Mercurial > repos > mgarnier > pangenome_cog_analysis

comparison pangenomeCogAnalysis.xml @ 16:3b12b1b1d67f draft

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author mgarnier
date Thu, 19 Aug 2021 19:12:05 +0000
parents ae68b2a86229
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15:ae68b2a86229 16:3b12b1b1d67f
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 $output8 $output9 19 perl ${__tool_directory__}/pangenomeCogAnalysis.pl $input $input2 $input_files $named_input_files $gff_files $output $output2 $output3 $output8 $output9
20 20
21 ]]></command> 21 ]]></command>
22 22
23 23
24 24
32 32
33 <outputs> 33 <outputs>
34 <data format="txt" name="output" label="List of group-specific clusters"/> 34 <data format="txt" name="output" label="List of group-specific clusters"/>
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="Core" />
41 </collection> 41 </collection>
42 <collection name="output6" type="list" label="Group specific genes coordinates"> 42 <collection name="output6" type="list" label="Group specific genes coordinates">
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"/> 48 <data format="tabular" name="output8" label="Odds ratio for core/accessory/unique"/>
49 <data format="txt" name="output9" label="Odds ratio comparison between groups"/> 49 <data format="tabular" name="output9" label="Odds ratio comparison between groups"/>
50 </outputs> 50 </outputs>
51 51
52 </tool> 52 </tool>