comparison pima_report.xml @ 28:27485e70ed2b draft

Uploaded

27:ddc056cf16bf

#for $i in $mutation_regions:
    #set file_name = $i.file_name
    #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
    ln -s $i 'mutation_regions_dir/$identifier' &&
#end for

python '${__tool_directory__}/pima_report.py' 
--amr_matrix_png_dir 'amr_matrix_png_dir'
--amr_deletions_file '$amr_deletions_file'
--analysis_name '$analysis_name'

    --illumina_reverse_read_file '$read_type_cond.illumina_reverse_read'
#end if
#if str($kraken2_report_file) not in ['None', '']:
    --kraken2_report_file '$kraken2_report_file'
    --kraken2_version '$kraken2_version'
#end if
#if str($minimap2_bam_file) not in ['None', '']:
    --minimap2_version '$minimap2_version'
#end if
--mutation_regions_dir 'mutation_regions_dir'

        <param name="features_bed" format="bed" type="data_collection" collection_type="list" label="Collection of best feature hits BED files"/>
        <param name="features_png" format="png" type="data_collection" collection_type="list" label="Collection of best feature hits PNG files"/>
        <param name="assembler_version_file" type="data" format="fasta,tabular,tsv" optional="true" label="Assembly version file" help="Optional, ignored if not selected"/>
        <param name="genome_insertions_file" type="data" format="bed" label="Genome insertions BED file"/>
        <param name="kraken2_report_file" type="data" format="tabular,tsv" optional="true" label="Kraken2 report tabular file" help="Optional, ignored if not selected"/>
        <param name="minimap2_bam_file" type="data" format="bam" label="Minimap2 BAM file"/>
        <param name="mutation_regions" format="tabular,tsv" type="data_collection" collection_type="list" label="Collection of mutation regions tabular files"/>
        <param name="mutation_regions_bed_file" type="data" format="mutations_regions,bed" label="Mutation regions BED file"/>
        <param name="quast_report_file" type="data" format="tabular" label="Quast report tabular file"/>
        <conditional name="read_type_cond">

28:27485e70ed2b

#for $i in $mutation_regions:
    #set file_name = $i.file_name
    #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
    ln -s $i 'mutation_regions_dir/$identifier' &&
#end for

#if $lrn_risk_amr_collection:
    #set lrn_risk_amr_file = 'lrn_risk_amr.tsv'
    touch $lrn_risk_amr_file &&
    #for $i in $lrn_risk_amr_collection:
        cat $i >> $lrn_risk_amr_file &&
    #end for
#end if

#if $lrn_risk_blacklist_collection:
    #set lrn_risk_blacklist_file = 'lrn_risk_blacklist.tsv'
    touch $lrn_risk_blacklist_file &&
    #for $i in $lrn_risk_blacklist_collection:
        cat $i >> $lrn_risk_blacklist_file &&
    #end for
#end if

#if $lrn_risk_vf_collection:
    #set lrn_risk_vf_file = 'lrn_risk_vf.tsv'
    touch $lrn_risk_vf_file &&
    #for $i in $lrn_risk_vf_collection:
        cat $i >> $lrn_risk_vf_file &&
    #end for
#end if

python '${__tool_directory__}/pima_report.py' 
--amr_matrix_png_dir 'amr_matrix_png_dir'
--amr_deletions_file '$amr_deletions_file'
--analysis_name '$analysis_name'

    --illumina_reverse_read_file '$read_type_cond.illumina_reverse_read'
#end if
#if str($kraken2_report_file) not in ['None', '']:
    --kraken2_report_file '$kraken2_report_file'
    --kraken2_version '$kraken2_version'
#end if
#if $lrn_risk_amr_collection:
    --lrn_risk_amr_file '$lrn_risk_amr_file'
#end if
#if $lrn_risk_blacklist_collection:
    --lrn_risk_blacklist_file '$lrn_risk_blacklist_file'
#end if
#if $lrn_risk_vf_collection:
    --lrn_risk_vf_file '$lrn_risk_vf_file'
#end if
#if str($minimap2_bam_file) not in ['None', '']:
    --minimap2_version '$minimap2_version'
#end if
--mutation_regions_dir 'mutation_regions_dir'

        <param name="features_bed" format="bed" type="data_collection" collection_type="list" label="Collection of best feature hits BED files"/>
        <param name="features_png" format="png" type="data_collection" collection_type="list" label="Collection of best feature hits PNG files"/>
        <param name="assembler_version_file" type="data" format="fasta,tabular,tsv" optional="true" label="Assembly version file" help="Optional, ignored if not selected"/>
        <param name="genome_insertions_file" type="data" format="bed" label="Genome insertions BED file"/>
        <param name="kraken2_report_file" type="data" format="tabular,tsv" optional="true" label="Kraken2 report tabular file" help="Optional, ignored if not selected"/>
        <param name="lrn_risk_amr_collection" format="tsv" type="data_collection" collection_type="list" optional="true" label="LRN Risk AMR collection"/>
        <param name="lrn_risk_blacklist_collection" format="tsv" type="data_collection" collection_type="list" optional="true" label="LRN Risk blacklist collection"/>
        <param name="lrn_risk_vf_collection" format="tsv" type="data_collection" collection_type="list" optional="true" label="LRN Risk virulence factors collection"/>
        <param name="minimap2_bam_file" type="data" format="bam" label="Minimap2 BAM file"/>
        <param name="mutation_regions" format="tabular,tsv" type="data_collection" collection_type="list" label="Collection of mutation regions tabular files"/>
        <param name="mutation_regions_bed_file" type="data" format="mutations_regions,bed" label="Mutation regions BED file"/>
        <param name="quast_report_file" type="data" format="tabular" label="Quast report tabular file"/>
        <conditional name="read_type_cond">