 <param name="genbank_files" type="data_collection" collection_type="list" format="genbank" label="GenBank File(s)"/> 36 <param name="genbank_files" type="data_collection" collection_type="list" format="genbank" label="GenBank File(s)"/>
37 <param name="domestication_csv" type="data" format="csv" label="Deomestication csv"/> 37 <param name="domestication_csv" type="data" format="csv" label="Deomestication csv"/>
38 <param name="methylation_protection" type="boolean" checked="False" label="Enabel Methylation Protection"/> 38 <param name="methylation_protection" type="boolean" checked="False" label="Enabel Methylation Protection"/>
43 the domesticaton will fail for this sequence (and this will be noted in 43 the domesticaton will fail for this sequence (and this will be noted in
44 the report."/> 44 the report."/>
45 </section> 45 </section>
46 </inputs> 46 </inputs>
47 <outputs> 47 <outputs>
48 <data format="zip" name="output_zip" label="domestication results"/> 48 <data format="zip" name="domesticated_zip" label="domestication results"/>
49 <collection name="domesticated_gb" type="list" label="Domesticated GenBank Files"> 49 <collection name="domesticated_gb" type="list" label="Domesticated GenBank Files">
50 <filter>methylation_protection == False</filter> 50 <filter>methylation_protection == False</filter>
51 <discover_datasets pattern="(?P&lt;name&gt;.*).gb" format="genbank" directory="outdir_gb" /> 51 <discover_datasets pattern="(?P&lt;name&gt;.*).gb" format="genbank" directory="outdir_gb" />
52 </collection> 52 </collection>
53 <collection name="methprot_gb" type="list" label="GenBank Files methylation protected"> 53 <collection name="methprot_gb" type="list" label="GenBank Files methylation protected">
71 </param> 71 </param>
72 <param name="domestication_csv" value="EMMA.csv" /> 72 <param name="domestication_csv" value="EMMA.csv" />
73 <param name='methylation_protection' value='false' /> 73 <param name='methylation_protection' value='false' />
74 <param name="adv|use_file_names_as_ids" value="True" /> 74 <param name="adv|use_file_names_as_ids" value="True" />
75 <param name="adv|allow_edits" value="True" /> 75 <param name="adv|allow_edits" value="True" />
76 <output name="output_zip" ftype='zip'> 76 <output name="domesticated_zip" ftype='zip'>
77 <assert_contents> 77 <assert_contents>
78 <has_archive_member path=".*" n="24"/> 78 <has_archive_member path=".*" n="24"/>
79 <has_archive_member path="order_ids.csv"> 79 <has_archive_member path="order_ids.csv">
80 <has_n_lines n="8" /> 80 <has_n_lines n="8" />
81 </has_archive_member> 81 </has_archive_member>
134 </param> 134 </param>
135 <param name="domestication_csv" value="EMMA.csv" /> 135 <param name="domestication_csv" value="EMMA.csv" />
136 <param name="methylation_protection" value="true" /> 136 <param name="methylation_protection" value="true" />
137 <param name="adv|use_file_names_as_ids" value="True" /> 137 <param name="adv|use_file_names_as_ids" value="True" />
138 <param name="adv|allow_edits" value="True" /> 138 <param name="adv|allow_edits" value="True" />
139 <output name="output_zip" ftype='zip'> 139 <output name="domesticated_zip" ftype='zip'>
140 <assert_contents> 140 <assert_contents>
141 <has_archive_member path=".*" n="24"/> 141 <has_archive_member path=".*" n="24"/>
142 <has_archive_member path="order_ids.csv"> 142 <has_archive_member path="order_ids.csv">
143 <has_n_lines n="8" /> 143 <has_n_lines n="8" />
144 </has_archive_member> 144 </has_archive_member>