# HG changeset patch
# User dereeper
# Date 1737982968 0
# Node ID b8ea3d2945b5475d4dabe19b616a86a74d37773b
# Parent  716821f47909c534d66590ae9cdc3537ce8cfc23
Uploaded

diff -r 716821f47909 -r b8ea3d2945b5 PanExplorer.xml
--- a/PanExplorer.xml	Tue Dec 17 13:19:43 2024 +0000
+++ b/PanExplorer.xml	Mon Jan 27 13:02:48 2025 +0000
@@ -1,13 +1,6 @@
 <tool id="pangenome_explorer" name="PanExplorer2" version="2.0">
   <description> Bacterial pan-genome analysis </description>
   <requirements>
-  <!--
- <requirement type="package" version="2.2.26">blast-legacy</requirement>
- <requirement type="package" version="7.480">mafft</requirement>
- <requirement type="package" version="14.137">mcl</requirement>
- <requirement type="package" version="3.697">phylip</requirement>
- <requirement type="package" version="1.7.2">perl-bioperl</requirement>
- -->
     <requirement type="package" version="1.30">perl-yaml</requirement>
     <requirement type="package" version="3.8.7">singularity</requirement>
     <container type="docker">docker.io/dereeper/panexplorer_workflow:latest</container>
@@ -27,55 +20,23 @@
 
 cat config.yaml >$logfile;
 
-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;
-
-
-
-
+touch $vcf;
 
 #if $software=="pgap"
-singularity exec ${__tool_directory__}/panexplorer_workflow_latest.sif cat \$PANEX_PATH/Snakemake_files/Snakefile_wget_PGAP_heatmap_upset_COG 1>snakefile 2>>$logfile;
+    snakemake --cores 1 --config identity=$min_identity -s \$PANEX_PATH/Snakemake_files/Snakefile_wget_PGAP_heatmap_upset_COG >>$logfile 2>&1;
 #else if $software=="roary"
-singularity exec ${__tool_directory__}/panexplorer_workflow_latest.sif cat \$PANEX_PATH/Snakemake_files/Snakefile_wget_roary_heatmap_upset_COG 1>snakefile 2>>$logfile;
+    snakemake --cores 1 --config identity=$min_identity -s \$PANEX_PATH/Snakemake_files/Snakefile_wget_roary_heatmap_upset_COG >>$logfile 2>&1;
 #else if $software=="orthofinder"
-singularity exec ${__tool_directory__}/panexplorer_workflow_latest.sif cat \$PANEX_PATH/Snakemake_files/Snakefile_orthofinder_heatmap_upset 1>snakefile 2>>$logfile;
+    snakemake --cores 1 --config identity=$min_identity -s \$PANEX_PATH/Snakemake_files/Snakefile_orthofinder_heatmap_upset >>$logfile 2>&1;
 #else if $software=="cactus"
-	    singularity exec ${__tool_directory__}/panexplorer_workflow_latest.sif cat \$PANEX_PATH/Snakemake_files/Snakefile_wget_cactus_heatmap_upset_COG2 1>snakefile 2>>$logfile;
+    snakemake --cores 1 --config identity=$min_identity -s \$PANEX_PATH/Snakemake_files/Snakefile_wget_cactus_heatmap_upset_COG2 >>$logfile 2>&1;
 #else if $software=="pggb"
-singularity exec ${__tool_directory__}/panexplorer_workflow_latest.sif cat \$PANEX_PATH/Snakemake_files/Snakefile_wget_pggb_heatmap_upset_COG 1>snakefile 2>>$logfile;
+    snakemake --cores 1 --config identity=$min_identity -s \$PANEX_PATH/Snakemake_files/Snakefile_wget_pggb_heatmap_upset_COG >>$logfile 2>&1;
 #else
-	    singularity exec ${__tool_directory__}/panexplorer_workflow_latest.sif cat \$PANEX_PATH/Snakemake_files/Snakefile_wget_panacota_heatmap_upset_COG 1>snakefile 2>>$logfile;
+    snakemake --cores 1 --config identity=$min_identity -s \$PANEX_PATH/Snakemake_files/Snakefile_wget_panacota_heatmap_upset_COG >>$logfile 2>&1;
 #end if
-
-singularity exec ${__tool_directory__}/panexplorer_workflow_latest.sif snakemake --cores 1 --config identity=$min_identity -s snakefile >>$logfile 2>&1;
-
+ 
 
