--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/coverm_contig.xml	Tue Apr 26 15:27:37 2022 +0000
@@ -0,0 +1,379 @@
+<tool id="coverm_contig" name="CoverM-CONTIG" version="@TOOL_VERSION@" python_template_version="3.5">
+    <macros>
+        <import>macros.xml</import>
+        <token name="@INPUT_FORMATS@">fasta,fastq,fastq.gz,fasta.gz</token>
+        <token name="@TOOL_VERSION@">0.2.1</token>
+    </macros>
+    <expand macro="requirements"/>
+    <command><![CDATA[
+         #if $reads.read_type == "single" or $reads.read_type == "interleaved"
+            mkdir -p reads1 &&
+            #set file_paths1 = []
+            #for $input_file in $reads.single
+                
+                #set $fname = $input_file.element_identifier.replace(" ","_")
+                #set $file_path = 'reads1/' + $fname
+                ln -s '$input_file' '$file_path' &&
+                $file_paths1.append($file_path)
+            #end for
+        #else if $reads.read_type == "bam"
+            mkdir -p bam &&
+            #set bam_files = []
+            #for $input_file in $reads.bam
+                
+                #set $fname = $input_file.element_identifier.replace(" ","_")
+                #set $file_path = 'bam/' + $fname
+                ln -s '$input_file' '$file_path' &&
+                $bam_files.append($file_path)
+            #end for
+        #else if $reads.read_type == "paired"
+            mkdir -p paired_reads1 &&
+            #set fw_reads1 = []
+            #for $input_file in $reads.read1
+                
+                #set $fname = $input_file.element_identifier.replace(" ","_")
+                #set $file_path = 'paired_reads1/' + str($fname)
+                ln -s '$input_file' '$file_path' &&
+                $fw_reads1.append($file_path)
+            #end for
+            #set rv_reads1 = []
+            #for $input_file in $reads.read2
+                
+                #set $fname = $input_file.element_identifier.replace(" ","_")
+                #set $file_path = 'paired_reads1/' + str($fname)
+                ln -s '$input_file' '$file_path' &&
+                $rv_reads1.append($file_path)
+            #end for
+            #silent $fw_reads1.sort()
+            #silent $rv_reads1.sort()
+        #else
+            mkdir -p paired_reads &&
+            #set paired_reads1 = []
+            #for $i, $input_file in enumerate($reads.paired_reads)
+                #set $file_path = 'paired_reads/fw' + str($i)
+                ln -s '$input_file.forward' '$file_path' &&
+                $paired_reads1.append($file_path)
+                #set $file_path = 'paired_reads/rv' + str($i)
+                ln -s '$input_file.reverse' '$file_path' &&
+                $paired_reads1.append($file_path)
+            #end for
+        #end if           
+        #if $add_reads.extra_read.read_type == "single" or $add_reads.extra_read.read_type == "interleaved"
+            mkdir -p add_reads1 &&
+            #set add_file_paths1 = []
+            #for $input_file in $add_reads.extra_read.single
+                #set $fname = $input_file.element_identifier.replace(" ","_")
+                #set $file_path = 'add_reads1/' + $fname
+                ln -s '$input_file' '$file_path' &&
+                $add_file_paths1.append($file_path)
+            #end for
+        #else if $add_reads.extra_read.read_type == "bam"
+            mkdir -p add_bam &&
+            #set add_bam_files = []
+            #for $input_file in $reads.bam
+                #set $fname = $input_file.element_identifier.replace(" ","_")
+                #set $file_path = 'add_bam/' + $fname
+                ln -s '$input_file' '$file_path' &&
+                $add_bam_files.append($file_path)
+            #end for
+        #else if $add_reads.extra_read.read_type == "paired"
+            mkdir -p add_paired_reads1 &&
+            #set add_fw_reads1 = []
+            #for $input_file in $add_reads.extra_read.read1
+                #set $fname = $input_file.element_identifier.replace(" ","_")
+                #set $file_path = 'add_paired_reads1/' + str($fname)
+                ln -s '$input_file' '$file_path' &&
+                $add_fw_reads1.append($file_path)
+            #end for
+            #set add_rv_reads1 = []
+            #for $input_file in $add_reads.extra_read.read2
+                #set $fname = $input_file.element_identifier.replace(" ","_")
