--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/salsa2.xml	Sun Jan 17 13:24:22 2021 +0000
@@ -0,0 +1,84 @@
+<tool id="salsa" name="SALSA" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
+    <description>scaffold long read assemblies with Hi-C</description>
+    <xrefs>
+        <xref type="bio.tools">SALSA</xref>
+    </xrefs>
+    <macros>
+        <token name="@TOOL_VERSION@">2.2</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">salsa2</requirement>
+        <requirement type="package" version="1.11">samtools</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+ln -s '$fasta_in' input.fasta &&
+samtools faidx input.fasta &&
+
+run_pipeline.py
+-a '$fasta_in'
+-l input.fasta.fai
+-b '$bed_file'
+-e '$enzyme'
+
+#if str($cutoff):
+    -c '$cutoff'
+#end if
+#if $gfa_file:
+    -g '$gfa_file'
+#end if
+#if $iter:
+    -i '$iter'
+#end if
+-o ./out
+    ]]></command>
+    <inputs>
+        <param name="fasta_in" type="data" format="fasta" label="Initial assembly file" help="Headers must not contain ':'."/>
+        <param name="bed_file" type="data" format="bed" label="Bed alignment" help="Sorted by read names"/>
+        <param name="cutoff" argument="-c" type="integer" min="1" label="Cutoff" optional="true" help="Minimum contig length to scaffold."/>
+        <param name="gfa_file" argument="-g" type="data" format="gfa1,gfa2" optional="true" label="Sequence graphs" help="Sequence graphs encoded in GFA format."/>
+        <param name="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>
+        <param name="iter" argument="-i" type="integer" min="0" label="Iterations" optional="true" help="Number of iterations to run"/>
+    </inputs>
+    <outputs>
+        <data name="scaffolds_fasta" format="fasta" from_work_dir="out/scaffolds_FINAL.fasta" label="${tool.name} on ${on_string}: FASTA assembly"/>
+        <data name="scaffolds_agp" format="tabular" from_work_dir="out/scaffolds_FINAL.agp" label="${tool.name} on ${on_string}: agp output"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="fasta_in" value="test.fasta"/>
+            <param name="length" value="test.fai"/>
+            <param name="bed_file" value="test.bed"/>
+            <param name="gfa_file" value="test.gfa1"/>
+            <param name="enzyme" value="GATC,GANTC"/> 
+            <param name="cutoff" value="1000"/>
+            <param name="iter" value="3"/>
+            <output name="scaffolds_fasta" file="out.fasta"/>
+            <output name="scaffolds_agp" file="out.agp"/>
+        </test>
+        <test>
+            <param name="fasta_in" value="test.fasta"/>
+            <param name="bed_file" value="test.bed"/>
+            <param name="gfa_file" value="test.gfa1"/>
+            <param name="enzyme" value="GATC,GANTC"/> 
+            <param name="cutoff" value="1000"/>
+            <param name="iter" value="3"/>
+            <output name="scaffolds_fasta" file="out.fasta"/>
+            <output name="scaffolds_agp" file="out.agp"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+**What is does**
+
+SALSA (Simple AssembLy ScAffolder) is a scaffolding tool based on a computational method that exploits the genomic proximity
+information in Hi-C data sets for long range scaffolding of de novo genome assemblies.
+
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1101/261149</citation>
+        <citation type="doi">10.1186/s12864-017-3879-z</citation>
+    </citations>
+</tool>