# HG changeset patch
# User p.lucas
# Date 1716903999 0
# Node ID e4b21e47cca62572cac3d5647b5f6fd268548372
# Parent  be17909bcbf06eae3a70ada0f538c02177c57ff4
Uploaded

diff -r be17909bcbf0 -r e4b21e47cca6 diamond_view.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/diamond_view.xml	Tue May 28 13:46:39 2024 +0000
@@ -0,0 +1,106 @@
+<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>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="daa" ftype="daa" value="diamond_results.daa" />
+            <section name="output_section">
+                <conditional name="output">
+                    <param name="outfmt" value="5"/>
+                </conditional>
+            </section>
+            <conditional name="hit_filter">
+                <param name="hit_filter_select" value="max"/>
+                <param name="max_target_seqs" value="1" />
+            </conditional>
+            <output name="blast_tabular" file="diamond_results.xml"/>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="daa" ftype="daa" value="diamond_results.daa" />
+            <section name="output_section">
+                <conditional name="output">
+                    <param name="outfmt" value="6"/>
+                    <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore,cigar,scovhsp"/>
+                </conditional>
+            </section>
+            <output name="blast_tabular" file="diamond_view_results.tabular"/>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="daa" ftype="daa" value="diamond_results.daa" />
+            <section name="output_section">
+                <conditional name="output">
+                    <param name="outfmt" value="101"/>
+                </conditional>
+            </section>
+            <conditional name="hit_filter">
+                <param name="hit_filter_select" value="top"/>
+                <param name="max_target_seqs" value="1" />
+            </conditional>
+            <param name="forwardonly" value="--forwardonly" />
+            <output name="blast_tabular" file="diamond_results.sam" lines_diff="2"/>
+        </test>
+    </tests>
+
+    <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>