+                #set $file_path = 'add_paired_reads1/' + str($fname)
+                ln -s '$input_file' '$file_path' &&
+                $add_rv_reads1.append($file_path)
+            #end for
+            #silent $add_fw_reads1.sort()
+            #silent $add_rv_reads1.sort()
+        #else if $add_reads.extra_read.read_type == "paired_collection"
+            mkdir -p add_paired_reads &&
+            #set add_paired_reads1 = []
+            #for $i, $input_file in enumerate($add_reads.extra_read.paired_reads)
+                #set $ext = $input_file.forward.ext
+                #set $file_path = 'add_paired_reads/fw' + str($i) + '.' + $ext
+                ln -s '$input_file.forward' '$file_path' &&
+                $add_paired_reads1.append($file_path)
+                #set $file_path = 'add_paired_reads/rv' + str($i) + '.' + $ext
+                ln -s '$input_file.reverse' '$file_path' &&
+                $add_paired_reads1.append($file_path)
+            #end for
+        #end if
+        
+        #if $reads.ref_fasta_history
+            mkdir -p reference &&
+            #set ref_files = []
+                #for $input_file in $reads.ref_fasta_history
+                    #set $fname = $input_file.element_identifier.replace(" ","_")
+                    #set $file_path = 'reference/' + $fname
+                    ln -s '$input_file' '$file_path' &&
+                    $ref_files.append($file_path)
+                #end for
+        #end if
+
+        coverm contig
+            #if $reads.read_type == 'paired'
+                -1
+                #for $read in $fw_reads1
+                    '${read}'
+                #end for
+                -2
+                #for $read in $rv_reads1
+                    '${read}'
+                #end for
+            #else if $reads.read_type == 'paired_collection'
+                --coupled
+                #for $read in $paired_reads1
+                    '${read}'
+                #end for
+            #else if $reads.read_type == 'single'
+                --single
+                #for $read in $file_paths1
+                    '${read}'
+                #end for
+            #else if $reads.read_type == 'interleaved'
+                --interleaved
+                #for $read in $file_paths1
+                    '${read}'
+                #end for
+            #else if $reads.read_type == 'bam'
+                -b
+                #for $read in $bam_files
+                    '${read}'
+                #end for
+            #end if
+
+            #if $add_reads.extra_read.read_type == 'paired'
+                -1
+                #for $read in $add_fw_reads1
+                    '${read}'
+                #end for
+                -2
+                #for $read in $add_rv_reads1
+                    '${read}'
+                #end for
+            #else if $add_reads.extra_read.read_type == 'paired_collection'
+                --coupled
+                #for $read in $add_paired_reads1
+                    '${read}'
+                #end for
+            #else if $add_reads.extra_read.read_type == 'single'
+                --single
+                #for $read in $add_file_paths1
+                    '${read}'
+                #end for
+            #else if $add_reads.extra_read.read_type == 'interleaved'
+                --interleaved
+                #for $read in $add_file_paths1
+                    '${read}'
+                #end for
+            #else if $add_reads.extra_read.read_type == 'bam'
+                #for $read in $add_bam_files
+                    '${read}'
+                #end for
+            #end if
+            
+
+            #if $reads.ref_fasta_history:
+                --reference
+                #for $reference in $ref_files
+                    '${reference}'
+                #end for
+            #end if
+
+            $shar.sharded
+
+            #if $mapping.mapper:
+                --mapper $mapping.mapper
+            #end if
+            #if $mapping.min_read_aligned_length:
+                --min-read-aligned-length $mapping.min_read_aligned_length
+            #end if
+            #if $mapping.min_read_percent_identity:
+                --min-read-percent-identity $mapping.min_read_percent_identity
+            #end if
+            #if $mapping.min_read_aligned_percent:
+                --min-read-aligned-percent $mapping.min_read_aligned_percent
+            #end if
+            #if $mapping.min_read_aligned_length_pair:
+                --min-read-aligned-length-pair $mapping.min_read_aligned_length_pair
+            #end if
+            #if $mapping.min_read_percent_identity_pair:
+                --min-read-percent-identity-pair $mapping.min_read_percent_identity_pair
+            #end if
+            #if $mapping.min_read_aligned_percent_pair:
+                --min-read-aligned-percent-pair $mapping.min_read_aligned_percent_pair
+            #end if
+            $mapping.proper_pairs_only
+            $mapping.exclude_supplementary
+
+            --methods $cov.relative_abundance $cov.mean $cov.cond_methods.trimmed_mean $cov.covered_bases $cov.covered_fraction
+            $cov.variance $cov.length $cov.count $cov.metabat $cov.coverage_histogram $cov.reads_per_base 
+            $cov.rpkm $cov.tpm
+            #if $cov.min_covered_fraction:
+                --min-covered-fraction $cov.min_covered_fraction
+            #end if
+            #if $cov.contig_end_exclusion:
+                --contig-end-exclusion $cov.contig_end_exclusion
+            #end if
+            #if $cov.cond_methods.trimmed_mean
+                #if $cov.cond_methods.trim_min:
+                    --trim-min $cov.cond_methods.trim_min
+                #end if
+                #if $cov.cond_methods.trim_max:
+                    --trim_max $cov.cond_methods.trim_max
+                #end if
+            #end if
+
+            #if $out.output_format:
+                --output-format $out.output_format
+            #end if
+            --output-file output.tsv
+            --threads \${GALAXY_SLOTS:-1}
+            2> stdout.txt
+    ]]></command>
+    <inputs>
+        <expand macro="reads_for_contig" />
+        <expand macro="add_reads" />
+        <section name="shar" title="Sharding" expanded="false">
+            <param name="sharded" type="boolean" optional="true" truevalue="--sharded" falsevalue="" label="If -b/--bam-files was used: Input BAM files are read-sorted alignments of a set of reads mapped to multiple reference contig sets. Choose the best hit for each read pair. Otherwise if mapping was carried out: Map reads to each reference, choosing the best hit for each pair." />
+        </section>
+            <expand macro="mapping"/>
+            <expand macro="coverage"/>
+        <section name="out" title="Output options" expanded="false">
+            <param name="output_format" type="select" label="Shape of output" help="'Sparse' for long format, 'dense' for species-by-site. Default: dense]">
+                <option value="dense" selected="true">Dense</option>
+                <option value="sparse">Sparse</option>
+            </param>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="output1" format="tsv" from_work_dir="./output.tsv"/>
+    </outputs>
+    <tests>
+        <test>
+            <conditional name="reads">
+                <param name="read_type" value="paired_collection"/>
+                <param name="paired_reads">
+                    <collection type="list:paired">
+                        <element name="reads_for_seq1_and_seq2..fq">
+                            <collection type="paired">
+                                <element name="forward" value="reads_for_seq1_and_seq2.1.fq.gz"/>
+                                <element name="reverse" value="reads_for_seq1_and_seq2.2.fq.gz"/>
+                            </collection>
+                        </element>
+                    </collection>
+                </param>
+                <param name="ref_fasta_history" value="7seqs.fna"/>
+            </conditional>
+            <output name="output1" file="contig_test1.tsv" ftype="tsv"/>
+        </test> 
+        <test>
+            <conditional name="reads">
+                <param name="read_type" value="single"/>
+                <param name="single" value="bad_reads.interleaved.fq"/>
+                <param name="ref_fasta_history" value="2seqs.fasta"/>
+            </conditional>
+            <section name="cov">
+                <param name="contig_end_exclusion" value="0"/>
+            </section>
+            <section name="out">
+                <param name="output_format" value="sparse"/>
+            </section>            
+            <output name="output1" file="contig_test2.tsv" ftype="tsv"/>
+        </test> 
+        <test>
+            <conditional name="reads">
+                <param name="read_type" value="interleaved"/>
