Mercurial > repos > dereeper > pangenome_explorer

comparison PanExplorer.xml @ 19:b8ea3d2945b5 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author dereeper
date Mon, 27 Jan 2025 13:02:48 +0000
parents 716821f47909
children e23149f1f55c
comparison
equal deleted inserted replaced
18:716821f47909 19:b8ea3d2945b5
1 <tool id="pangenome_explorer" name="PanExplorer2" version="2.0"> 1 <tool id="pangenome_explorer" name="PanExplorer2" version="2.0">
2 <description> Bacterial pan-genome analysis </description> 2 <description> Bacterial pan-genome analysis </description>
3 <requirements> 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="1.30">perl-yaml</requirement> 4 <requirement type="package" version="1.30">perl-yaml</requirement>
12 <requirement type="package" version="3.8.7">singularity</requirement> 5 <requirement type="package" version="3.8.7">singularity</requirement>
13 <container type="docker">docker.io/dereeper/panexplorer_workflow:latest</container> 6 <container type="docker">docker.io/dereeper/panexplorer_workflow:latest</container>
14 </requirements> 7 </requirements>
15 8
25 perl ${__tool_directory__}/generateConfig.pl '$private_genomes' 'None' config.yaml '$private_genomes_fasta'; 18 perl ${__tool_directory__}/generateConfig.pl '$private_genomes' 'None' config.yaml '$private_genomes_fasta';
26 #end if 19 #end if
27 20
28 cat config.yaml >$logfile; 21 cat config.yaml >$logfile;
29 22
30 if [ ! -f ${__tool_directory__}/panexplorer_workflow_latest.sif ]; then wget -O ${__tool_directory__}/panexplorer_workflow_latest.sif https://panexplorer.southgreen.fr/singularity/panexplorer_workflow_latest.sif >>$logfile 2>&1;fi; 23 touch $vcf;
31
32
33
34
35 24
36 #if $software=="pgap" 25 #if $software=="pgap"
37 singularity exec ${__tool_directory__}/panexplorer_workflow_latest.sif cat \$PANEX_PATH/Snakemake_files/Snakefile_wget_PGAP_heatmap_upset_COG 1>snakefile 2>>$logfile; 26 snakemake --cores 1 --config identity=$min_identity -s \$PANEX_PATH/Snakemake_files/Snakefile_wget_PGAP_heatmap_upset_COG >>$logfile 2>&1;
38 #else if $software=="roary" 27 #else if $software=="roary"
39 singularity exec ${__tool_directory__}/panexplorer_workflow_latest.sif cat \$PANEX_PATH/Snakemake_files/Snakefile_wget_roary_heatmap_upset_COG 1>snakefile 2>>$logfile; 28 snakemake --cores 1 --config identity=$min_identity -s \$PANEX_PATH/Snakemake_files/Snakefile_wget_roary_heatmap_upset_COG >>$logfile 2>&1;
40 #else if $software=="orthofinder" 29 #else if $software=="orthofinder"
41 singularity exec ${__tool_directory__}/panexplorer_workflow_latest.sif cat \$PANEX_PATH/Snakemake_files/Snakefile_orthofinder_heatmap_upset 1>snakefile 2>>$logfile; 30 snakemake --cores 1 --config identity=$min_identity -s \$PANEX_PATH/Snakemake_files/Snakefile_orthofinder_heatmap_upset >>$logfile 2>&1;
42 #else if $software=="cactus" 31 #else if $software=="cactus"
43 singularity exec ${__tool_directory__}/panexplorer_workflow_latest.sif cat \$PANEX_PATH/Snakemake_files/Snakefile_wget_cactus_heatmap_upset_COG2 1>snakefile 2>>$logfile; 32 snakemake --cores 1 --config identity=$min_identity -s \$PANEX_PATH/Snakemake_files/Snakefile_wget_cactus_heatmap_upset_COG2 >>$logfile 2>&1;
44 #else if $software=="pggb" 33 #else if $software=="pggb"
45 singularity exec ${__tool_directory__}/panexplorer_workflow_latest.sif cat \$PANEX_PATH/Snakemake_files/Snakefile_wget_pggb_heatmap_upset_COG 1>snakefile 2>>$logfile; 34 snakemake --cores 1 --config identity=$min_identity -s \$PANEX_PATH/Snakemake_files/Snakefile_wget_pggb_heatmap_upset_COG >>$logfile 2>&1;
46 #else 35 #else
47 singularity exec ${__tool_directory__}/panexplorer_workflow_latest.sif cat \$PANEX_PATH/Snakemake_files/Snakefile_wget_panacota_heatmap_upset_COG 1>snakefile 2>>$logfile; 36 snakemake --cores 1 --config identity=$min_identity -s \$PANEX_PATH/Snakemake_files/Snakefile_wget_panacota_heatmap_upset_COG >>$logfile 2>&1;
48 #end if 37 #end if
38
49 39
50 singularity exec ${__tool_directory__}/panexplorer_workflow_latest.sif snakemake --cores 1 --config identity=$min_identity -s snakefile >>$logfile 2>&1;
51
52
53 cp -rf outputs/upsetr.svg $upset;
54 cp -rf outputs/pav_matrix.tsv $output;
55 cp -rf outputs/heatmap.svg.gz $heatmap;
56 cp -rf outputs/heatmap.svg.heatmap_plotly.html $heatmap_html;
57 cp -rf outputs/rarefaction_curves.txt $rarefaction_curves;
58 cp -rf outputs/rarefaction_curves.svg $rarefaction_curves_svg;
59 cp -rf outputs/heaps.tsv $heaps;
60 cp -rf outputs/heatmap.svg.complete.pdf.distance_matrix.txt $distance_matrix;
61 cp -rf outputs/heatmap.svg.complete.pdf.distance_matrix.hclust.newick $njtree;
