diff sendsketch.xml @ 0:23ecfa3e5eff draft

"planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit fec9224232f4fe1200df4f66e1fa064533b3f21e"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sendsketch.xml	Mon Nov 25 11:28:06 2019 +0000
@@ -0,0 +1,70 @@
+<tool id="bbmap_sendsketch" name="sendsketch" version="@VERSION@">
+    <description> Identifying species using sketch</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+
+    <command detect_errors="exit_code"><![CDATA[
+        ln -sf '$input' '$input.element_identifier' &&
+        sendsketch.sh
+        #if $printall
+            printall=t
+        #end if
+        #if $translate
+            translate=t
+        #end if
+        in='$input.element_identifier'
+        out=output.txt
+        outsketch=sketch
+        minhits=$minhits
+        minani=$minani
+        format=$format
+        score=t
+        $db
+    ]]>    </command>
+
+    <inputs>
+        <param name="input" type="data" format="fasta,fasta.gz" label="Input sequence"/>
+        <param name="db" type="select" label="Sketch Database">
+            <option value="refseq" selected="true">Refseq</option> 
+            <option value="nt">nt</option> 
+            <option value="silva">silva</option> 
+            <option value="protein">RefSeq prokaryotic amino acid sketches</option> 
+        </param>
+        <param name="format" type="select" label="Output Format">
+            <option value="2" selected="true">Default format with, per query, one query header line;
+                   one column header line; and one reference line per hit</option>
+            <option value="3">One line per hit, with columns query, reference, ANI,
+                   and sizeRatio</option>
+            <option value="4">JSON</option>
+        </param>
+        <param name="minhits" type="integer" min="1" value="3" label="Only report records with at least this many hits"/>
+        <param name="minani" type="float" min="0" value="0.0" max="1" label="Only report records with at least this ANI"/>
+        <param name="minwkid" type="float" min="0" value="0.0001" max="1" label="Only report records with at least this WKID"/>
+        <param name="minbases" type="integer" min="0" value="0" label="Ignore ref sketches of sequences shortert than this"/>
+        <param name="minsizeratio" type="float" min="0" value="0.0" max="1" label="Don't compare sketches if the smaller genome is less than
+                this fraction of the size of the larger"/>
+        <param name="records" type="integer" min="1" value="20" label="Report at most this many best-matching records"/>
+        <param name="write_sketch" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Write sketch?"/>
+        <param name="translate" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Call genes and translate to proteins.  Input should be
+                nucleotides"/>
+        <param name="printall" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Print all column?"/>
+    </inputs>
+
+    <outputs>
+        <data name="Output" format="txt" from_work_dir="output.txt"/>
+        <data name="Sketch" format="binary" from_work_dir="sketch">
+            <filter>write_sketch is True</filter>
+        </data>
+    </outputs>
+    <help><![CDATA[
+    Compares query sketches to reference sketches hosted on a
+    remote server via the Internet.  The input can be sketches made by sketch.sh,
+    or fasta/fastq files from which SendSketch will generate sketches.
+    Only sketches will sent, not sequences.
+    ]]>    </help>
+    <expand macro="citations" />
+
+</tool>