--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/yahs.xml	Wed Jun 29 13:06:23 2022 +0000
@@ -0,0 +1,227 @@
+<tool id="yahs" name="YAHS" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
+    <description>yet another HI-C scaffolding tool</description>
+    <macros>
+        <token name="@VERSION@">1.1a.2</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@VERSION@">yahs</requirement>
+        <requirement type="package" version="1.11">samtools</requirement>
+        <requirement type="package" version="3.9">python</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        #if $function.function_select == "yahs":
+            ln -s '$function.fasta' input.fasta &&
+            #if $function.bfile.ext == "bam":
+                ln -s '$function.bfile' input.bam &&
+            #else if $function.bfile.ext == "bed":
+                ln -s '$function.bfile' input.bed &&
+            #end if
+            #if $function.agp:
+                ln -s '$function.agp' input.agp &&
+            #end if
+            samtools faidx input.fasta &&
+            mkdir initial_break agp_out agp_break final_outs &&
+            yahs input.fasta 
+            #if $function.bfile.ext == "bam":
+                input.bam
+            #else if $function.bfile.ext == "bed":
+                input.bed
+            #end if
+            #if $agp:
+                -a input.agp
+            #end if
+            #if $function.res:
+                -r $function.res
+            #end if
+            #if $function.enzyme_conditional.enzyme_options == 'preconfigured':
+                #if $function.enzyme_conditional.preconfigured_enzymes == 'dovetail'
+                    -e 'GATC'
+                #else if $function.enzyme_conditional.preconfigured_enzymes == 'arima1'
+                    -e 'GATC,GANTC'
+                #else
+                    -e 'GATC,GANTC,CTNAG,TTAA'
+                #end if
+            #else if $function.enzyme_conditional.enzyme_options == 'specific':
+                -e '${function.enzyme_conditional.manual_enzyme}'
+            #end if
+            #if $function.length:
+                -l $function.length
+            #end if
+            #if $function.quality:
+                -q $function.quality
+            #end if
+            $function.no_contig_ec
+            $function.no_scaffold_ec
+            -o yahs_out &&
+            ls -lah &&
+            python '$__tool_directory__/move_files.py'
+            && ls -lah ./*
+        #else:
+            ln -s '$function.fasta' input.fasta &&
+            ln -s '$function.agp' input.agp &&
+            agp_to_fasta input.agp input.fasta
+            #if $function.length:
+                -l $function.length
+            #end if
+            -o output.fasta
+        #end if
+    ]]></command>
+    <inputs>
+        <conditional name="function">
+            <param name="function_select" type="select" label="Which function would you like to run?">
+                <option value="yahs">YAHS</option>
+                <option value="agp_to_fasta">AGP to fasta</option>
+            </param>
+            <when value="yahs">
+                <param name="fasta" type="data" format="fasta" label="Input contig sequences"/>
+                <param name="bfile" type="data" format="bam,bed" label="Alignment file of Hi-C reads to contigs"/>
+                <param name="agp" argument="-a" type="data" format="agp" optional="true" label="Input AGP file (for rescaffolding)"
+                    help="You can specify a AGP format file to ask YaHS to do scaffolding with the scaffolds in the AGP file as the start point"/>
+                <param name="res" argument="-r" type="text" label="Resolutions" optional="true" 
+                    help="Comma separated, ascending list of range of resolutions with no spaces. Ex. 50000,100000,200000,500000,1000000,2000000,5000000. By default and the upper limit is automatically adjusted with the genome size"/>
+                <conditional name="enzyme_conditional">
+                    <param name="enzyme_options" type="select" label="Restriction enzyme used in Hi-C experiment" help="Hi-C experiments can use different restriction enzymes.
