Mercurial > repos > mgarnier > pangenome_cog_analysis
comparison pangenomeCogAnalysis.xml @ 0:731fb6cb324b draft
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author | mgarnier |
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date | Wed, 30 Jun 2021 13:30:19 +0000 |
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children | 27c5a6f2301c |
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-1:000000000000 | 0:731fb6cb324b |
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1 <tool id="pangenome_cog_analysis" name="Pangenome COG Analysis" version="1.0"> | |
2 <description>Provide statistics from pangenome matrix and COG annotations </description> | |
3 <!-- <requirements> | |
4 <requirement type="package" version=""></requirement> | |
5 </requirements> --> | |
6 <command detect_errors="aggressive"><![CDATA[ | |
7 #import re | |
8 | |
9 ## Creates symlinks for each input file based on the Galaxy 'element_identifier' | |
10 ## Used so that a human-readable name appears in the output table (instead of 'dataset_xyz.dat') | |
11 #set $named_input_files = '' | |
12 #for $input_file in $input_files | |
13 ## Add single quotes around each input file identifier | |
14 #set $_input_file = "'{}'".format($input_file.element_identifier) | |
15 ln -s '${input_file}' ${_input_file} && | |
16 #set $named_input_files = $named_input_files + ',' + $_input_file | |
17 #end for | |
18 | |
19 perl ${__tool_directory__}/pangenomeCogAnalysis_V1.pl $input $input2 $named_input_files $input_files $gff_files order $output $output2 $output3 $output4 $output5 | |
20 ]]></command> | |
21 | |
22 | |
23 | |
24 <inputs> | |
25 <param format="tabular" name="input" type="data" label="Pangenome Matrix" help="Headers must be: Cluster,genes_strain1,genes_strain2..."/> | |
26 <param format="tabular" name="input2" type="data" label="Strains group file (example species information)" help="Headers must be: strain1,groupinfo"/> | |
27 <param type="data" name="input_files" format="txt" multiple="true" label="Collection of COG files" help="Each files must be named with the same strain name as defined in Strain group file. Headers must be Gene,COG,COGcategory"/> | |
28 <param type="data" name="gff_files" format="gff3" multiple="true" label="Collection of GFF files for preparing Circos track" help="Not necessarily annotations from all strains, only those that you want to be represented as Circos tracks"/> | |
29 <!--<param format="tabular" name="input_files" type="data" multiple="true" label="Annotation files"/>--> | |
30 </inputs> | |
31 | |
32 <outputs> | |
33 <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="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="output5" label="Core-genes coordinates"/> | |
38 </outputs> | |
39 | |
40 </tool> |