# HG changeset patch
# User greg
# Date 1677881183 0
# Node ID 0a558f444c98160e03aed31d7dc157fd9301a9de

Uploaded

diff -r 000000000000 -r 0a558f444c98 .shed.yml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/.shed.yml	Fri Mar 03 22:06:23 2023 +0000
@@ -0,0 +1,9 @@
+name: pima_report
+owner: greg
+description: Generates the PIMA analysis summary report
+long_description: Generates the PIMA analysis summary report
+categories: 
+- Nanopore
+remote_repository_url: https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/pima/pima_report
+homepage_url: https://github.com/gregvonkuster/galaxy_tools
+type: unrestricted
diff -r 000000000000 -r 0a558f444c98 macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Fri Mar 03 22:06:23 2023 +0000
@@ -0,0 +1,22 @@
+<macros>
+    <token name="@TOOL_VERSION@">1.0.0</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">21.01</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="1.79">biopython</requirement>
+            <requirement type="package" version="5.1.0">gawk</requirement>
+            <requirement type="package" version="3.4">grep</requirement>
+            <requirement type="package" version="1.5.0">mdutils</requirement>
+            <requirement type="package" version="1.5.2">pandas</requirement>
+            <requirement type="package" version="1.10">pypandoc</requirement>
+            <requirement type="package" version="57.1">weasyprint</requirement>
+        </requirements>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1101/2020.01.09.900589</citation>
+        </citations>
+    </xml>
+</macros>
+
diff -r 000000000000 -r 0a558f444c98 pima.css
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pima.css	Fri Mar 03 22:06:23 2023 +0000
@@ -0,0 +1,143 @@
+html {
+    line-height: 1.5;
+    font-family: Georgia, serif;
+    font-size: 20px;
+    color: #1a1a1a;
+    background-color: #fdfdfd;
+}
+body {
+    margin: 0 auto;
+    max-width: 50em;
+    padding-left: 20px;
+    padding-right: 20px;
+    padding-top: 20px;
+    padding-bottom: 20px;
+    hyphens: auto;
+    overflow-wrap: break-word;
+    font-kerning: normal;
+}
+@media print {
+    body {
+        background-color: transparent;
+        color: black;
+        font-size: 10pt;
+    }
+    p, h2, h3 {
+        orphans: 3;
+        widows: 3;
+    }
+    h2, h3, h4 {
+        page-break-after: avoid;
+    }
+}
+p {
+    margin: 1em 0;
+}
+a {
+    color: #3333FF;
+}
+a:visited {
+    color: #1a1a1a;
+}
+img {
+    max-width: 100%;
+}
+h1, h2, h3, h4, h5, h6 {
+    margin-top: 1.4em;
+}
+h5, h6 {
+    font-size: .8em;
+    font-style: italic;
+}
+h6 {
+    font-weight: normal;
+}
+ol, ul {
+    padding-left: 1.7em;
+    margin-top: 1em;
+}
+li > ol, li > ul {
+    margin-top: 0;
+}
+blockquote {
+    margin: 1em 0 1em 1.7em;
+    padding-left: 1em;
+    border-left: 2px solid #e6e6e6;
+    color: #606060;
+}
+code {
+    font-family: Menlo, Monaco, 'Lucida Console', Consolas, monospace;
+    font-size: 85%;
+    margin: 0;
+}
+pre {
+    margin: 1em 0;
+    overflow: auto;
+}
+pre code {
+    padding: 0;
+    overflow: visible;
+    overflow-wrap: normal;
+}
+.sourceCode {
+    background-color: transparent;
+    overflow: visible;
+}
+hr {
+    background-color: #1a1a1a;
+    border: none;
+    height: 1px;
+    margin: 1em 0;
+}
+table {
+    border-collapse: collapse;
+    font-variant-numeric: lining-nums tabular-nums;
+    /*
+    margin-left: auto;
+    margin-right: auto; */
+}
+
+table caption {
+    margin-bottom: 0.75em;
+}
+tbody {
+    margin-top: 0.5em;
+    border-top: 1px solid #1a1a1a;
+    border-bottom: 1px solid #1a1a1a;
+    text-align: center;
+}
+th {
+    border-top: 1px solid #1a1a1a;
+    padding: 0.25em 0.5em 0.25em 0.5em;
+}
+td {
+    padding: 0.125em 0.5em 0.25em 0.5em;
+
+}
+
+tr:nth-child(even) {background: #CCC}
+tr:nth-child(odd) {background: #FFF}
+
+header {
+    margin-bottom: 4em;
+    text-align: center;
+}
+#TOC li {
+    list-style: none;
+}
+#TOC ul {
+    padding-left: 1.3em;
+}
+#TOC > ul {
+    padding-left: 0;
+}
+#TOC a:not(:hover) {
+    text-decoration: none;
+}
+code{white-space: pre-wrap;}
+span.smallcaps{font-variant: small-caps;}
+span.underline{text-decoration: underline;}
+div.column{display: inline-block; vertical-align: top; width: 50%;}
+div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
+ul.task-list{list-style: none;}
+.display.math{display: block; text-align: center; margin: 0.5rem auto;}
diff -r 000000000000 -r 0a558f444c98 pima_report.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pima_report.py	Fri Mar 03 22:06:23 2023 +0000
@@ -0,0 +1,733 @@
+import argparse
+import os
+import pandas
+import pypandoc
+import re
+import subprocess
+import sys
+
+from Bio import SeqIO
+from datetime import date
+from mdutils.mdutils import MdUtils
+
+CDC_ADVISORY = 'The analysis and report presented here should be treated as preliminary.  Please contact the CDC/BDRD with any results regarding _Bacillus anthracis_.'
