Merge pull request #2955 from bgruening/seqwish

add seqwish

Author: bgruening

tools/seqwish/.shed.yml

@@ -0,0 +1,10 @@
+categories:
+  - Sequence Analysis
+  - Variant Analysis
+homepage_url: https://github.com/ekg/seqwish
+description: Alignment to variation graph inducer
+long_description: |
+  seqwish implements a lossless conversion from pairwise alignments between sequences to a variation graph encoding the sequences and their alignments.
+owner: iuc
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/
+type: unrestricted

tools/seqwish/seqwish.xml

@@ -0,0 +1,72 @@
+<tool id="seqwish" name="seqwish" version="@TOOL_VERSION@" >
+    <description>Alignment to variation graph inducer</description>
+    <macros>
+        <token name="@TOOL_VERSION@">0.4</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">seqwish</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+seqwish
+-p '$paf_alns'
+-s ${ ' '.join(["'%s'" % x for x in $seqs]) }
+--gfa='$out_gfa'
+#if $m:
+    -m '$m'
+#end if
+--threads=\${GALAXY_SLOTS:-1}
+#if str($r):
+    -r $r
+#end if
+#if str($k):
+    -k $k
+#end if
+#if str($B):
+    -B $B
+#end if
+    ]]></command>
+    <inputs>
+        <param argument="--paf-alns" type="data" format="paf" label="Induce the graph from these PAF formatted alignments" />
+        <param argument="--seqs" type="data" format="fasta,fasta.gz,fastq,fastq.gz" multiple="true" label="The sequences used to generate the alignments" />
+        <param argument="-m" type="data" optional="true" format="txt,tabular" label="Subset the input alignments"
+            help="" />
+        <param argument="-r" type="integer" min="1" optional="true" label="Limit copies of a given input base"
+            help="Limit transitive closure to include no more than N copies of a given input base" />
+        <param argument="-k" type="integer" min="1" optional="true" label="Filter exact matches below this length"
+            help="This can smooth the graph locally and prevent the formation of complex local graph topologies from forming due to differential alignments." />
+        <param argument="-B" type="integer" min="1" optional="true" label="Number of bp to use for transitive closure batch"
+            help="" />
+    </inputs>
+
+    <outputs>
+        <data name="out_gfa" format="gfa1" label="${tool.name} on ${on_string}" />
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="seqs" value="A-3105.fa.gz" />
+            <param name="paf_alns" value="A-3105.paf.gz" />
+            <output name="out_gfa" md5="176f9b4be76a2e69550da9b9c39ac5eb" />
+        </test>
+        <test>
+            <param name="seqs" value="A-3105.fa.gz" />
+            <param name="paf_alns" value="A-3105.paf.gz" />
+            <param name="r" value="3000" />
+            <param name="k" value="1" />
+            <param name="B" value="1000000" />
+            <output name="out_gfa" md5="176f9b4be76a2e69550da9b9c39ac5eb" />
+        </test>
+    </tests>
+    <help><![CDATA[
+These **seq**uences **wish** they were squished into a graph.
+
+seqwish implements a lossless conversion from pairwise alignments between sequences to a variation graph encoding the sequences
+and their alignments. As input we typically take all-versus-all alignments, but the exact structure of the alignment set may
+be defined in an application specific way. This algorithm uses a series of disk-backed sorts and passes over the alignment
+and sequence inputs to allow the graph to be constructed from very large inputs that are commonly encountered when working with
+large numbers of noisy input sequences. Memory usage during construction and traversal is limited by the use of sorted
+disk-backed arrays and succinct rank/select dictionaries to record a queryable version of the graph.
+    ]]></help>
+    <citations>
+    </citations>
+</tool>