+                        The enzyme frequency in contigs is used to normalize the Hi-C interaction frequency. Note that you need to specify the actual 
+                        sequence of the cutting site for a restriction enzyme and not the enzyme name. You can also specify DNASE as an enzyme if you 
+                        use an enzyme-free prep, e.g. Omin-C.">
+                        <option value="not_especified">Not especified</option>
+                        <option value="preconfigured">Preconfigured restriction enzymes</option>
+                        <option value="specific">Enter a specific sequence</option>
+                    </param>
+                    <when value="not_especified"/>
+                    <when value="preconfigured">
+                        <param name="preconfigured_enzymes" argument="-e" type="select" label="Preconfigured enzymes">
+                            <option value="dovetail">Dovetail Chicago, Dovetail Hi-C or Phase: GATC</option>
+                            <option value="arima1">Arima Hi-C 1.0: GATC, GANTC</option>
+                            <option value="arima2">Arima Hi-C 2.0: GATC, GANTC, CTNAG, TTAA</option>
+                        </param>
+                    </when>
+                    <when value="specific">
+                        <param name="manual_enzyme" argument="-e" type="text" label="Restriction enzyme sequence(s)"
+                            help="Restriction enzyme sequence. If multiple were used, include all as a comma separated list without spaces (ex. 'GATC,AAGCTT').">
+                            <validator type="expression" message="Only alphabetical letters and the comma can be used in to define restriction enzym sequences.">value.replace(',', '').isalpha()</validator>
+                        </param>
+                    </when>
+                </conditional>
+                <param name="length" argument="-l" type="integer" label="Minimum contig length included for scaffolding" min="1" optional="true"/>
+                <param name="quality" argument="-q" type="integer" label="Minimum read mapping quality (for BAM input only)" min="1" optional="true"/>
+                <param argument="--no-contig-ec" type="boolean" label="Skip assembly error correction step" truevalue="--no-contig-ec" falsevalue="" help="Automatically active if AGP output is set"/>
+                <param argument="--no-scaffold-ec" type="boolean" label="Skip assembly/scaffolding error check each round" truevalue="--no-scaffold-ec" falsevalue="" help="Will also prevent any break.agp output files"/>
+            </when>
+            <when value="agp_to_fasta">
+                <param name="agp" type="data" format="agp" label="Input AGP file"/>
+                <param name="fasta" type="data" format="fasta" label="Contig fasta file"/>
+                <param name="length" type='integer' label="Output fasta line length" value="60" min="1"/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <!-- INITIAL ROUNDS -->
+        <collection name="initial_agp_break" type="list" label="${tool.name} on ${on_string}: AGP initial break files">
+            <filter>function['function_select'] == "yahs"</filter>
+            <discover_datasets pattern="__name_and_ext__" directory="initial_break" ext="agp"/>
+        </collection>
+        <collection name="agp_break" type="list" label="${tool.name} on ${on_string}: AGP break files">
+            <filter> function['function_select'] == "yahs"</filter>
+            <discover_datasets pattern="__name_and_ext__" directory="agp_break" ext="agp"/>
+        </collection>
+        <collection name="agp_out" type="list" label="${tool.name} on ${on_string}: AGP scaffolding results files">
+            <filter>function['function_select'] == "yahs"</filter>
+            <discover_datasets pattern="__name_and_ext__" directory="agp_out" ext="agp"/>
+        </collection>
+        <!-- FINAL FILES -->
+        <data format="agp" name="final_agp_out" label="${tool.name} on ${on_string}: Final scaffolds agp output" from_work_dir="final_outs/yahs_out_scaffolds_final.agp">
+            <filter>function['function_select'] == "yahs"</filter>
+        </data>
+        <data format="fasta" name="final_fasta_out" label="${tool.name} on ${on_string}: Final scaffolds fasta output" from_work_dir="final_outs/yahs_out_scaffolds_final.fa">
+            <filter>function['function_select'] == "yahs"</filter>
+        </data>
+        <data format="fasta" name="fasta_from_agp" label="${tool.name} on ${on_string}: agp to fasta" from_work_dir="output.fasta">
+            <filter>function['function_select'] == "agp_to_fasta"</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="5">
+            <conditional name="function">
+                <param name="function_select" value="yahs"/>
+                <param name="fasta" value="test.fasta"/>