+                <param name="single" value="bad_reads.all.interleaved.fa"/>
+                <param name="ref_fasta_history" value="2seqs.fasta"/>
+            </conditional>
+            <section name="cov">
+                <param name="contig_end_exclusion" value="0"/>
+            </section>
+            <section name="mapping">
+                <param name="min_read_aligned_length_pair" value="300"/>
+                <param name="proper_pairs_only" value="true"/>
+            </section>
+            <section name="out">
+                <param name="output_format" value="sparse"/>
+            </section>            
+            <output name="output1" file="contig_test3.tsv" ftype="tsv"/>
+        </test> 
+        <test>
+            <conditional name="reads">
+                <param name="read_type" value="paired"/>
+                <param name="read1" value="reads_for_seq1_and_seq2.1.fq.gz"/>
+                <param name="read2" value="reads_for_seq1_and_seq2.2.fq.gz"/>
+                <param name="ref_fasta_history" value="2seqs.fasta"/>
+            </conditional>
+            <section name="add_reads">
+                <conditional name="extra_read">
+                    <param name="read_type" value="paired_collection"/>
+                    <param name="paired_reads">
+                        <collection type="list:paired">
+                            <element name="reads_for_seq1_and_seq2..fq">
+                                <collection type="paired">
+                                    <element name="forward" value="reads_for_seq1_and_seq2.1.fq.gz"/>
+                                    <element name="reverse" value="reads_for_seq1_and_seq2.2.fq.gz"/>
+                                </collection>
+                            </element>
+                        </collection>
+                    </param>
+                </conditional>
+            </section>
+            <section name="cov">
+                <param name="contig_end_exclusion" value="0"/>
+            </section>
+            <section name="mapping">
+                <param name="--min-read-percent-identity" value="0.95"/>
+            </section>
+            <output name="output1" file="contig_test4.tsv" ftype="tsv"/>
+        </test> 
+        <test>
+            <conditional name="reads">
+                <param name="read_type" value="bam"/>
+                <param name="bam" value="tpm_test.bam"/>
+            </conditional>
+            <section name="cov">
+                <param name="mean" value="true"/>
+                <param name="tpm" value="true"/>
+            </section>
+            <section name="out">
+                <param name="output_format" value="sparse"/>
+            </section>            
+            <output name="output1" file="contig_test5.tsv" ftype="tsv"/>
+        </test> 
+        </tests>
+    <help><![CDATA[
+.. class:: infomark
+    
+**Method for calculating coverage**
+
+Calculation of genome-wise coverage (genome mode) is similar to calculating contig-wise (contig mode) coverage, except that the unit of reporting is per-genome rather than per-contig. For calculation methods which exclude base positions based on their coverage, all positions from all contigs are considered together. 
+
+- Relative abundance: Percentage relative abundance of each genome, and the unmapped read percentage
+- Mean: Average number of aligned reads overlapping each position on the genome
+- Trimmed mean: Average number of aligned reads overlapping each position after removing the most deeply and shallowly covered positions.
+- Covered fraction: Fraction of genome covered by 1 or more reads
+- Covered bases: Number of bases covered by 1 or more reads
+- Variance: Variance of coverage depths
+- Length: Length of each genome in base pairs
+- Count: Number of reads aligned toq each genome. Note that a single read may be aligned to multiple genomes with supplementary alignments
+- Reads per base: Number of reads aligned divided by the length of the genome
+- MetaBAT: Reproduction of the `MetaBAT <https://bitbucket.org/berkeleylab/metabat>`_ tool output
+- Coverage histogram: Histogram of coverage depths
+- RPKM: Reads mapped per kilobase of genome, per million mapped reads
+- TPM: Transcripts Per Million as described in `Li et al 2010 <https://doi.org/10.1093/bioinformatics/btp692>`_
+
+    ]]></help>
+    <expand macro="citation"/>
+</tool>
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