+
+
+class PimaReport:
+
+    def __init__(self, analysis_name=None, assembly_fasta_file=None, assembly_name=None, feature_bed_files=None, feature_png_files=None,
+                 contig_coverage_file=None, dbkey=None, gzipped=None, illumina_fastq_file=None, mutation_regions_bed_file=None,
+                 mutation_regions_tsv_files=None, pima_css=None):
+        self.ofh = open("process_log.txt", "w")
+
+        self.ofh.write("analysis_name: %s\n" % str(analysis_name))
+        self.ofh.write("assembly_fasta_file: %s\n" % str(assembly_fasta_file))
+        self.ofh.write("assembly_name: %s\n" % str(assembly_name))
+        self.ofh.write("feature_bed_files: %s\n" % str(feature_bed_files))
+        self.ofh.write("feature_png_files: %s\n" % str(feature_png_files))
+        self.ofh.write("contig_coverage_file: %s\n" % str(contig_coverage_file))
+        self.ofh.write("dbkey: %s\n" % str(dbkey))
+        self.ofh.write("gzipped: %s\n" % str(gzipped))
+        self.ofh.write("illumina_fastq_file: %s\n" % str(illumina_fastq_file))
+        self.ofh.write("mutation_regions_bed_file: %s\n" % str(mutation_regions_bed_file))
+        self.ofh.write("mutation_regions_tsv_files: %s\n" % str(mutation_regions_tsv_files))
+        self.ofh.write("pima_css: %s\n" % str(pima_css))
+
+        # General
+        self.doc = None
+        self.report_md = 'pima_report.md'
+
+        # Inputs
+        self.analysis_name = analysis_name
+        self.assembly_fasta_file = assembly_fasta_file
+        self.assembly_name = assembly_name
+        self.feature_bed_files = feature_bed_files
+        self.feature_png_files = feature_png_files
+        self.contig_coverage_file = contig_coverage_file
+        self.dbkey = dbkey
+        self.gzipped = gzipped
+        self.illumina_fastq_file = illumina_fastq_file
+        self.mutation_regions_bed_file = mutation_regions_bed_file
+        self.mutation_regions_tsv_files = mutation_regions_tsv_files
+        self.read_type = 'Illumina'
+        self.ont_bases = None
+        self.ont_n50 = None
+        self.ont_read_count = None
+        self.pima_css = pima_css
+
+        # Titles
+        self.alignment_title = 'Comparison with reference'
+        self.alignment_notes_title = 'Alignment notes'
+        self.amr_matrix_title = 'AMR matrix'
+        self.assembly_methods_title = 'Assembly'
+        self.assembly_notes_title = 'Assembly notes'
+        self.basecalling_title = 'Basecalling'
+        self.basecalling_methods_title = 'Basecalling'
+        self.contamination_methods_title = 'Contamination check'
+        self.contig_alignment_title = 'Alignment vs. reference contigs'
+        self.feature_title = 'Features found in the assembly'
+        self.feature_methods_title = 'Feature annotation'
+        self.feature_plot_title = 'Feature annotation plots'
+        self.large_indel_title = 'Large insertions & deletions'
+        self.methods_title = 'Methods'
+        self.mutation_title = 'Mutations found in the sample'
+        self.mutation_methods_title = 'Mutation screening'
+        self.plasmid_methods_title = 'Plasmid annotation'
+        self.reference_methods_title = 'Reference comparison'
+        self.snp_indel_title = 'SNPs and small indels'
+        #self.summary_title = 'Summary'
+        self.summary_title = 'Analysis of %s' % analysis_name
+
+        # Methods
+        self.methods = pandas.Series(dtype='float64')
+        self.methods[self.contamination_methods_title] = pandas.Series(dtype='float64')
+        self.methods[self.assembly_methods_title] = pandas.Series(dtype='float64')
+        self.methods[self.reference_methods_title] = pandas.Series(dtype='float64')
+        self.methods[self.mutation_methods_title] = pandas.Series(dtype='float64')
+        self.methods[self.feature_methods_title] = pandas.Series(dtype='float64')
+        self.methods[self.plasmid_methods_title] = pandas.Series(dtype='float64')
+
+        # Contamination
+        self.kraken_fracs = pandas.Series(dtype=object)
+
+        # Notes
+        self.assembly_notes = pandas.Series(dtype=object)
+        self.alignment_notes = pandas.Series(dtype=object)
+        self.contig_alignment = pandas.Series(dtype=object)
+
+        # Values
+        self.assembly_size = 0
+        self.contig_info = None
+        self.did_flye_ont_fastq = False
+        self.did_medaka_ont_assembly = False
