move panaroo to iuc repo #6811
move panaroo to iuc repo #6811
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| ]]></command> | ||
| <inputs> | ||
| <param name="gff_input_collection" type="data_collection" format="gff" collection_type="list" label="GFF Input Collection" help="A list of gff files (i.e prokka)"/> |
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Shouldn't this be gff3? I think this was a question from a Galaxy user as well.
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A lot of users did ask about this as well. I did have a look at Different input formats and it's required to add all the gff3 into a text file first . In other words, the input is a tab delimited text file contaings gff3 and fasta file (see the different input formats in details) . We'll need to find a way to implement this to support gff3 file
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So in this case, would it be a good idea to keep both gff and gff3 as input file formats in Galaxy?
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Hi @mthang,
Thanks for your PR for moving Panaroo to IUC. I have reviewed the tool and left some of the comments. Feel free to ping me if something is unclear.
| <section name="graph_correction_option" title="Graph Correction" expanded="false"> | ||
| <param argument="--min_trailing_support" type="integer" value="2" label="Minimum cluster size to keep a gene called at the end of a contig" help="--min_traiiing_support [relexed mode : 2 is used]"/> | ||
| <param argument="--trailing_recursive" type="integer" value="1" label="Number of times to perform recursive trimming of low support nodes near the end of contigs" help="--trailing_recursive [relaxed mode: 1 is used]"/> | ||
| <param name="edge_support_threshold" type="integer" value="1" label="Edge support threshold" help="--edge_support_threshold [ Minimal edge 1 is used ]"/> |
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Can all the below params be arguments? (For eg "--edge_support_threshold", "--remove_by_consensus", etc)
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Sure. I can make the changes.
| <param argument="-a" type="select" label="Output alignments of core genes or all genes." help="-a [optional: core or pan; default: None"> | ||
| <expand macro="gene_alignment"/> | ||
| </param> | ||
| <param argument="--aligner" type="select" label="Specify an aligner" help="--aligner [mafft|prank|clustal][default: mafft]"> |
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Can we also add prank and clustal to tool requirements? AFAIK, prank and clustal are not internally present in Panaroo and relies on external tool.
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Prank has already been included in the macro file, but not the clustal. In memroy, there are many version of clustal (i.e clustalw, clustalo and etc), so I have not added it to the wrapper yet. As you mentioned, both prank and clustal are depending on external tool. It requires Galaxy admin to install them on Galaxy prior to test the wrapper.
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I think if we add the requirements, those tools would be automatically installed in the biocontainer and the tool can use it further.
| <element name="gff11.gff" value="11_small.gff"/> | ||
| </collection> | ||
| </param> | ||
| <output_collection name="output" count="13"/> |
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Can we capture contents of some important outputs such gene_presence_absence.csv, etc? This will help to maintain the tool in longer run.
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No worries! Let me have a look and update the test section
| **INPUTS** | ||
| Panaroo now supports multiple input formats. To use non-standard GFF3 files you must profile the input file as a list in a text file (one per line). Separate GFF and FASTA files can be provided per isolate by providing each file delimited by a space or a tab. Genbank file formats are also supported with extensions '.gbk', '.gb' or '.gbff'. These must compliant with Genbank/ENA/DDJB. This can be forced in Prokka by specifying the --compliance parameter. | ||
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| - a list of gff format in a collection |
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gff3?
| - a list of gff format in a collection | |
| - a list of gff3 format in a collection |
| </test> | ||
| </tests> | ||
| <help><
FOR CONTRIBUTOR:
@SaimMomin12 I am moving this panaroo to iuc repo. Please review and merge it when you can. Please let me know after you merged it into IUC repo.