changeset 59:697cd919b711 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/diamond_view.xml	Mon Jun 10 13:10:53 2024 +0000
@@ -0,0 +1,66 @@
+<tool id="pl_diamond_view" name="PL_Diamond view" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="19.01">
+    <description>generate formatted output from DAA files</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="stdio" />
+    <expand macro="version_command" />
+    <command detect_errors="aggressive"><![CDATA[
+    ## need to link because diamont tries to open dataset_xxx.dat.daa
+    ln -s '$daa' input.daa &&
+    /usr/bin/diamond
+        view
+        --threads \${GALAXY_SLOTS:-1}
+        --daa input.daa
+        @OUTPUT_ARGS@
+        @HITFILTER_ARGS@
+        $forwardonly
+        --compress '0'
+    ]]>
+    </command>
+    <inputs>
+        <param argument="--daa" type="data" format="daa" label="input file in DAA format" />
+        <section name="output_section" title="Output options">
+            <expand macro="output_type_macro" />
+        </section>
+        <expand macro="hit_filter_macro" />
+        <param argument="--forwardonly" type="boolean" truevalue="--forwardonly" falsevalue="" checked="false" label="only show alignments of forward strand" help=""/>
+    </inputs>
+    <outputs>
+        <expand macro="output_macro" />
+    </outputs>
+    <help>
+<![CDATA[
+
+**What it does**
+
+Converts diamond daa files to multiple other formats.
+
+**Input**
+
+Input data is a daa file.
+
+
+**Output**
+
+Alignment results in BLAST format (pairwise/tabular), xml, sam, taxonomic (Note the latter does not work with the current diamond version. )
+
+BLAST tables contain the following columns.
+
+Column 	Description
+1 	    Query Seq-id (ID of your sequence)
+2 	    Subject Seq-id (ID of the database hit)
+3 	    Percentage of identical matches
+4 	    Alignment length
+5 	    Number of mismatches
+6 	    Number of gap openings
+7 	    Start of alignment in query
+8 	    End of alignment in query
+9 	    Start of alignment in subject (database hit)
+10 	    End of alignment in subject (database hit)
+11 	    Expectation value (E-value)
+12 	    Bit score
+]]>
+    </help>
+    <expand macro="citations" />
+</tool>