+        self.feature_hits = pandas.Series(dtype='float64')
+        self.illumina_length_mean = 0
+        self.illumina_read_count = 0
+        self.illumina_bases = 0
+        self.mean_coverage = 0
+        self.num_assembly_contigs = 0
+
+        # Actions
+        self.did_guppy_ont_fast5 = False
+        self.did_qcat_ont_fastq = False
+        self.info_illumina_fastq()
+        self.load_contig_info()
+
+    def run_command(self, command):
+        self.ofh.write("\nXXXXXX In run_command, command:\n%s\n\n" % str(command))
+        try:
+            return re.split('\\n', subprocess.check_output(command, shell=True).decode('utf-8'))
+        except Exception:
+            message = 'Command %s failed: exiting...' % command
+            sys.exit(message)
+
+    def format_kmg(self, number, decimals=0):
+        self.ofh.write("\nXXXXXX In format_kmg, number:\n%s\n" % str(number))
+        self.ofh.write("XXXXXX In format_kmg, decimals:\n%s\n\n" % str(decimals))
+        if number == 0:
+            return '0'
+        magnitude_powers = [10**9, 10**6, 10**3, 1]
+        magnitude_units = ['G', 'M', 'K', '']
+        for i in range(len(magnitude_units)):
+            if number >= magnitude_powers[i]:
+                magnitude_power = magnitude_powers[i]
+                magnitude_unit = magnitude_units[i]
+                return ('{:0.' + str(decimals) + 'f}').format(number / magnitude_power) + magnitude_unit
+
+    def load_contig_info(self):
+        self.contig_info = pandas.Series(dtype=object)
+        self.contig_info[self.read_type] = pandas.read_csv(self.contig_coverage_file, header=None, index_col=None, sep='\t').sort_values(1, axis=0, ascending=False)
+        self.contig_info[self.read_type].columns = ['contig', 'size', 'coverage']
+        self.mean_coverage = (self.contig_info[self.read_type].iloc[:, 1] * self.contig_info[self.read_type].iloc[:, 2]).sum() / self.contig_info[self.read_type].iloc[:, 1].sum()
+
+    def load_fasta(self, fasta):
+        sequence = pandas.Series(dtype=object)
+        for contig in SeqIO.parse(fasta, 'fasta'):
+            sequence[contig.id] = contig
+        return sequence
+
+    def load_assembly(self):
+        self.assembly = self.load_fasta(self.assembly_fasta_file)
+        self.num_assembly_contigs = len(self.assembly)
+        for i in self.assembly:
+            self.assembly_size += len(i.seq)
+        self.assembly_size = self.format_kmg(self.assembly_size, decimals=1)
+
+    def info_illumina_fastq(self):
+        self.ofh.write("\nXXXXXX In info_illumina_fastq\n\n")
+        if self.gzipped:
+            opener = 'gunzip -c'
+        else:
+            opener = 'cat'
+        command = ' '.join([opener,
+                            self.illumina_fastq_file,
+                            '| awk \'{getline;s += length($1);getline;getline;}END{print s/(NR/4)"\t"(NR/4)"\t"s}\''])
+        output = self.run_command(command)
+        self.ofh.write("output:\n%s\n" % str(output))
+        self.ofh.write("re.split('\\t', self.run_command(command)[0]:\n%s\n" % str(re.split('\\t', self.run_command(command)[0])))
+        values = []
+        for i in re.split('\\t', self.run_command(command)[0]):
+            if i == '':
+                values.append(float('nan'))
+            else:
+                values.append(float(i))
+        self.ofh.write("values:\n%s\n" % str(values))
+        self.ofh.write("values[0]:\n%s\n" % str(values[0]))
+        self.illumina_length_mean += values[0]
+        self.ofh.write("values[1]:\n%s\n" % str(values[1]))
+        self.illumina_read_count += int(values[1])
+        self.ofh.write("values[2]:\n%s\n" % str(values[2]))
+        self.illumina_bases += int(values[2])
+        # The original PIMA code inserts self.illumina_fastq into
+        # a list for no apparent reason.  We don't do that here.
+        # self.illumina_length_mean /= len(self.illumina_fastq)
+        self.illumina_length_mean /= 1
+        self.illumina_bases = self.format_kmg(self.illumina_bases, decimals=1)
+
+    def start_doc(self):
+        #header_text = 'Analysis of %s' % self.analysis_name
+        self.doc = MdUtils(file_name=self.report_md, title='')
+
+    def add_run_information(self):
+        self.ofh.write("\nXXXXXX In add_run_information\n\n")
+        self.doc.new_line()
+        self.doc.new_header(1, 'Run information')
+        # Tables in md.utils are implemented as a wrapping function.
