Mercurial > repos > mgarnier > pangenome_cog_analysis

comparison pangenomeCogAnalysis.xml @ 15:ae68b2a86229 draft

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author mgarnier
date Thu, 19 Aug 2021 13:39:39 +0000
parents 9ac1a58fda89
children 3b12b1b1d67f
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14:ef012cfc41e8 15:ae68b2a86229
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 $input_files $named_input_files $gff_files $output $output2 $output3 $output4 19 perl ${__tool_directory__}/pangenomeCogAnalysis_V1.pl $input $input2 $input_files $named_input_files $gff_files $output $output2 $output3 $output4 $output8 $output9
20 20
21 ]]></command> 21 ]]></command>
22 22
23 23
24 24
43 <discover_datasets pattern="__name_and_ext__" directory="GroupSpecific" /> 43 <discover_datasets pattern="__name_and_ext__" directory="GroupSpecific" />
44 </collection> 44 </collection>
45 <collection name="output7" type="list" label="Strain specific genes coordinates"> 45 <collection name="output7" type="list" label="Strain specific genes coordinates">
46 <discover_datasets pattern="__name_and_ext__" directory="StrainSpecific" /> 46 <discover_datasets pattern="__name_and_ext__" directory="StrainSpecific" />
47 </collection> 47 </collection>
48 <data format="txt" name="output8" label="Odds ratio for core/accessory/unique"/>
49 <data format="txt" name="output9" label="Odds ratio comparison between groups"/>
48 </outputs> 50 </outputs>
49 51
50 </tool> 52 </tool>