Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

update panaroo.xml #119

Merged
merged 1 commit into from
Aug 1, 2024
Merged

update panaroo.xml #119

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
66 changes: 56 additions & 10 deletions tools/panaroo/panaroo.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -131,15 +131,25 @@
</conditional>
</inputs>
<outputs>
<collection name="output" type="list" label="${tool.name} on ${on_string}: Pangenome output">
<collection name="output" type="list" label="${tool.name} on ${on_string}: Pangenome output">
<discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;clstr)" directory="outdir" format="txt" visible="false" />
<discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;txt)" directory="outdir" format="txt" visible="false" />
<discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;gml)" directory="outdir" format="txt" visible="false" />
<discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;Rtab)" directory="outdir" format="tabular" visible="false" />
<discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;csv)" directory="outdir" format="csv" visible="false" />
<discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;fasta)" directory="outdir" format="fasta" visible="false" />
<discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;fa)" directory="outdir" format="fasta" visible="false" />
<filter>advanced['adv_options_selector'] != 'set'</filter>
</collection>
<collection name="output_advance" type="list" label="${tool.name} on ${on_string}: Pangenome output (advance)">
<discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;clstr)" directory="outdir" format="txt" visible="false" />
<discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;txt)" directory="outdir" format="txt" visible="false" />
<discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;gml)" directory="outdir" format="txt" visible="false" />
<discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;Rtab)" directory="outdir" format="tabular" visible="false" />
<discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;csv)" directory="outdir" format="csv" visible="false" />
<discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;fasta)" directory="outdir" format="fasta" visible="false" />
<discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;fa)" directory="outdir" format="fasta" visible="false" />
<filter>advanced['gene_alignment_option']['a'] == 'None' </filter>
<filter>advanced['adv_options_selector'] == 'set' and advanced['gene_alignment_option']['a'] == 'None'</filter>
</collection>
<collection name="output_pangenome" type="list" label="${tool.name} on ${on_string}: Pangenome alignment output">
<discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;clstr)" directory="outdir" format="txt" visible="false" />
Expand All @@ -151,17 +161,33 @@
<discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;fa)" directory="outdir" format="fasta" visible="false" />
<discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;aln)" directory="outdir" format="aln" visible="false" />
<discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;embl)" directory="outdir" format="embl" visible="false" />
<filter>advanced['gene_alignment_option']['a'] != 'None' </filter>
<filter>advanced['adv_options_selector'] == 'set' and advanced['gene_alignment_option']['a'] != 'None' </filter>
</collection>
<collection name="output_pangenome_fasta" type="list" label="${tool.name} on ${on_string}: Pangenom alignment fasta">
<discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;fas)" directory="outdir/aligned_gene_sequences" format="fasta" visible="false" />
<filter>advanced['gene_alignment_option']['a'] != 'None' </filter>
<filter>advanced['adv_options_selector'] == 'set' and advanced['gene_alignment_option']['a'] != 'None'</filter>
</collection>

<data name="log" format="txt" label="${tool.name} on ${on_string}: log"/>
<data name="log" format="txt" label="${tool.name} on ${on_string}: log"/>
</outputs>
<tests>
<!-- run panaroo with default parameters (i.e panaroo -t 2 -i *.gff -o default \-\-clean-mode strict \-\-remove-invalid-genes) -->
<!-- run panaroo with default parameters (i.e panaroo -t 2 -i *.gff -o default \-\-clean-mode strict \-\-remove-invalid-genes) -->
<test expect_num_outputs="2">
<param name="gen_code" value="11"/>
<param name="mode" value="strict"/>
<param name="adv_options_selector" value="do_not_set"/>
<param name="gff_input_collection">
<collection type="list">
<element name="gff10.gff" value="10_small.gff"/>
<element name="gff11.gff" value="11_small.gff"/>
</collection>
</param>
<output_collection name="output" count="13"/>
<output name="log">
<assert_contents>
<has_text text="pre-processing gff3 files..."/>
</assert_contents>
</output>
</test>
<test expect_num_outputs="2">
<param name="gen_code" value="11"/>
<param name="mode" value="strict"/>
Expand All @@ -173,7 +199,7 @@
<element name="gff11.gff" value="11_small.gff"/>
</collection>
</param>
<output_collection name="output" count="13"/>
<output_collection name="output_advance" count="13"/>
<output name="log">
<assert_contents>
<has_text text="pre-processing gff3 files..."/>
Expand Down Expand Up @@ -206,7 +232,7 @@ Panaroo_ is A Bacterial Pangenome Analysis Pipeline.
**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.

- data file in gff format
- a list of gff format in a collection

**OUTPUTS**

Expand All @@ -216,14 +242,34 @@ Panaroo now supports multiple input formats. To use non-standard GFF3 files you
- gene_data.csv
- combined_protein_CDS.fasta
- combined_DNA_CDS.fasta
- gene_presence_absence.Rtab
- gene_presence_absence_rtab.Rtab
- gene_presence_absence_roary.csv
- gene_presence_absence.csv
- summary_statistics.txt
- pan_genome_reference.fa
- struct_presence_absence.Rtab
- final_graph.gml

**OUTPUTS with Advance parameters**

- combined_protein_cdhit_out.txt
- combined_protein_cdhit_out.txt.clstr
- pre_filt_graph.gml
- gene_data.csv
- combined_protein_CDS.fasta
- combined_DNA_CDS.fasta
- gene_presence_absence_rtab.Rtab
- gene_presence_absence_roary.csv
- gene_presence_absence.csv
- summary_statistics.txt
- pan_genome_reference.fa
- struct_presence_absence.Rtab
- final_graph.gml
- core_gene_alignment
- core_gene_alignment_filtered
- core_alignment_filtered_header
- core_alignment_header
- a collection of fasta files

.. _Panaroo: https://gthlab.au/panaroo/#/gettingstarted/quickstart

Expand Down
Loading