+        Table_list = [
+            "Category",
+            "Information",
+            "Date",
+            date.today(),
+            "ONT FAST5",
+            "N/A",
+            "ONT FASTQ",
+            "N/A",
+            "Illumina FASTQ",
+            self.wordwrap_markdown(self.analysis_name),
+            "Assembly",
+            self.wordwrap_markdown(self.assembly_name),
+            "Reference",
+            self.wordwrap_markdown(self.dbkey),
+        ]
+        self.doc.new_table(columns=2, rows=7, text=Table_list, text_align='left')
+        self.doc.new_line()
+        self.doc.new_line()
+
+    def add_ont_library_information(self):
+        self.ofh.write("\nXXXXXX In add_ont_library_information\n\n")
+        if self.ont_n50 is None:
+            return
+        self.doc.new_line()
+        self.doc.new_header(2, 'ONT library statistics')
+        Table_List = [
+            "Category",
+            "Quantity",
+            "ONT N50",
+            '{:,}'.format(self.ont_n50),
+            "ONT reads",
+            '{:,}'.format(self.ont_read_count),
+            "ONT bases",
+            '{:s}'.format(self.ont_bases),
+            "Illumina FASTQ",
+            self.wordwrap_markdown(self.illumina_fastq_file),
+            "Assembly",
+            self.wordwrap_markdown(self.assembly_name),
+            "Reference",
+            self.wordwrap_markdown(self.dbkey),
+        ]
+        self.doc.new_table(columns=2, rows=7, text=Table_List, text_align='left')
+        self.doc.new_line()
+
+    def add_illumina_library_information(self):
+        self.ofh.write("\nXXXXXX In add_illumina_library_information\n\n")
+        if self.illumina_length_mean is None:
+            return
+        self.doc.new_line()
+        self.doc.new_header(2, 'Illumina library statistics')
+        Table_List = [
+            "Illumina Info.",
+            "Quantity",
+            'Illumina mean length',
+            '{:.1f}'.format(self.illumina_length_mean),
+            'Illumina reads',
+            '{:,}'.format(self.illumina_read_count),
+            'Illumina bases',
+            '{:s}'.format(self.illumina_bases)
+        ]
+        self.doc.new_table(columns=2, rows=4, text=Table_List, text_align='left')
+
+    def add_assembly_information(self):
+        self.ofh.write("\nXXXXXX In add_assembly_information\n\n")
+        if self.assembly_fasta_file is None:
+            return
+        self.load_assembly()
+        self.doc.new_line()
+        self.doc.new_header(2, 'Assembly statistics')
+        Table_List = [
+            "Category",
+            "Information",
+            "Contigs",
+            str(self.num_assembly_contigs),
+            "Assembly size",
+            str(self.assembly_size),
+        ]
+        self.doc.new_table(columns=2, rows=3, text=Table_List, text_align='left')
+
+    def info_ont_fastq(self, fastq_file):
+        self.ofh.write("\nXXXXXX In info_ont_fastq, fastq_file:\n%s\n\n" % str(fastq_file))
+        opener = 'cat'
+        if self.gzipped:
+            opener = 'gunzip -c'
+        else:
+            opener = 'cat'
+        command = ' '.join([opener,
+                            fastq_file,
+                            '| awk \'{getline;print length($0);s += length($1);getline;getline;}END{print "+"s}\'',
+                            '| sort -gr',
+                            '| awk \'BEGIN{bp = 0;f = 0}',
+                            '{if(NR == 1){sub(/+/, "", $1);s=$1}else{bp += $1;if(bp > s / 2 && f == 0){n50 = $1;f = 1}}}',
+                            'END{printf "%d\\t%d\\t%d\\n", n50, (NR - 1), s;exit}\''])
+        result = list(re.split('\\t', self.run_command(command)[0]))
+        if result[1] == '0':
+            self.error_out('No ONT reads found')
+        ont_n50, ont_read_count, ont_raw_bases = [int(i) for i in result]
+
+        command = ' '.join([opener,
+                            fastq_file,
+                            '| awk \'{getline;print length($0);getline;getline;}\''])
+        result = self.run_command(command)
+        result = list(filter(lambda x: x != '', result))
+        ont_read_lengths = [int(i) for i in result]
+
+        return ([ont_n50, ont_read_count, ont_raw_bases, ont_read_lengths])
+
+    def wordwrap_markdown(self, string):
+        if string:
+            if len(string) < 35:
+                return string
+            else:
+                if '/' in string:
+                    adjust = string.split('/')
+                    out = ''
+                    max = 35
+                    for i in adjust:
+                        out = out + '/' + i
+                        if len(out) > max:
+                            out += '<br>'
+                            max += 35
+                    return out
+                else:
+                    out = [string[i:i + 35] for i in range(0, len(string), 50)]
+                    return '<br>'.join(out)
+        else:
+            return string
+
+    def add_contig_info(self):
+        self.ofh.write("\nXXXXXX In add_contig_info\n\n")
+        if self.contig_info is None:
+            return
+        for method in ['ONT', 'Illumina']:
+            if method not in self.contig_info.index:
+                continue
+            self.doc.new_line()
+            self.doc.new_header(2, 'Assembly coverage by ' + method)
+            Table_List = ["Contig", "Length (bp)", "Coverage (X)"]
+            formatted = self.contig_info[method].copy()
+            formatted.iloc[:, 1] = formatted.iloc[:, 1].apply(lambda x: '{:,}'.format(x))
+            for i in range(self.contig_info[method].shape[0]):
+                Table_List = Table_List + formatted.iloc[i, :].values.tolist()
+            row_count = int(len(Table_List) / 3)
+            self.doc.new_table(columns=3, rows=row_count, text=Table_List, text_align='left')
+
+    def add_assembly_notes(self):
+        self.ofh.write("\nXXXXXX In add_assembly_notes\n\n")
+        if len(self.assembly_notes) == 0:
+            return
+        self.doc.new_line()
+        self.doc.new_line('<div style="page-break-after: always;"></div>')
+        self.doc.new_line()
+        self.doc.new_header(2, self.assembly_notes_title)
+        #for note in self.analysis.assembly_notes:
+        #    self.doc.new_line(note)
+
+    def add_contamination(self):
+        self.ofh.write("\nXXXXXX In add_contamination\n\n")
+        if len(self.kraken_fracs) == 0:
+            return
+        self.doc.new_line()
+        self.doc.new_header(2, 'Contamination check')
+        for read_type, kraken_fracs in self.kraken_fracs.iteritems():
+            self.doc.new_line(read_type + ' classifications')
+            self.doc.new_line()
+            Table_List = ["Percent of Reads", "Reads", "Level", "Label"]
+            for index, row in kraken_fracs.iterrows():
+                Table_List = Table_List + row.tolist()
+            row_count = int(len(Table_List) / 4)
+            self.doc.new_table(columns=4, rows=row_count, text=Table_List, text_align='left')
+            if self.contamination_methods_title not in self.methods:
+                self.methods[self.contamination_methods_title] = ''
+        method = 'Kraken2 was used to assign the raw reads into taxa.'
