Mercurial > repos > dereeper > pangenome_explorer
comparison PanExplorer.xml @ 2:97e4e3e818b6 draft
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author | dereeper |
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date | Thu, 30 May 2024 11:48:09 +0000 |
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children | 4157f435fa89 |
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1:032f6b3806a3 | 2:97e4e3e818b6 |
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1 <tool id="PanExplorer2" name="PanExplorer2" version="2.0"> | |
2 <description> Bacterial pan-genome analysis </description> | |
3 <requirements> | |
4 <!-- | |
5 <requirement type="package" version="2.2.26">blast-legacy</requirement> | |
6 <requirement type="package" version="7.480">mafft</requirement> | |
7 <requirement type="package" version="14.137">mcl</requirement> | |
8 <requirement type="package" version="3.697">phylip</requirement> | |
9 <requirement type="package" version="1.7.2">perl-bioperl</requirement> | |
10 --> | |
11 <requirement type="package" version="2.4.2">singularity</requirement> | |
12 | |
13 </requirements> | |
14 | |
15 <command><![CDATA[ | |
16 module load system/singularity/3.6.0; | |
17 export PANEX_PATH=${__tool_directory__}; | |
18 | |
19 perl ${__tool_directory__}/Perl/generateConfig.pl '$private_genomes' '$input' config.yaml '$private_genomes_fasta'; | |
20 | |
21 cat config.yaml >$logfile; | |
22 | |
23 if [ -f \$PANEX_PATH/panexplorer.sif ]; then; else; wget -O \$PANEX_PATH/panexplorer.sif https://panexplorer.southgreen.fr/singularity/panexplorer.sif; fi; | |
24 | |
25 | |
26 | |
27 #if $software=="pgap" | |
28 sed "s/identity\=80/identity\=$min_identity/g" \$PANEX_PATH/Snakemake_files/Snakefile_wget_PGAP_heatmap_upset_COG >snakefile; | |
29 #else if $software=="roary" | |
30 sed "s/identity\=80/identity\=$min_identity/g" \$PANEX_PATH/Snakemake_files/Snakefile_wget_roary_heatmap_upset_COG >snakefile; | |
31 #else if $software=="orthofinder" | |
32 sed "s/identity\=80/identity\=$min_identity/g" \$PANEX_PATH/Snakemake_files/Snakefile_orthofinder_heatmap_upset >snakefile; | |
33 #else if $software=="cactus" | |
34 cp -rf \$PANEX_PATH/Snakemake_files/Snakefile_wget_cactus_heatmap_upset_COG2 snakefile; | |
35 #else if $software=="pggb" | |
36 sed "s/identity\=30/identity\=$min_identity/g" \$PANEX_PATH/Snakemake_files/Snakefile_wget_pggb_heatmap_upset_COG >snakefile; | |
37 #else | |
38 sed "s/identity\=80/identity\=$min_identity/g" \$PANEX_PATH/Snakemake_files/Snakefile_wget_panacota_heatmap_upset_COG >snakefile; | |
39 #end if | |
40 | |
41 singularity exec \$PANEX_PATH/panexplorer.sif snakemake --cores 1 -s snakefile >>$logfile 2>&1; | |
42 | |
43 | |
44 cp -rf outputs/upsetr.svg $upset; | |
45 cp -rf outputs/pav_matrix.tsv $output; | |
46 cp -rf outputs/heatmap.svg.gz $heatmap; | |
47 cp -rf outputs/heatmap.svg.heatmap_plotly.html $heatmap_html; | |
48 cp -rf outputs/rarefaction_curves.txt $rarefaction_curves; | |
49 cp -rf outputs/rarefaction_curves.svg $rarefaction_curves_svg; | |
50 cp -rf outputs/heaps.tsv $heaps; | |
51 cp -rf outputs/heatmap.svg.complete.pdf.distance_matrix.txt $distance_matrix; | |
52 cp -rf outputs/heatmap.svg.complete.pdf.distance_matrix.hclust.newick $njtree; | |
53 | |
54 #if $software!="orthofinder" | |
55 cp -rf outputs/GCskew.txt $gcfile; | |
56 cp -rf outputs/cog_output.txt $cogfile; | |
57 cp -rf outputs/cog_stats.txt $outcog_stat; | |
58 cp -rf outputs/cog_stats2.txt $outcog_stat2; | |
59 cp -rf outputs/cog_of_clusters.txt $outcog_clusters; | |
60 cp -rf outputs/genomes/genes.txt $genes; | |
61 cp -rf outputs/fastani.out.matrix.complete $fastani; | |
62 cp -rf outputs/fastani.out.svg $ani_svg; | |
63 #end if | |
64 | |
65 #if $software=="pggb" | |
66 cp -rf outputs/all_genomes.vcf $vcf; | |
67 #else | |
68 touch $vcf; | |
69 #end if | |
70 ]]></command> | |
71 | |
72 | |
73 <inputs> | |
74 <param name="input" type="text" multiple="true" label="List of genbank identifiers" help="Coma separated list (ex: CP000235.1,CP001079.1,CP001759.1,CP015994.2)"/> | |
75 <param name="private_genomes" type="data" format="zip" label="Zip of genbank or GFF files" optional="true"/> | |
76 <param name="private_genomes_fasta" type="data" format="zip" label="Zip of Fasta files" optional="true"/> | |
77 <param name="min_identity" type="text" value="80" label="Minimum percentage identity for BlastP" /> | |
78 <param type="select" name="software" label="Choose the pan-genome software"> | |
79 <option value="pgap">PGAP</option> | |
80 <option value="roary">Roary</option> | |
81 <option value="panacota">PanACoTA</option> | |
82 <option value="orthofinder">OrthoFinder</option> | |
83 <option value="cactus">Minigraph-Cactus</option> | |
84 <option value="pggb">PanGenome Graph Builder (PGGB)</option> | |
85 </param> | |
86 </inputs> | |
87 | |
88 <outputs> | |
89 <data format="txt" name="output" label="Pangenome presence absence matrix"/> | |
90 <data format="newick" name="njtree" label="PanBased NJ tree"/> | |
91 <data format="txt" name="genes" label="Genes"/> | |
92 <data format="txt" name="cogfile" label="COG assignation"/> | |
93 <data format="txt" name="gcfile" label="GC_percent"/> | |
94 <data format="svg" name="upset" label="Upset Diagram"/> | |
95 <data format="svg" name="heatmap" label="Presence Absence Heatmap"/> | |
96 <data format="html" name="heatmap_html" label="Presence Absence Heatmap interactive"/> | |
97 <data format="tabular" name="outcog_stat" label="COG category counts"/> | |
98 <data format="tabular" name="outcog_stat2" label="COG category 2 counts"/> | |
99 <data format="tabular" name="outcog_clusters" label="COG of clusters"/> | |
100 <data format="tabular" name="fastani" label="ANI" /> | |
101 <data format="svg" name="ani_svg" label="ANI heatmap" /> | |
102 <data format="txt" name="rarefaction_curves" label="Rarefaction curves data"/> | |
103 <data format="svg" name="rarefaction_curves_svg" label="Rarefaction curves"/> | |
104 <data format="txt" name="heaps" label="Heaps law alpha"/> | |
105 <data format="txt" name="distance_matrix" label="Accessory based distance matrix"/> | |
106 <data format="vcf" name="vcf" label="VCF file"/> | |
107 <data format="txt" name="logfile" label="Logfile"/> | |
108 <data format="txt" name="roary_log" label="Roary Logfile"/> | |
109 </outputs> | |
110 | |
111 </tool> |