-cp -rf outputs/upsetr.svg $upset;
-cp -rf outputs/pav_matrix.tsv $output;
-cp -rf outputs/heatmap.svg.gz $heatmap;
-cp -rf outputs/heatmap.svg.heatmap_plotly.html $heatmap_html;
-cp -rf outputs/rarefaction_curves.txt $rarefaction_curves;
-cp -rf outputs/rarefaction_curves.svg $rarefaction_curves_svg;
-cp -rf outputs/heaps.tsv $heaps;
-cp -rf outputs/heatmap.svg.complete.pdf.distance_matrix.txt $distance_matrix;
-cp -rf outputs/heatmap.svg.complete.pdf.distance_matrix.hclust.newick $njtree;
-
-#if $software!="orthofinder"
-cp -rf outputs/GCskew.txt $gcfile;
-cp -rf outputs/cog_output.txt $cogfile;
-cp -rf outputs/cog_stats.txt $outcog_stat;
-cp -rf outputs/cog_stats2.txt $outcog_stat2;
-cp -rf outputs/cog_of_clusters.txt $outcog_clusters;
-cp -rf outputs/genomes/genes.txt $genes;
-cp -rf outputs/fastani.out.matrix.complete $fastani;
-cp -rf outputs/fastani.out.svg $ani_svg;
-#end if
-
-#if $software=="pggb"
-cp -rf outputs/all_genomes.vcf $vcf;
-#else
-touch $vcf;
-#end if
 ]]></command>
 
 
@@ -117,24 +78,24 @@
  </inputs>
 
  <outputs>
- <data format="txt" name="output" label="Pangenome presence absence matrix"/>
- <data format="newick" name="njtree" label="PanBased NJ tree"/>
- <data format="txt" name="genes" label="Genes"/>
- <data format="txt" name="cogfile" label="COG assignation"/>
- <data format="txt" name="gcfile" label="GC_percent"/>
- <data format="svg" name="upset" label="Upset Diagram"/>
- <data format="svg" name="heatmap" label="Presence Absence Heatmap"/>
- <data format="html" name="heatmap_html" label="Presence Absence Heatmap interactive"/>
- <data format="tabular" name="outcog_stat" label="COG category counts"/>
- <data format="tabular" name="outcog_stat2" label="COG category 2 counts"/>
- <data format="tabular" name="outcog_clusters" label="COG of clusters"/>
- <data format="tabular" name="fastani" label="ANI" />
- <data format="svg" name="ani_svg" label="ANI heatmap" />
- <data format="txt" name="rarefaction_curves" label="Rarefaction curves data"/>
- <data format="svg" name="rarefaction_curves_svg" label="Rarefaction curves"/>
- <data format="txt" name="heaps" label="Heaps law alpha"/>
- <data format="txt" name="distance_matrix" label="Accessory based distance matrix"/>
- <data format="vcf" name="vcf" label="VCF file"/>
+ <data from_work_dir="outputs/pav_matrix.tsv" format="txt" name="output" label="Pangenome presence absence matrix"/>
+ <data from_work_dir="outputs/heatmap.svg.complete.pdf.distance_matrix.hclust.newick" format="newick" name="njtree" label="PanBased NJ tree"/>
+ <data from_work_dir="outputs/genomes/genes.txt" format="txt" name="genes" label="Genes"/>
+ <data from_work_dir="outputs/cog_output.txt" format="txt" name="cogfile" label="COG assignation"/>
+ <data from_work_dir="outputs/GCskew.txt" format="txt" name="gcfile" label="GC_percent"/>
+ <data from_work_dir="outputs/upsetr.svg" format="svg" name="upset" label="Upset Diagram"/>
+ <data from_work_dir="outputs/heatmap.svg.gz" format="svg" name="heatmap" label="Presence Absence Heatmap"/>
+ <data from_work_dir="outputs/heatmap.svg.heatmap_plotly.html" format="html" name="heatmap_html" label="Presence Absence Heatmap interactive"/>
+ <data from_work_dir="outputs/cog_stats.txt" format="tabular" name="outcog_stat" label="COG category counts"/>
+ <data from_work_dir="outputs/cog_stats2.txt" format="tabular" name="outcog_stat2" label="COG category 2 counts"/>
+ <data from_work_dir="outputs/cog_of_clusters.txt" format="tabular" name="outcog_clusters" label="COG of clusters"/>
+ <data from_work_dir="outputs/fastani.out.matrix.complete" format="tabular" name="fastani" label="ANI" />
+ <data from_work_dir="outputs/fastani.out.svg" format="svg" name="ani_svg" label="ANI heatmap" />
+ <data from_work_dir="outputs/rarefaction_curves.txt" format="txt" name="rarefaction_curves" label="Rarefaction curves data"/>
+ <data from_work_dir="outputs/rarefaction_curves.svg" format="svg" name="rarefaction_curves_svg" label="Rarefaction curves"/>
+ <data from_work_dir="outputs/heaps.tsv" format="txt" name="heaps" label="Heaps law alpha"/>
+ <data from_work_dir="outputs/heatmap.svg.complete.pdf.distance_matrix.txt" format="txt" name="distance_matrix" label="Accessory based distance matrix"/>
+ <data from_work_dir="outputs/all_genomes.vcf" format="vcf" name="vcf" label="VCF file"/>
  <data format="txt" name="logfile" label="Logfile"/>
  <data format="txt" name="roary_log" label="Roary Logfile"/>
 </outputs>