diff PanExplorer.xml @ 16:1e0698511c9f draft

Uploaded

--- a/PanExplorer.xml	Wed Dec 11 08:25:06 2024 +0000
+++ b/PanExplorer.xml	Sun Dec 15 21:30:16 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="pangenome_explorer" name="Pangenome Explorer2" version="2.0">
+<tool id="PanExplorer2" name="PanExplorer2" version="2.0">
   <description> Bacterial pan-genome analysis </description>
   <requirements>
   <!--
@@ -10,45 +10,42 @@
  -->
     <requirement type="package" version="1.30">perl-yaml</requirement>
     <requirement type="package" version="3.8.7">singularity</requirement>
- 
+    <!--    <container type="docker">ghcr.io/pangenome/pggb:latest</container> -->
  </requirements>
 
     <command><![CDATA[
 
-export PANEX_PATH=${__tool_directory__};
-
+export PANEX_PATH=/usr/local/bin/PanExplorer_workflow;
 
 #if str($mode.mode) == "accessions":
-	    perl ${__tool_directory__}/Perl/generateConfig.pl 'None' '$input' config.yaml 'None';
+	    perl ${__tool_directory__}/generateConfig.pl 'None' '$input' config.yaml 'None';
 #else if str($mode.mode) == "genbanks":
-	    perl ${__tool_directory__}/Perl/generateConfig.pl '$private_genomes' 'None' config.yaml 'None';
+	    perl ${__tool_directory__}/generateConfig.pl '$private_genomes' 'None' config.yaml 'None';
 #else if str($mode.mode) == "fasta":
-            perl ${__tool_directory__}/Perl/generateConfig.pl '$private_genomes' 'None' config.yaml '$private_genomes_fasta';
+            perl ${__tool_directory__}/generateConfig.pl '$private_genomes' 'None' config.yaml '$private_genomes_fasta';
 #end if
 
 cat config.yaml >$logfile;
 
-
-
-if [ ! -f \$PANEX_PATH/panexplorer.sif ]; then wget -O \$PANEX_PATH/panexplorer.sif https://panexplorer.southgreen.fr/singularity/panexplorer.sif >>$logfile 2>&1;fi;
+if [ ! -f ${__tool_directory__}/panexplorer.sif ]; then wget -O ${__tool_directory__}/panexplorer.sif https://panexplorer.southgreen.fr/singularity/panexplorer.sif >>$logfile 2>&1;fi;
 
 
 
 #if $software=="pgap"
-sed "s/identity\=80/identity\=$min_identity/g" \$PANEX_PATH/Snakemake_files/Snakefile_wget_PGAP_heatmap_upset_COG >snakefile;
+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;
 #else if $software=="roary"
-sed "s/identity\=80/identity\=$min_identity/g" \$PANEX_PATH/Snakemake_files/Snakefile_wget_roary_heatmap_upset_COG >snakefile;
+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;
 #else if $software=="orthofinder"
-sed "s/identity\=80/identity\=$min_identity/g" \$PANEX_PATH/Snakemake_files/Snakefile_orthofinder_heatmap_upset >snakefile;
+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;
 #else if $software=="cactus"
-cp -rf \$PANEX_PATH/Snakemake_files/Snakefile_wget_cactus_heatmap_upset_COG2 snakefile;
+	    singularity exec ${__tool_directory__}/panexplorer.sif cp -rf \$PANEX_PATH/Snakemake_files/Snakefile_wget_cactus_heatmap_upset_COG2 1>snakefile 2>>$logfile;
 #else if $software=="pggb"
-sed "s/identity\=30/identity\=$min_identity/g" \$PANEX_PATH/Snakemake_files/Snakefile_wget_pggb_heatmap_upset_COG >snakefile;
+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>>$logfile;
 #else
-sed "s/identity\=80/identity\=$min_identity/g" \$PANEX_PATH/Snakemake_files/Snakefile_wget_panacota_heatmap_upset_COG >snakefile;
+	    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;
 #end if
 
-singularity exec \$PANEX_PATH/panexplorer.sif snakemake --cores 1 -s snakefile >>$logfile 2>&1;
+singularity exec ${__tool_directory__}/panexplorer.sif snakemake --cores 1 -s snakefile >>$logfile 2>&1;
 
 
 cp -rf outputs/upsetr.svg $upset;