Mercurial > repos > mgarnier > pangenome_cog_analysis

comparison pangenomeCogAnalysis.xml @ 7:3f4e4e7d77ff draft

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author mgarnier
date Fri, 02 Jul 2021 19:25:36 +0000
parents 27c5a6f2301c
children ede0f548b6ec
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6:cf9da93e4145 7:3f4e4e7d77ff
10 ## Used so that a human-readable name appears in the output table (instead of 'dataset_xyz.dat') 10 ## Used so that a human-readable name appears in the output table (instead of 'dataset_xyz.dat')
11 #set $named_input_files = '' 11 #set $named_input_files = ''
12 #for $input_file in $input_files 12 #for $input_file in $input_files
13 ## Add single quotes around each input file identifier 13 ## Add single quotes around each input file identifier
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 19 perl ${__tool_directory__}/pangenomeCogAnalysis_V1.pl $input $input2 $input_files $named_input_files $gff_files $output $output2 $output3 $output4
20 20
21 ]]></command> 21 ]]></command>
22 22
23 23
24 24
35 <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"/>
36 <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"/>
37 <data format="tabular" name="output4" label="COG category count average"/> 37 <data format="tabular" name="output4" label="COG category count average"/>
38 <!--<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"> 39 <collection name="output5" type="list" label="Core-genes coordinates">
40 <discover_datasets pattern="__name_and_ext__" directory="Core" /> 40 <discover_datasets pattern="__name_and_ext__" directory="SampleDataset" />
41 </collection> 41 </collection>
42 <collection name="output6" type="list" label="Group specific genes coordinates">
43 <discover_datasets pattern="__name_and_ext__" directory="GroupSpecific" />
44 </collection>
45 </outputs> 42 </outputs>
46 43
47 </tool> 44 </tool>