comparison PanExplorer.xml @ 16:1e0698511c9f draft

Uploaded

15:dbde253606c5

<tool id="pangenome_explorer" name="Pangenome Explorer2" 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="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>
 
 </requirements>

    <command><![CDATA[

export PANEX_PATH=${__tool_directory__};


#if str($mode.mode) == "accessions":
	    perl ${__tool_directory__}/Perl/generateConfig.pl 'None' '$input' config.yaml 'None';
#else if str($mode.mode) == "genbanks":
	    perl ${__tool_directory__}/Perl/generateConfig.pl '$private_genomes' 'None' config.yaml 'None';
#else if str($mode.mode) == "fasta":
            perl ${__tool_directory__}/Perl/generateConfig.pl '$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 $software=="pgap"
sed "s/identity\=80/identity\=$min_identity/g" \$PANEX_PATH/Snakemake_files/Snakefile_wget_PGAP_heatmap_upset_COG >snakefile;
#else if $software=="roary"
sed "s/identity\=80/identity\=$min_identity/g" \$PANEX_PATH/Snakemake_files/Snakefile_wget_roary_heatmap_upset_COG >snakefile;
#else if $software=="orthofinder"
sed "s/identity\=80/identity\=$min_identity/g" \$PANEX_PATH/Snakemake_files/Snakefile_orthofinder_heatmap_upset >snakefile;
#else if $software=="cactus"
cp -rf \$PANEX_PATH/Snakemake_files/Snakefile_wget_cactus_heatmap_upset_COG2 snakefile;
#else if $software=="pggb"
sed "s/identity\=30/identity\=$min_identity/g" \$PANEX_PATH/Snakemake_files/Snakefile_wget_pggb_heatmap_upset_COG >snakefile;
#else
sed "s/identity\=80/identity\=$min_identity/g" \$PANEX_PATH/Snakemake_files/Snakefile_wget_panacota_heatmap_upset_COG >snakefile;
#end if

singularity exec \$PANEX_PATH/panexplorer.sif snakemake --cores 1 -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;

16:1e0698511c9f

<tool id="PanExplorer2" 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="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">ghcr.io/pangenome/pggb:latest</container> -->
 </requirements>

    <command><![CDATA[

export PANEX_PATH=/usr/local/bin/PanExplorer_workflow;

#if str($mode.mode) == "accessions":
	    perl ${__tool_directory__}/generateConfig.pl 'None' '$input' config.yaml 'None';
#else if str($mode.mode) == "genbanks":
	    perl ${__tool_directory__}/generateConfig.pl '$private_genomes' 'None' config.yaml 'None';
#else if str($mode.mode) == "fasta":
            perl ${__tool_directory__}/generateConfig.pl '$private_genomes' 'None' config.yaml '$private_genomes_fasta';
#end if

cat config.yaml >$logfile;

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"
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"
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"
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"
	    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"
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
	    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 ${__tool_directory__}/panexplorer.sif snakemake --cores 1 -s snakefile >>$logfile 2>&1;


cp -rf outputs/upsetr.svg $upset;
cp -rf outputs/pav_matrix.tsv $output;
cp -rf outputs/heatmap.svg.gz $heatmap;