62
63 #if $software!="orthofinder"
64 cp -rf outputs/GCskew.txt $gcfile;
65 cp -rf outputs/cog_output.txt $cogfile;
66 cp -rf outputs/cog_stats.txt $outcog_stat;
67 cp -rf outputs/cog_stats2.txt $outcog_stat2;
68 cp -rf outputs/cog_of_clusters.txt $outcog_clusters;
69 cp -rf outputs/genomes/genes.txt $genes;
70 cp -rf outputs/fastani.out.matrix.complete $fastani;
71 cp -rf outputs/fastani.out.svg $ani_svg;
72 #end if
73
74 #if $software=="pggb"
75 cp -rf outputs/all_genomes.vcf $vcf;
76 #else
77 touch $vcf;
78 #end if
79 ]]></command> 40 ]]></command>
80 41
81 42
82 <inputs> 43 <inputs>
83 <conditional name="mode"> 44 <conditional name="mode">
115 76
116 <param name="min_identity" type="text" value="80" label="Minimum percentage identity for BlastP" /> 77 <param name="min_identity" type="text" value="80" label="Minimum percentage identity for BlastP" />
117 </inputs> 78 </inputs>
118 79
119 <outputs> 80 <outputs>
120 <data format="txt" name="output" label="Pangenome presence absence matrix"/> 81 <data from_work_dir="outputs/pav_matrix.tsv" format="txt" name="output" label="Pangenome presence absence matrix"/>
121 <data format="newick" name="njtree" label="PanBased NJ tree"/> 82 <data from_work_dir="outputs/heatmap.svg.complete.pdf.distance_matrix.hclust.newick" format="newick" name="njtree" label="PanBased NJ tree"/>
122 <data format="txt" name="genes" label="Genes"/> 83 <data from_work_dir="outputs/genomes/genes.txt" format="txt" name="genes" label="Genes"/>
123 <data format="txt" name="cogfile" label="COG assignation"/> 84 <data from_work_dir="outputs/cog_output.txt" format="txt" name="cogfile" label="COG assignation"/>
124 <data format="txt" name="gcfile" label="GC_percent"/> 85 <data from_work_dir="outputs/GCskew.txt" format="txt" name="gcfile" label="GC_percent"/>
125 <data format="svg" name="upset" label="Upset Diagram"/> 86 <data from_work_dir="outputs/upsetr.svg" format="svg" name="upset" label="Upset Diagram"/>
126 <data format="svg" name="heatmap" label="Presence Absence Heatmap"/> 87 <data from_work_dir="outputs/heatmap.svg.gz" format="svg" name="heatmap" label="Presence Absence Heatmap"/>
127 <data format="html" name="heatmap_html" label="Presence Absence Heatmap interactive"/> 88 <data from_work_dir="outputs/heatmap.svg.heatmap_plotly.html" format="html" name="heatmap_html" label="Presence Absence Heatmap interactive"/>
128 <data format="tabular" name="outcog_stat" label="COG category counts"/> 89 <data from_work_dir="outputs/cog_stats.txt" format="tabular" name="outcog_stat" label="COG category counts"/>
129 <data format="tabular" name="outcog_stat2" label="COG category 2 counts"/> 90 <data from_work_dir="outputs/cog_stats2.txt" format="tabular" name="outcog_stat2" label="COG category 2 counts"/>
130 <data format="tabular" name="outcog_clusters" label="COG of clusters"/> 91 <data from_work_dir="outputs/cog_of_clusters.txt" format="tabular" name="outcog_clusters" label="COG of clusters"/>
131 <data format="tabular" name="fastani" label="ANI" /> 92 <data from_work_dir="outputs/fastani.out.matrix.complete" format="tabular" name="fastani" label="ANI" />
132 <data format="svg" name="ani_svg" label="ANI heatmap" /> 93 <data from_work_dir="outputs/fastani.out.svg" format="svg" name="ani_svg" label="ANI heatmap" />
133 <data format="txt" name="rarefaction_curves" label="Rarefaction curves data"/> 94 <data from_work_dir="outputs/rarefaction_curves.txt" format="txt" name="rarefaction_curves" label="Rarefaction curves data"/>
134 <data format="svg" name="rarefaction_curves_svg" label="Rarefaction curves"/> 95 <data from_work_dir="outputs/rarefaction_curves.svg" format="svg" name="rarefaction_curves_svg" label="Rarefaction curves"/>
135 <data format="txt" name="heaps" label="Heaps law alpha"/> 96 <data from_work_dir="outputs/heaps.tsv" format="txt" name="heaps" label="Heaps law alpha"/>
136 <data format="txt" name="distance_matrix" label="Accessory based distance matrix"/> 97 <data from_work_dir="outputs/heatmap.svg.complete.pdf.distance_matrix.txt" format="txt" name="distance_matrix" label="Accessory based distance matrix"/>
137 <data format="vcf" name="vcf" label="VCF file"/> 98 <data from_work_dir="outputs/all_genomes.vcf" format="vcf" name="vcf" label="VCF file"/>
138 <data format="txt" name="logfile" label="Logfile"/> 99 <data format="txt" name="logfile" label="Logfile"/>
139 <data format="txt" name="roary_log" label="Roary Logfile"/> 100 <data format="txt" name="roary_log" label="Roary Logfile"/>
140 </outputs> 101 </outputs>
141 <tests> 102 <tests>
142 <test> 103 <test>