Mercurial > repos > gga > apollo_feat_from_gff3

comparison create_features_from_gff3.xml @ 13:bb562d95b6cd draft

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"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 7bf18c69becc57152efdadedf7ebd0bcfa382a15"
author gga
date Mon, 29 Jun 2020 09:17:58 -0400
parents 5d1cf95ade8a
children 250745643de2
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12:d022c003c7a3 13:bb562d95b6cd
13 @ORG_OR_GUESS@ 13 @ORG_OR_GUESS@
14 14
15 '$__user_email__' 15 '$__user_email__'
16 '$gff3_data' 16 '$gff3_data'
17 --source '${__app__.config.galaxy_infrastructure_url}/history/view/${__app__.security.encode_id($gff3_data.history_id)}' 17 --source '${__app__.config.galaxy_infrastructure_url}/history/view/${__app__.security.encode_id($gff3_data.history_id)}'
18 $use_name
19 $disable_cds_recalculation
18 20
19 > '$output']]></command> 21 > '$output']]></command>
20 <inputs> 22 <inputs>
21 <expand macro="org_or_guess" /> 23 <expand macro="org_or_guess" />
22 <expand macro="gff3_input" /> 24 <expand macro="gff3_input" />
25 <param name="use_name" type="boolean" truevalue="--user_name" falsevalue="" label="Use the given name instead of generating one" />
26 <param name="disable_cds_recalculation" type="boolean" truevalue="--disable_cds_recalculation" falsevalue="" label="Disable CDS recalculation and instead use the one provided" />
23 </inputs> 27 </inputs>
24 <outputs> 28 <outputs>
25 <data format="tabular" name="output" label="Process and Error Log"> 29 <data format="txt" name="output" label="Process and Error Log"/>
26 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" format="tabular" visible="true"/>
27 </data>
28 </outputs> 30 </outputs>
29 <tests> 31 <tests>
30 <test> 32 <test>
31 <conditional name="org_source"> 33 <conditional name="org_source">
32 <param name="source_select" value="direct"/> 34 <param name="source_select" value="direct"/>
33 <param name="org_raw" value="Test org" /> 35 <param name="org_raw" value="Test org" />
34 </conditional> 36 </conditional>
35 <param name="gff3_data" value="merlin.gff"/> 37 <param name="gff3_data" value="merlin.gff"/>
36 <output name="output" file="load_gff3/output.tsv" compare="sim_size"/> 38 <output name="output" file="load_gff3/output.txt" compare="sim_size"/>
37 </test> 39 </test>
38 </tests> 40 </tests>
39 <help><![CDATA[ 41 <help><![CDATA[
40 **NOTA BENE**
41
42 This is **incredibly, highly experimental**
43
44 DO NOT:
45
46 - Run on gff3 referencing multiple reference sequences/contigs
47 - Expect it to work well
48 - Expect it to work at all
49
50 @REFERENCES@ 42 @REFERENCES@
51 ]]></help> 43 ]]></help>
52 <expand macro="citations"/> 44 <expand macro="citations"/>
53 </tool> 45 </tool>