Mercurial > repos > dereeper > pangenome_explorer

comparison PanExplorer.xml @ 16:1e0698511c9f draft

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author dereeper
date Sun, 15 Dec 2024 21:30:16 +0000
parents dbde253606c5
children db83eb7c8f78
comparison
equal deleted inserted replaced
15:dbde253606c5 16:1e0698511c9f
1 <tool id="pangenome_explorer" name="Pangenome Explorer2" version="2.0"> 1 <tool id="PanExplorer2" name="PanExplorer2" version="2.0">
2 <description> Bacterial pan-genome analysis </description> 2 <description> Bacterial pan-genome analysis </description>
3 <requirements> 3 <requirements>
4 <!-- 4 <!--
5 <requirement type="package" version="2.2.26">blast-legacy</requirement> 5 <requirement type="package" version="2.2.26">blast-legacy</requirement>
6 <requirement type="package" version="7.480">mafft</requirement> 6 <requirement type="package" version="7.480">mafft</requirement>
8 <requirement type="package" version="3.697">phylip</requirement> 8 <requirement type="package" version="3.697">phylip</requirement>
9 <requirement type="package" version="1.7.2">perl-bioperl</requirement> 9 <requirement type="package" version="1.7.2">perl-bioperl</requirement>
10 --> 10 -->
11 <requirement type="package" version="1.30">perl-yaml</requirement> 11 <requirement type="package" version="1.30">perl-yaml</requirement>
12 <requirement type="package" version="3.8.7">singularity</requirement> 12 <requirement type="package" version="3.8.7">singularity</requirement>
13 13 <!-- <container type="docker">ghcr.io/pangenome/pggb:latest</container> -->
14 </requirements> 14 </requirements>
15 15
16 <command><![CDATA[ 16 <command><![CDATA[
17 17
18 export PANEX_PATH=${__tool_directory__}; 18 export PANEX_PATH=/usr/local/bin/PanExplorer_workflow;
19
20 19
21 #if str($mode.mode) == "accessions": 20 #if str($mode.mode) == "accessions":
22 perl ${__tool_directory__}/Perl/generateConfig.pl 'None' '$input' config.yaml 'None'; 21 perl ${__tool_directory__}/generateConfig.pl 'None' '$input' config.yaml 'None';
23 #else if str($mode.mode) == "genbanks": 22 #else if str($mode.mode) == "genbanks":
24 perl ${__tool_directory__}/Perl/generateConfig.pl '$private_genomes' 'None' config.yaml 'None'; 23 perl ${__tool_directory__}/generateConfig.pl '$private_genomes' 'None' config.yaml 'None';
25 #else if str($mode.mode) == "fasta": 24 #else if str($mode.mode) == "fasta":
26 perl ${__tool_directory__}/Perl/generateConfig.pl '$private_genomes' 'None' config.yaml '$private_genomes_fasta'; 25 perl ${__tool_directory__}/generateConfig.pl '$private_genomes' 'None' config.yaml '$private_genomes_fasta';
27 #end if 26 #end if
28 27
29 cat config.yaml >$logfile; 28 cat config.yaml >$logfile;
30 29
31 30 if [ ! -f ${__tool_directory__}/panexplorer.sif ]; then wget -O ${__tool_directory__}/panexplorer.sif https://panexplorer.southgreen.fr/singularity/panexplorer.sif >>$logfile 2>&1;fi;
32
33 if [ ! -f \$PANEX_PATH/panexplorer.sif ]; then wget -O \$PANEX_PATH/panexplorer.sif https://panexplorer.southgreen.fr/singularity/panexplorer.sif >>$logfile 2>&1;fi;
34 31
35 32
36 33
37 #if $software=="pgap" 34 #if $software=="pgap"
38 sed "s/identity\=80/identity\=$min_identity/g" \$PANEX_PATH/Snakemake_files/Snakefile_wget_PGAP_heatmap_upset_COG >snakefile; 35 singularity exec ${__tool_directory__}/panexplorer.sif sed "s/identity\=80/identity\=$min_identity/g" \$PANEX_PATH/Snakemake_files/Snakefile_wget_PGAP_heatmap_upset_COG 1>snakefile 2>>$logfile;
39 #else if $software=="roary" 36 #else if $software=="roary"
40 sed "s/identity\=80/identity\=$min_identity/g" \$PANEX_PATH/Snakemake_files/Snakefile_wget_roary_heatmap_upset_COG >snakefile; 37 singularity exec ${__tool_directory__}/panexplorer.sif sed "s/identity\=80/identity\=$min_identity/g" \$PANEX_PATH/Snakemake_files/Snakefile_wget_roary_heatmap_upset_COG 1>snakefile 2>>$logfile;
41 #else if $software=="orthofinder" 38 #else if $software=="orthofinder"
42 sed "s/identity\=80/identity\=$min_identity/g" \$PANEX_PATH/Snakemake_files/Snakefile_orthofinder_heatmap_upset >snakefile; 39 singularity exec ${__tool_directory__}/panexplorer.sif sed "s/identity\=80/identity\=$min_identity/g" \$PANEX_PATH/Snakemake_files/Snakefile_orthofinder_heatmap_upset 1>snakefile 2>>$logfile;
43 #else if $software=="cactus" 40 #else if $software=="cactus"
44 cp -rf \$PANEX_PATH/Snakemake_files/Snakefile_wget_cactus_heatmap_upset_COG2 snakefile; 41 singularity exec ${__tool_directory__}/panexplorer.sif cp -rf \$PANEX_PATH/Snakemake_files/Snakefile_wget_cactus_heatmap_upset_COG2 1>snakefile 2>>$logfile;
45 #else if $software=="pggb" 42 #else if $software=="pggb"
46 sed "s/identity\=30/identity\=$min_identity/g" \$PANEX_PATH/Snakemake_files/Snakefile_wget_pggb_heatmap_upset_COG >snakefile; 43 singularity exec ${__tool_directory__}/panexplorer.sif sed "s/identity\=30/identity\=$min_identity/g" \$PANEX_PATH/Snakemake_files/Snakefile_wget_pggb_heatmap_upset_COG 1>snakefile 2>>$logfile;
47 #else 44 #else
48 sed "s/identity\=80/identity\=$min_identity/g" \$PANEX_PATH/Snakemake_files/Snakefile_wget_panacota_heatmap_upset_COG >snakefile; 45 singularity exec ${__tool_directory__}/panexplorer.sif sed "s/identity\=80/identity\=$min_identity/g" \$PANEX_PATH/Snakemake_files/Snakefile_wget_panacota_heatmap_upset_COG 1>snakefile 2>>$logfile;
49 #end if 46 #end if
50 47
51 singularity exec \$PANEX_PATH/panexplorer.sif snakemake --cores 1 -s snakefile >>$logfile 2>&1; 48 singularity exec ${__tool_directory__}/panexplorer.sif snakemake --cores 1 -s snakefile >>$logfile 2>&1;
52 49
53 50
54 cp -rf outputs/upsetr.svg $upset; 51 cp -rf outputs/upsetr.svg $upset;
55 cp -rf outputs/pav_matrix.tsv $output; 52 cp -rf outputs/pav_matrix.tsv $output;
56 cp -rf outputs/heatmap.svg.gz $heatmap; 53 cp -rf outputs/heatmap.svg.gz $heatmap;