diff pima_report.xml @ 12:99613333fd1f draft

Uploaded
author greg
date Fri, 10 Mar 2023 16:35:16 +0000
parents 7177d81eb7cb
children f03c80bb22e9
line wrap: on
line diff
--- a/pima_report.xml	Thu Mar 09 18:34:01 2023 +0000
+++ b/pima_report.xml	Fri Mar 10 16:35:16 2023 +0000
@@ -10,17 +10,29 @@
 #set analysis_name = re.sub('[^\s\w\-]', '_', str($illumina_fastq_file.element_identifier))
 #set assembly_name = re.sub('[^\s\w\-]', '_', str($assembly_fasta_file.element_identifier))
 
-#set blastn_version = re.sub('[^\s\w\-]', '_', str($blastn_features.element_identifier))
-#set blastn_version = $blastn_version.rstrip('(features)')
-#set dnadiff_version = re.sub('[^\s\w\-]', '_', str($dnadiff_snps_file.element_identifier))
-#set dnadiff_version = $dnadiff_version.rstrip('(snps)')
+#if str($bedtools_complementbed_file) not in ['None', '']:
+    #set bedtools_version = re.sub('[^\s\w\-]', '_', str($bedtools_complementbed_file.element_identifier))
+#end if
+#if str($blastn_features) not in ['None', '']:
+    #set blastn_version = re.sub('[^\s\w\-]', '_', str($blastn_features.element_identifier))
+#end if
+#if str($dnadiff_snps_file) not in ['None', '']:
+    #set dnadiff_version = re.sub('[^\s\w\-]', '_', str($dnadiff_snps_file.element_identifier))
+#end if
 #if str($flye_assembly_info_file) not in ['None', '']:
     #set flye_version = re.sub('[^\s\w\-]', '_', str($flye_assembly_info_file.element_identifier))
-    #set flye_version = $flye_version.rstrip('(assembly info)')
 #end if
 #if str($kraken2_report_file) not in ['None', '']:
     #set kraken2_version = re.sub('[^\s\w\-]', '_', str($kraken2_report_file.element_identifier))
-    #set kraken2_version = $kraken2_version.rstrip('(report)')
+#end if
+#if str($minimap2_bam_file) not in ['None', '']:
+    #set minimap2_version = re.sub('[^\s\w\-]', '_', str($minimap2_bam_file.element_identifier))
+#end if
+#if str($samtools_pileup_file) not in ['None', '']:
+    #set samtools_version = re.sub('[^\s\w\-]', '_', str($samtools_pileup_file.element_identifier))
+#end if
+#if str($varscan_vcf_file) not in ['None', '']:
+    #set varscan_version = re.sub('[^\s\w\-]', '_', str($varscan_vcf_file.element_identifier))
 #end if
 
 mkdir amr_matrix_png_dir &&
@@ -56,12 +68,19 @@
 --analysis_name '$analysis_name'
 --assembly_fasta_file '$assembly_fasta_file'
 --assembly_name '$assembly_name'
---blastn_version '$blastn_version'
+#if str($bedtools_complementbed_file) not in ['None', '']:
+    --bedtools_version '$bedtools_version'
+#end if
+#if str($blastn_features) not in ['None', '']:
+    --blastn_version '$blastn_version'
+#end if
 --compute_sequence_length_file '$compute_sequence_length_file'
 --contig_coverage_file '$contig_coverage_file'
 --dbkey '$aligned_sample.metadata.dbkey'
 --dnadiff_snps_file '$dnadiff_snps_file'
---dnadiff_version '$dnadiff_version'
+#if str($dnadiff_snps_file) not in ['None', '']:
+    --dnadiff_version '$dnadiff_version'
+#end if
 --feature_bed_dir 'feature_bed_dir'
 --feature_png_dir 'feature_png_dir'
 #if str($flye_assembly_info_file) not in ['None', '']:
@@ -77,11 +96,20 @@
     --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'
 --mutation_regions_bed_file '$mutation_regions_bed_file'
 --pima_css '${__tool_directory__}/pima.css'
 --plasmids_file '$plasmids_file'
 --reference_insertions_file '$reference_insertions_file'
+#if str($samtools_pileup_file) not in ['None', '']:
+    --samtools_version '$samtools_version'
+#end if
+#if str($varscan_vcf_file) not in ['None', '']:
+    --varscan_version '$varscan_version'
+#end if
 && mv 'pima_report.pdf' '$output'
     ]]></command>
     <inputs>
@@ -89,6 +117,7 @@
         <param name="aligned_sample" type="data" format="bam" label="Aligned sample BAM file"/>
         <param name="amr_deletions_file" type="data" format="bed" label="AMR deletions BED file"/>
         <param name="assembly_fasta_file" type="data" format="fasta" label="Assembly FASTA file"/>
+        <param name="bedtools_complementbed_file" type="data" format="bed" label="Bedtools ComplementBed BED file"/>
         <param name="blastn_features" format="tabular" type="data_collection" collection_type="list" label="Collection of blastn tabular files"/>
         <param name="compute_sequence_length_file" type="data" format="tabular,tsv" label="Compute sequence length tabular file"/>
         <param name="contig_coverage_file" type="data" format="tabular,tsv" label="Contig coverage tabular file"/>
@@ -99,10 +128,13 @@
         <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="illumina_fastq_file" type="data" format="fastqsanger,fastqsanger.gz" label="Fastq sample file"/>
+        <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="reference_insertions_file" type="data" format="bed" label="Reference insertions BED file"/>
         <param name="plasmids_file" type="data" format="tsv" label="pChunks plasmids TSV file"/>
+        <param name="samtools_pileup_file" type="data" format="pileup" label="Samtools pileup file"/>
+        <param name="varscan_vcf_file" type="data" format="vcf" label="Varscan VCF file"/>
     </inputs>
     <outputs>
         <data name="output" format="pdf"/>