+        self.methods[self.contamination_methods_title] = self.methods[self.contamination_methods_title].append(pandas.Series(method))
+
+    def add_alignment(self):
+        self.ofh.write("\nXXXXXX In add_alignment\n\n")
+        # TODO: implement the draw_circos function for this.
+        if len(self.contig_alignment) > 0:
+            alignments = self.contig_alignment
+        else:
+            return
+        self.doc.new_line()
+        self.doc.new_header(level=2, title=self.alignment_title)
+        self.doc.new_line()
+        self.doc.new_header(level=3, title=self.snp_indel_title)
+        Table_1 = [
+            "Category",
+            "Quantity",
+            'SNPs',
+            #'{:,}'.format(self.analysis.quast_mismatches),
+            'NA'
+            'Small indels',
+            #'{:,}'.format(self.analysis.quast_indels)
+            'NA'
+        ]
+        self.doc.new_table(columns=2, rows=3, text=Table_1, text_align='left')
+        self.doc.new_line('<div style="page-break-after: always;"></div>')
+        self.doc.new_line()
+        if len(self.alignment_notes) > 0:
+            self.doc.new_header(level=3, title=self.alignment_notes_title)
+            for note in self.alignment_notes:
+                self.doc.new_line(note)
+        for contig in alignments.index.tolist():
+            contig_title = 'Alignment to %s' % contig
+            image_png = alignments[contig]
+            self.doc.new_line()
+            self.doc.new_header(level=3, title=contig_title)
+            self.doc.new_line(self.doc.new_inline_image(text='contig_title', path=os.path.abspath(image_png)))
+            self.doc.new_line('<div style="page-break-after: always;"></div>')
+            self.doc.new_line()
+        method = 'The genome assembly was aligned against the reference sequencing using dnadiff.'
+        self.methods[self.reference_methods_title] = self.methods[self.reference_methods_title].append(pandas.Series(method))
+
+    def add_features(self):
+        self.ofh.write("\nXXXXXX In add_features\n\n")
+        if len(self.feature_bed_files) == 0:
+            return
+        for bbf in self.feature_bed_files:
+            if os.path.getsize(bbf) > 0:
+                best = pandas.read_csv(filepath_or_buffer=bbf, sep='\t', header=None)
+                self.feature_hits[os.path.basename(bbf)] = best
+        if len(self.feature_hits) == 0:
+            return
+        self.ofh.write("self.feature_hits: %s\n" % str(self.feature_hits))
+        self.doc.new_line()
+        self.doc.new_header(level=2, title=self.feature_title)
+        for feature_name in self.feature_hits.index.tolist():
+            self.ofh.write("feature_name: %s\n" % str(feature_name))
+            features = self.feature_hits[feature_name].copy()
+            self.ofh.write("features: %s\n" % str(features))
+            if features.shape[0] == 0:
+                continue
+            features.iloc[:, 1] = features.iloc[:, 1].apply(lambda x: '{:,}'.format(x))
+            features.iloc[:, 2] = features.iloc[:, 2].apply(lambda x: '{:,}'.format(x))
+            self.doc.new_line()
+            self.doc.new_header(level=3, title=feature_name)
+            if (features.shape[0] == 0):
+                continue
+            for contig in pandas.unique(features.iloc[:, 0]):
+                self.ofh.write("contig: %s\n" % str(contig))
+                self.doc.new_line(contig)
+                contig_features = features.loc[(features.iloc[:, 0] == contig), :]
+                self.ofh.write("contig_features: %s\n" % str(contig_features))
+                Table_List = ['Start', 'Stop', 'Feature', 'Identity (%)', 'Strand']
+                for i in range(contig_features.shape[0]):
+                    self.ofh.write("i: %s\n" % str(i))
+                    feature = contig_features.iloc[i, :].copy(deep=True)
+                    self.ofh.write("feature: %s\n" % str(feature))
+                    feature[4] = '{:.3f}'.format(feature[4])
+                    Table_List = Table_List + feature[1:].values.tolist()
+                self.ofh.write("Table_List: %s\n" % str(Table_List))
+                row_count = int(len(Table_List) / 5)
+                self.ofh.write("row_count: %s\n" % str(row_count))
+                self.doc.new_line()
+                self.doc.new_table(columns=7, rows=row_count, text=Table_List, text_align='left')
+        blastn_version = 'The genome assembly was queried for features using blastn.'
+        bedtools_version = 'Feature hits were clustered using bedtools and the highest scoring hit for each cluster was reported.'
+        method = '%s  %s' % (blastn_version, bedtools_version)
+        self.methods[self.feature_methods_title] = self.methods[self.feature_methods_title].append(pandas.Series(method))
+
+    def add_feature_plots(self):
+        self.ofh.write("\nXXXXXX In add_feature_plots\n\n")
+        if len(self.feature_png_files) == 0:
+            return
+        self.doc.new_line()
+        self.doc.new_header(level=2, title='Feature Plots')
+        self.doc.new_paragraph('Only contigs with features are shown')
+        for feature_png_file in self.feature_png_files:
+            self.doc.new_line(self.doc.new_inline_image(text='Analysis', path=os.path.abspath(feature_png_file)))
+
+    def add_mutations(self):
+        self.ofh.write("\nXXXXXX In add_mutations\n\n")
+        if len(self.mutation_regions_tsv_files) == 0:
+            return
+        try:
+            mutation_regions = pandas.read_csv(self.mutation_regions_bed_file, sep='\t', header=0, index_col=False)
+        except Exception:
+            # Likely an empty file.