+                <param name="bfile" value="test.bed"/>
+                <param name="agp" value="test.agp"/>
+                <param name="res" value="50000,100000,150000,2000000,1000000"/>
+            </conditional>
+            <output name="final_agp_out" file="test_01_scaffolds_final.agp" ftype="agp"/>
+            <output name="final_fasta_out" file="test_01_scaffolds_final.fa" ftype="fasta"/>
+            <!-- COMMAND:   yahs test.fasta test.bed -r 50000,100000,150000,2000000,1000000 -a test.agp -o test_1 -->
+        </test>
+        <test expect_num_outputs="5">
+            <conditional name="function">
+                <param name="function_select" value="yahs"/>
+                <param name="fasta" value="test.fasta"/>
+                <param name="bfile" value="test.bed"/>
+                <param name="no_contig_ec" value="--no-contig-ec"/>
+                <param name="no_scaffold_ec" value="--no-scaffold-ec"/>
+            </conditional>
+            <output name="final_agp_out" file="test_02_scaffolds_final.agp" ftype="agp"/>
+            <output name="final_fasta_out" file="test_02_scaffolds_final.fa" ftype="fasta"/>
+            <output_collection name="agp_break">
+                <element name="yahs_out_no_break" file="test_02_no_break.agp" ftype="agp"/>
+            </output_collection>
+            <!-- COMMAND:  yahs test.fasta test.bed -\-no-contig-ec -\-no-scaffold-ec -o test_2 -->
+        </test>
+        <test expect_num_outputs="5">
+            <conditional name="function">
+                <param name="function_select" value="yahs"/>
+                <param name="fasta" value="test.fasta"/>
+                <param name="bfile" value="test.bam"/>
+                <param name="qual" value="10"/>
+                <param name="length" value="20"/>
+                <conditional name="enzyme_conditional">
+                    <param name="enzyme_options" value="specific"/>
+                    <param name="manual_enzyme" value="GATC,GANT"/>
+                </conditional>
+            </conditional>
+            <output name="final_agp_out" file="test_03_scaffolds_final.agp" ftype="agp"/>
+            <output name="final_fasta_out" file="test_03_scaffolds_final.fa" ftype="fasta"/>
+            <output_collection name="initial_agp_break">
+                <element name="yahs_out_inital_break_01" file="test_03_initial_break.agp" ftype="agp"/>
+            </output_collection>
+            <!-- COMMAND:  yahs test.fasta test.bed -q 10 -l 20 -e 'GATC,GANT' -o test_3 -->
+        </test>
+                <test expect_num_outputs="5">
+            <conditional name="function">
+                <param name="function_select" value="yahs"/>
+                <param name="fasta" value="test.fasta"/>
+                <param name="bfile" value="test.bam"/>
+                <param name="qual" value="10"/>
+                <param name="length" value="20"/>
+                <conditional name="enzyme_conditional">
+                    <param name="enzyme_options" value="preconfigured"/>
+                    <param name="preconfigured_enzymes" value="arima1"/>
+                </conditional>
+            </conditional>
+            <output name="final_agp_out" file="test_03_scaffolds_final.agp" ftype="agp"/>
+            <output name="final_fasta_out" file="test_03_scaffolds_final.fa" ftype="fasta"/>
+            <output_collection name="initial_agp_break">
+                <element name="yahs_out_inital_break_01" file="test_04_initial_break.agp" ftype="agp"/>
+            </output_collection>
+            <!-- COMMAND:  yahs test.fasta test.bed -q 10 -l 20 -e 'GATC,GANT' -o test_3 -->
+        </test>
+        <test expect_num_outputs="1">
+            <conditional name="function">
+                <param name="function_select" value="agp_to_fasta"/>
+                <param name="fasta" value="test.fasta"/>
+                <param name="agp" value="test.agp"/>
+                <param name="length" value="20"/>
+            </conditional>
+            <output name="fasta_from_agp" file="test_05.fasta" ftype="fasta"/>
+            <!-- COMMAND: agp_to_fasta teast.fasta test.agp -l 20 -o test_4 -->
+        </test>
+    </tests>
+    <help><![CDATA[
+        YaHS is scaffolding tool using Hi-C data. It relies on a new algothrim for contig joining detection which considers the topological distribution of Hi-C signals aiming to distingush real interaction signals from mapping nosies. YaHS has been tested in a wide range of genome assemblies. Compared to other Hi-C scaffolding tools, it usually generates more contiguous scaffolds - especially with a higher N90 and L90 statistics. It is also super fast - takes less than 5 minutes to reconstruct the human genome from an assembly of 5,483 contigs with ~45X Hi-C data.
+    ]]></help>
+    <citations>
+        <citation type="doi">10.5281/zenodo.5848772</citation>
+    </citations>
+</tool>