--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tatajuba.xml	Wed Jun 15 07:47:02 2022 +0000
@@ -0,0 +1,85 @@
+<tool id="tatajuba" name="tatajuba" version="@VERSION@">
+    <description> Polishing genome assemblies with short reads</description>
+    <macros>
+        <token name="@VERSION@">1.0.4</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@VERSION@">tatajuba</requirement>
+    </requirements>
+    <version_command>tatajuba --version</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+        #if $reads.sr_type == "paired"
+            ln -s '$reads.R1' read1.fastq.gz &&
+            ln -s '$reads.R2' read2.fastq.gz &&
+        #end if
+        #if $reads.sr_type == "collection"
+            ln -s '$reads.input1.forward' read1.fastq.gz &&
+            ln -s '$reads.input1.reverse' read2.fastq.gz &&
+        #end if
+        ln -s '$gff' 'ref.gff' &&
+        ln -s '$fasta' 'ref.fasta' &&
+        tatajuba
+        $keep_bias
+        $vcf
+        --kmer=$kmer
+        --minsize=$minsize
+        --minreads=$minreads
+        --maxdist=$maxdist
+        #if $leven > 0
+        --level $leven
+        #end if
+        --nthreads=\${GALAXY_SLOTS:-4}
+        --gff=ref.gff
+        --fasta=ref.fasta
+        *.fastq.gz
+        --outdir=output
+    ]]>    </command>
+
+    <inputs>
+        <conditional name="reads">
+            <param name="sr_type" type="select" label="Input reads type or collection" help="Select 'paired end' for a single library or 'collection' for a paired end collection">
+                <option value="paired" selected="true">Paired End</option>
+                <option value="collection">Paired Collection</option>
+            </param>
+            <when value="paired">
+                <param name="R1" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Forward reads (R1)" help="The file of forward reads in FASTQ format"/>
+                <param name="R2" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Reverse reads (R2)" help="The file of reverse reads in FASTQ format"/>
+            </when>
+            <when value="collection">
+                <param name="input1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data_collection" collection_type="paired" label="Paired collection" help="See help section for an explanation of dataset collections"/>
+            </when>
+        </conditional>
+        <param name="gff" type="data" format="gff" label="Reference in GFF format"/>
+        <param name="fasta" type="data" format="fasta,fasta.gz" label="Reference in fasta format"/>
+        <param argument="kmer" type="integer" value="25" min="2" max="32" label="Kmer size flanking each side of homopolymer" />
+        <param argument="minsize" type="integer" value="4" min="1" max="32" label="Fraction value of the read depth to be considered invalid" />
+        <param argument="minreads" type="integer" value="5" min="1" label="Minimum number of reads for tract+context to be considered" />
+        <param argument="maxdist" type="integer" value="1" min="1" label="Maximum distance between kmers of a flanking region to merge them into one context" />
+        <param argument="leven" type="integer" value="0" min="0" label="Levenshtein distance between flanking regions to merge them into one context" />
+        <param argument="vcf" type="boolean" truevalue="--vcf" falsevalue="" checked="false" label="generate VCF files for each sample, around the HT regions" />
+        <param argument="keep_bias" type="boolean" truevalue="--keep_bias" falsevalue="" checked="false" label="Keep biased tracts" />
+    </inputs>
+    <outputs>
+        <data name="variable_tracts" format="tabular" from_work_dir="output/variable_tracts.bed" label="${tool.name} on ${on_string} BED file with tract locations" />
+        <data name="tract_list" format="tabular" from_work_dir="output/tract_list.tsv" label="${tool.name} on ${on_string} list of all HTs found" />
+        <data name="selected_tracts_unknown" format="tabular" from_work_dir="output/selected_tracts_unknown.tsv" label="${tool.name} on ${on_string} debug file with difference stats per tract for tracts outside annotated regions" />
+        <data name="selected_tracts_annotated" format="tabular" from_work_dir="output/selected_tracts_annotated.tsv" label="${tool.name} on ${on_string} debug file with difference stats per tract for tracts in annotated regions" />
+        <data name="per_sample_proportional_coverage" format="tabular" from_work_dir="output/per_sample_proportional_coverage.tsv" label="${tool.name} on ${on_string} feature matrix of proportional coverage depth of HT" />
+        <data name="per_sample_proportional_coverage" format="tabular" from_work_dir="output/per_sample_modal_frequency.tsv" label="${tool.name} on ${on_string} feature matrix with histogram bar length of modal tract length" />
+        <data name="per_sample_average_length" format="tabular" from_work_dir="output/per_sample_average_length.tsv" label="${tool.name} on ${on_string} feature matrix with average HT length" />
+        <data name="vcf1" format="vcf" from_work_dir="output/1.vcf.gz" label="${tool.name} on ${on_string} VCF-1" />
+        <data name="vcf2" format="vcf" from_work_dir="output/2.vcf.gz" label="${tool.name} on ${on_string} VCF-2" />
+    </outputs>
+    <tests>
+        <test name="test-paired-end">
+            <param name="sr_type" value="paired" />
+            <param name="R1" value="r1.fastq.gz" ftype="fastqsanger.gz" />
+            <param name="R2" value="r2.fastq.gz" ftype="fastqsanger.gz" />
+            <param name="gff" value="GCF_000009085.1_ASM908v1_genomic.gff" ftype="gff" />
+            <param name="fasta" value="GCF_000009085.1_ASM908v1_genomic.fna" ftype="fasta" />
+            <output name="per_sample_average_length" file="output/per_sample_average_length.tsv" ftype="tabular" compare="contains" />
+        </test>
+    </tests>
+    <help><![CDATA[
+    ]]>    </help>
+</tool>