+            return
+        amr_mutations = pandas.Series(dtype=object)
+        for region_i in range(mutation_regions.shape[0]):
+            region = mutation_regions.iloc[region_i, :]
+            region_name = str(region['name'])
+            self.ofh.write("Processing mutations for region %s\n" % region_name)
+            region_mutations_tsv_name = '%s_mutations.tsv' % region_name
+            if region_mutations_tsv_name not in self.mutation_regions_tsv_files:
+                continue
+            region_mutations_tsv = self.mutation_regions_tsv_files[region_mutations_tsv_name]
+            try:
+                region_mutations = pandas.read_csv(region_mutations_tsv, sep='\t', header=0, index_col=False)
+            except Exception:
+                region_mutations = pandas.DataFrame()
+            if region_mutations.shape[0] == 0:
+                continue
+            # Figure out what kind of mutations are in this region
+            region_mutation_types = pandas.Series(['snp'] * region_mutations.shape[0], name='TYPE', index=region_mutations.index)
+            region_mutation_types[region_mutations['REF'].str.len() != region_mutations['ALT'].str.len()] = 'small-indel'
+            region_mutation_drugs = pandas.Series(region['drug'] * region_mutations.shape[0], name='DRUG', index=region_mutations.index)
+            region_notes = pandas.Series(region['note'] * region_mutations.shape[0], name='NOTE', index=region_mutations.index)
+            region_mutations = pandas.concat([region_mutations, region_mutation_types, region_mutation_drugs, region_notes], axis=1)
+            region_mutations = region_mutations[['#CHROM', 'POS', 'TYPE', 'REF', 'ALT', 'DRUG', 'NOTE']]
+            amr_mutations[region['name']] = region_mutations
+        # Report the mutations.
+        self.doc.new_line()
+        self.doc.new_header(level=2, title=self.mutation_title)
+        for region_name in amr_mutations.index.tolist():
+            region_mutations = amr_mutations[region_name].copy()
+            self.doc.new_line()
+            self.doc.new_header(level=3, title=region_name)
+            if (region_mutations.shape[0] == 0):
+                self.doc.append('None')
+                continue
+            region_mutations.iloc[:, 1] = region_mutations.iloc[:, 1].apply(lambda x: '{:,}'.format(x))
+            Table_List = ['Reference contig', 'Position', 'Reference', 'Alternate', 'Drug', 'Note']
+            for i in range(region_mutations.shape[0]):
+                Table_List = Table_List + region_mutations.iloc[i, [0, 1, 3, 4, 5, 6]].values.tolist()
+            row_count = int(len(Table_List) / 6)
+            self.doc.new_table(columns=6, rows=row_count, text=Table_List, text_align='left')
+        method = '%s reads were mapped to the reference sequence using minimap2.' % self.read_type
+        self.methods[self.mutation_methods_title] = self.methods[self.mutation_methods_title].append(pandas.Series(method))
+        method = 'Mutations were identified using samtools mpileup and varscan.'
+        self.methods[self.mutation_methods_title] = self.methods[self.mutation_methods_title].append(pandas.Series(method))
+
+    def add_amr_matrix(self):
+        self.ofh.write("\nXXXXXX In add_amr_matrix\n\n")
+        # Make sure that we have an AMR matrix to plot
+        #if not getattr(self.analysis, 'did_draw_amr_matrix', False):
+        #    return
+        #amr_matrix_png = self.analysis.amr_matrix_png
+        #self.doc.new_line()
+        #self.doc.new_header(level=2, title=self.amr_matrix_title)
+        #self.doc.new_line('AMR genes and mutations with their corresponding drugs.')
+        #self.doc.new_line(
+        #    self.doc.new_inline_image(
+        #        text='AMR genes and mutations with their corresponding drugs',
+        #        path=amr_matrix_png
+        #    )
+        #)
+        pass
+
+    def add_large_indels(self):
+        self.ofh.write("\nXXXXXX In add_large_indels\n\n")
+        # Make sure we looked for mutations
+        #if len(self.analysis.large_indels) == 0:
+        #    return
+        #large_indels = self.analysis.large_indels
+        #self.doc.new_line()
+        #self.doc.new_header(level=2, title=self.large_indel_title)
+        #for genome in ['Reference insertions', 'Query insertions']:
+        #    genome_indels = large_indels[genome].copy()
+        #    self.doc.new_line()
+        #    self.doc.new_header(level=3, title=genome)
+        #    if (genome_indels.shape[0] == 0):
+        #        continue
+        #    genome_indels.iloc[:, 1] = genome_indels.iloc[:, 1].apply(lambda x: '{:,}'.format(x))
+        #    genome_indels.iloc[:, 2] = genome_indels.iloc[:, 2].apply(lambda x: '{:,}'.format(x))
+        #    genome_indels.iloc[:, 3] = genome_indels.iloc[:, 3].apply(lambda x: '{:,}'.format(x))
+        #    Table_List = [
+        #        'Reference contig', 'Start', 'Stop', 'Size (bp)'
+        #    ]
+        #    for i in range(genome_indels.shape[0]):
+        #        Table_List = Table_List + genome_indels.iloc[i, :].values.tolist()
+        #    row_count = int(len(Table_List) / 4)
+        #    self.doc.new_table(columns=4, rows=row_count, text=Table_List, text_align='left')
+        #method = 'Large insertions or deletions were found as the complement of aligned regions using bedtools.'
