Mercurial > repos > dereeper > pangenome_explorer

comparison PanExplorer.xml @ 25:963038acf999 draft default tip

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author dereeper
date Fri, 12 Sep 2025 16:14:44 +0000
parents bf77c62428fc
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24:bf77c62428fc 25:963038acf999
26 touch $coregenes_alignment; 26 touch $coregenes_alignment;
27 27
28 #if $software=="pgap" 28 #if $software=="pgap"
29 snakemake --cores 1 --config identity=$min_identity -s \$PANEX_PATH/Snakemake_files/Snakefile_wget_PGAP_heatmap_upset_COG >>$logfile 2>&1; 29 snakemake --cores 1 --config identity=$min_identity -s \$PANEX_PATH/Snakemake_files/Snakefile_wget_PGAP_heatmap_upset_COG >>$logfile 2>&1;
30 #else if $software=="roary" 30 #else if $software=="roary"
31 snakemake --cores 1 --config identity=$min_identity generate_core_genes_alignment=$generate_core_genes_alignment -s \$PANEX_PATH/Snakemake_files/Snakefile_wget_roary_heatmap_upset_COG >>$logfile 2>&1; 31 #else if $software=="roary" and $generate_core_genes_alignment=="true"
32 snakemake --cores 1 --config identity=$min_identity generate_core_genes_alignment=True -s \$PANEX_PATH/Snakemake_files/Snakefile_wget_roary_heatmap_upset_COG >>$logfile 2>&1;
33 #else if $software=="roary"
34 snakemake --cores 1 --config identity=$min_identity generate_core_genes_alignment=False -s \$PANEX_PATH/Snakemake_files/Snakefile_wget_roary_heatmap_upset_COG >>$logfile 2>&1;
32 #else if $software=="orthofinder" 35 #else if $software=="orthofinder"
33 snakemake --cores 1 --config identity=$min_identity -s \$PANEX_PATH/Snakemake_files/Snakefile_orthofinder_heatmap_upset >>$logfile 2>&1; 36 snakemake --cores 1 --config identity=$min_identity -s \$PANEX_PATH/Snakemake_files/Snakefile_orthofinder_heatmap_upset >>$logfile 2>&1;
34 #else if $software=="cactus" 37 #else if $software=="cactus"
35 snakemake --cores 1 --config identity=$min_identity -s \$PANEX_PATH/Snakemake_files/Snakefile_wget_cactus_heatmap_upset_COG2 >>$logfile 2>&1; 38 snakemake --cores 1 --config identity=$min_identity -s \$PANEX_PATH/Snakemake_files/Snakefile_wget_cactus_heatmap_upset_COG2 >>$logfile 2>&1;
36 #else if $software=="pggb" 39 #else if $software=="pggb"
99 <data from_work_dir="outputs/rarefaction_curves.svg" format="svg" name="rarefaction_curves_svg" label="Rarefaction curves"/> 102 <data from_work_dir="outputs/rarefaction_curves.svg" format="svg" name="rarefaction_curves_svg" label="Rarefaction curves"/>
100 <data from_work_dir="outputs/heaps.tsv" format="txt" name="heaps" label="Heaps law alpha"/> 103 <data from_work_dir="outputs/heaps.tsv" format="txt" name="heaps" label="Heaps law alpha"/>
101 <data from_work_dir="outputs/heatmap.svg.complete.pdf.distance_matrix.txt" format="txt" name="distance_matrix" label="Accessory based distance matrix"/> 104 <data from_work_dir="outputs/heatmap.svg.complete.pdf.distance_matrix.txt" format="txt" name="distance_matrix" label="Accessory based distance matrix"/>
102 <data from_work_dir="outputs/all_genomes.vcf" format="vcf" name="vcf" label="VCF file"/> 105 <data from_work_dir="outputs/all_genomes.vcf" format="vcf" name="vcf" label="VCF file"/>
103 <data from_work_dir="outputs/pggb_out/all_genomes.fa.smooth.final.gfa" format="gfa1" name="gfa_file" label="GFA file"/> 106 <data from_work_dir="outputs/pggb_out/all_genomes.fa.smooth.final.gfa" format="gfa1" name="gfa_file" label="GFA file"/>
107 <data from_work_dir="outputs/roary_outdir/core_gene_alignment.aln" format="fasta" name="coregenes_alignment" label="Coregenes FASTA alignment"/>
104 <data format="txt" name="logfile" label="Logfile"/> 108 <data format="txt" name="logfile" label="Logfile"/>
105 <data format="txt" name="roary_log" label="Roary Logfile"/> 109 <data format="txt" name="roary_log" label="Roary Logfile"/>
106 </outputs> 110 </outputs>
107 <tests> 111 <tests>
108 <test> 112 <test>