Mercurial > repos > mgarnier > pangenome_cog_analysis

comparison pangenomeCogAnalysis.xml @ 3:27c5a6f2301c draft

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author mgarnier
date Fri, 02 Jul 2021 14:54:40 +0000
parents 731fb6cb324b
children 3f4e4e7d77ff
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2:0428ce25da81 3:27c5a6f2301c
14 #set $_input_file = "'{}'".format($input_file.element_identifier) 14 #set $_input_file = "'{}'".format($input_file.element_identifier)
15 ln -s '${input_file}' ${_input_file} && 15 ln -s '${input_file}' ${_input_file} &&
16 #set $named_input_files = $named_input_files + ',' + $_input_file 16 #set $named_input_files = $named_input_files + ',' + $_input_file
17 #end for 17 #end for
18 18
19 perl ${__tool_directory__}/pangenomeCogAnalysis_V1.pl $input $input2 $named_input_files $input_files $gff_files order $output $output2 $output3 $output4 $output5 19 perl ${__tool_directory__}/pangenomeCogAnalysis_V1.pl $input $input2 $named_input_files $input_files $gff_files order $output $output2 $output3 $output4
20
20 ]]></command> 21 ]]></command>
21 22
22 23
23 24
24 <inputs> 25 <inputs>
32 <outputs> 33 <outputs>
33 <data format="txt" name="output" label="List of group-specific clusters"/> 34 <data format="txt" name="output" label="List of group-specific clusters"/>
34 <data format="tabular" name="output2" label="COG category count average per group"/> 35 <data format="tabular" name="output2" label="COG category count average per group"/>
35 <data format="tabular" name="output3" label="Detailed COG category count values per group"/> 36 <data format="tabular" name="output3" label="Detailed COG category count values per group"/>
36 <data format="tabular" name="output4" label="COG category count average"/> 37 <data format="tabular" name="output4" label="COG category count average"/>
37 <data format="tabular" name="output5" label="Core-genes coordinates"/> 38 <!--<data format="tabular" name="output5" label="Core-genes coordinates"/>-->
39 <collection name="output5" type="list" label="Core-genes coordinates">
40 <discover_datasets pattern="__name_and_ext__" directory="Core" />
41 </collection>
42 <collection name="output6" type="list" label="Group specific genes coordinates">
43 <discover_datasets pattern="__name_and_ext__" directory="GroupSpecific" />
44 </collection>
38 </outputs> 45 </outputs>
39 46
40 </tool> 47 </tool>