+        #self.methods[self.reference_methods_title] = self.methods[self.reference_methods_title].append(
+        #    pandas.Series(method))
+        #self.doc.new_line()
+        #self.doc.new_line('<div style="page-break-after: always;"></div>')
+        #self.doc.new_line()
+        pass
+
+    def add_plasmids(self):
+        self.ofh.write("\nXXXXXX In add_plasmids\n\n")
+        """
+        if not getattr(self.analysis, 'did_call_plasmids', False):
+            return
+        # Make sure we looked for mutations
+        #plasmids = self.analysis.plasmids
+        if plasmids is None:
+            return
+        plasmids = plasmids.copy()
+        self.doc.new_line()
+        #self.doc.new_header(level=2, title=self.analysis.plasmid_title)
+        if (plasmids.shape[0] == 0):
+            self.doc.new_line('None')
+            return
+        plasmids.iloc[:, 3] = plasmids.iloc[:, 3].apply(lambda x: '{:,}'.format(x))
+        plasmids.iloc[:, 4] = plasmids.iloc[:, 4].apply(lambda x: '{:,}'.format(x))
+        plasmids.iloc[:, 5] = plasmids.iloc[:, 5].apply(lambda x: '{:,}'.format(x))
+        Table_List = [
+            'Genome contig',
+            'Plasmid hit',
+            'Plasmid acc.',
+            'Contig size',
+            'Aliged',
+            'Plasmid size'
+        ]
+        for i in range(plasmids.shape[0]):
+            Table_List = Table_List + plasmids.iloc[i, 0:6].values.tolist()
+        row_count = int(len(Table_List) / 6)
+        self.doc.new_table(columns=6, rows=row_count, text=Table_List, text_align='left')
+        method = 'The plasmid reference database was queried against the genome assembly using minimap2.'
+        self.methods[self.plasmid_methods_title] = self.methods[self.plasmid_methods_title].append(pandas.Series(method))
+        method = 'The resulting SAM was converted to a PSL using a custom version of sam2psl.'
+        self.methods[self.plasmid_methods_title] = self.methods[self.plasmid_methods_title].append(pandas.Series(method))
+        method = 'Plasmid-to-genome hits were resolved using the pChunks algorithm.'
+        self.methods[self.plasmid_methods_title] = self.methods[self.plasmid_methods_title].append(pandas.Series(method))
+        """
+        pass
+
+    def add_methods(self):
+        self.ofh.write("\nXXXXXX In add_methods\n\n")
+        self.doc.new_line('<div style="page-break-after: always;"></div>')
+        self.doc.new_line()
+        if len(self.methods) == 0:
+            return
+        self.doc.new_line()
+        self.doc.new_header(level=2, title=self.methods_title)
+
+        for methods_section in self.methods.index.tolist():
+            if self.methods[methods_section] is None or len(self.methods[methods_section]) == 0:
+                continue
+            self.doc.new_line()
+            self.doc.new_header(level=3, title=methods_section)
+            self.doc.new_paragraph(' '.join(self.methods[methods_section]))
+
+    def add_summary(self):
+        self.ofh.write("\nXXXXXX In add_summary\n\n")
+        # Add summary title
+        self.doc.new_header(level=1, title=self.summary_title)
+        # First section of Summary
+        self.doc.new_header(level=1, title='CDC Advisory')
+        self.doc.new_paragraph(CDC_ADVISORY)
+        self.doc.new_line()
+        self.add_run_information()
+        self.add_ont_library_information()
+        methods = []
+        if self.did_guppy_ont_fast5:
+            methods += ['ONT reads were basecalled using guppy']
+        if self.did_qcat_ont_fastq:
+            methods += ['ONT reads were demultiplexed and trimmed using qcat']
+        self.methods[self.basecalling_methods_title] = pandas.Series(methods)
+        self.add_illumina_library_information()
+        self.add_assembly_information()
+        self.add_contig_info()
+        self.add_assembly_notes()
+        if self.did_flye_ont_fastq:
+            method = 'ONT reads were assembled using Flye.'
+            self.methods[self.assembly_methods_title] = self.methods[self.assembly_methods_title].append(pandas.Series(method))
+        if self.did_medaka_ont_assembly:
+            method = 'the genome assembly was polished using ont reads and medaka.'
+            self.methods[self.assembly_methods_title] = self.methods[self.assembly_methods_title].append(pandas.series(method))
+
+    def make_tex(self):
+        self.doc.new_table_of_contents(table_title='detailed run information', depth=2, marker="tableofcontents")
+        text = self.doc.file_data_text
+        text = text.replace("##--[", "")
+        text = text.replace("]--##", "")
+        self.doc.file_data_text = text
+        self.doc.create_md_file()
+
+    def make_report(self):
+        self.ofh.write("\nXXXXXX In make_report\n\n")
+        self.start_doc()
+        self.add_summary()
+        self.add_contamination()
+        self.add_alignment()
+        self.add_features()
+        self.add_feature_plots()
+        self.add_mutations()
+        # TODO stuff working to here...
+        self.add_large_indels()
+        self.add_plasmids()
+        self.add_amr_matrix()
+        # self.add_snps()
+        self.add_methods()
+        self.make_tex()
+        # It took me quite a long time to find out that the value of the -t
+        # (implied) argument in the following command must be 'html' instead of
+        # the more logical 'pdf'.  see the answer from snsn in this thread:
+        # https://github.com/jessicategner/pypandoc/issues/186
+        self.ofh.write("\nXXXXX In make_report, calling pypandoc.convert_file...\n\n")
+        pypandoc.convert_file(self.report_md,
+                              'html',
+                              extra_args=['--pdf-engine=weasyprint', '-V', '-css=%s' % self.pima_css],
+                              outputfile='pima_report.pdf')
+        self.ofh.close()
+
+
+parser = argparse.ArgumentParser()
+
+parser.add_argument('--analysis_name', action='store', dest='analysis_name', help='Sample identifier')
+parser.add_argument('--assembly_fasta_file', action='store', dest='assembly_fasta_file', help='Assembly fasta file')
+parser.add_argument('--assembly_name', action='store', dest='assembly_name', help='Assembly identifier')
+parser.add_argument('--feature_bed_dir', action='store', dest='feature_bed_dir', help='Directory of best feature hits bed files')
+parser.add_argument('--feature_png_dir', action='store', dest='feature_png_dir', help='Directory of best feature hits png files')
+parser.add_argument('--contig_coverage_file', action='store', dest='contig_coverage_file', help='Contig coverage TSV file')
+parser.add_argument('--dbkey', action='store', dest='dbkey', help='Reference genome')
+parser.add_argument('--gzipped', action='store_true', dest='gzipped', default=False, help='Input sample is gzipped')
+parser.add_argument('--illumina_fastq_file', action='store', dest='illumina_fastq_file', help='Input sample')
+parser.add_argument('--mutation_regions_bed_file', action='store', dest='mutation_regions_bed_file', help='AMR mutation regions BRD file')
+parser.add_argument('--mutation_regions_dir', action='store', dest='mutation_regions_dir', help='Directory of mutation regions TSV files')
+parser.add_argument('--pima_css', action='store', dest='pima_css', help='PIMA css stypesheet')
+
+args = parser.parse_args()
+
+# Prepare the features BED files.
+feature_bed_files = []
+for file_name in sorted(os.listdir(args.feature_bed_dir)):
+    file_path = os.path.abspath(os.path.join(args.feature_bed_dir, file_name))
+    feature_bed_files.append(file_path)
+# Prepare the features PNG files.
+feature_png_files = []
+for file_name in sorted(os.listdir(args.feature_png_dir)):
+    file_path = os.path.abspath(os.path.join(args.feature_png_dir, file_name))
+    feature_png_files.append(file_path)
+# Prepare the mutation regions TSV files.
+mutation_regions_files = []
+for file_name in sorted(os.listdir(args.mutation_regions_dir)):
+    file_path = os.path.abspath(os.path.join(args.feature_png_dir, file_name))
+    mutation_regions_files.append(file_path)
+
+markdown_report = PimaReport(args.analysis_name,
+                             args.assembly_fasta_file,
+                             args.assembly_name,
+                             feature_bed_files,
+                             feature_png_files,
+                             args.contig_coverage_file,
+                             args.dbkey,
+                             args.gzipped,
+                             args.illumina_fastq_file,
+                             args.mutation_regions_bed_file,
+                             mutation_regions_files,
+                             args.pima_css)
+markdown_report.make_report()
diff -r 000000000000 -r 0a558f444c98 pima_report.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pima_report.xml	Fri Mar 03 22:06:23 2023 +0000
@@ -0,0 +1,80 @@
+<tool id="pima_report" name="PIMA: summary report" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+  <description></description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+#import re
+
+#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))
+
+mkdir feature_bed_dir &&
+mkdir feature_png_dir &&
+mkdir mutation_regions_dir &&
+touch 'pima_report.pdf' &&
+
+#for $i in $features_bed:
+    #set file_name = $i.file_name
+    #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
+    ln -s $i 'feature_bed_dir/$identifier' &&
+#end for
+#for $i in $features_png:
+    #set file_name = $i.file_name
+    #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
+    ln -s $i 'feature_png_dir/$identifier' &&
+#end for
+#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 '${__tool_directory__}/pima_report.py' 
+--analysis_name '$analysis_name'
+--assembly_fasta_file '$assembly_fasta_file'
+--assembly_name '$assembly_name'
+--contig_coverage_file '$contig_coverage_file'
+--dbkey '$aligned_sample.metadata.dbkey'
+--feature_bed_dir 'feature_bed_dir'
+--feature_png_dir 'feature_png_dir'
+#if $illumina_fastq_file.ext.endswith(".gz"):
+    --gzipped
+#end if
+--illumina_fastq_file '$illumina_fastq_file'
+--mutation_regions_dir 'mutation_regions_dir'
+--mutation_regions_bed_file '$mutation_regions_bed_file'
+--pima_css '${__tool_directory__}/pima.css'
+&& mv 'pima_report.pdf' '$output'
+    ]]></command>
+    <inputs>
+        <param name="aligned_sample" type="data" format="bam" label="Aligned sample BAM file"/>
+        <param name="assembly_fasta_file" type="data" format="fasta" label="Assembly FASTA file"/>
+        <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="contig_coverage_file" type="data" format="tabular,tsv" label="Contig coverage tabular file"/>
+        <param name="illumina_fastq_file" type="data" format="fastqsanger,fastqsanger.gz" label="Fastq sample 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"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="pdf"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="aligned_sample" value="aligned_sample.bam" ftype="bam"/>
+            <param name="assembly_fasta_file" value="assembly_fasta.fasta" ftype="fasta"/>
+            <param name="contig_coverage_file" value="contig_coverage.tabular" ftype="tabular"/>
+            <param name="illumina_fastq_file" value="illumina_fastq.fastq" ftype="fastq"/>
+            <output name="output" value="output.pdf" ftype="pdf"/>
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+Generates the PIMA analysis summary report.
+    </help>
+    <expand macro="citations"/>
+</tool>
+