diff daa2rma.xml @ 0:e13ac00e6a4d draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 374a2824a264468316f04281ed211079015503b5"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/daa2rma.xml	Tue Dec 07 10:16:58 2021 +0000
@@ -0,0 +1,107 @@
+<tool id="megan_daa2rma" name="MEGAN: Generate a MEGAN rma6 file" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>from a DIAMOND daa file</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="bio_tools"/>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+#set input_identifier = 'input.' + $in.ext
+ln -s '${in}' '${input_identifier}' &&
+
+daa2rma
+--in '${input_identifier}'
+#if $advanced_options.metaDataFile:
+    --metaDataFile '$advanced_options.metaDataFile'
+#end if
+#if str($advanced_options.paired_reads_cond.paired_reads) == 'yes':
+    --paired
+    $advanced_options.paired_reads_cond.pairedSuffixLength
+#end if
+$advanced_options.longReads
+--maxMatchesPerRead $advanced_options.maxMatchesPerRead
+$advanced_options.classify
+--minScore $advanced_options.minScore
+--maxExpected $advanced_options.maxExpected
+--minPercentIdentity $advanced_options.minPercentIdentity
+--topPercent $advanced_options.topPercent
+--minSupportPercent $advanced_options.minSupportPercent
+--minSupport $advanced_options.minSupport
+--minPercentReadCover $advanced_options.minPercentReadCover
+--minPercentReferenceCover $advanced_options.minPercentReferenceCover
+--minReadLength $advanced_options.minReadLength
+--lcaAlgorithm '$advanced_options.lcaAlgorithm'
+--lcaCoveragePercent $advanced_options.lcaCoveragePercent
+--readAssignmentMode '$advanced_options.readAssignmentMode'
+#if $advanced_options.conFile:
+    --conFile '$advanced_options.conFile'
+#end if
+#if $advanced_options.mapDB:
+    --mapDB '$advanced_options.mapDB'
+#end if
+#if str($advanced_options.only) != '':
+    --only '$advanced_options.only'
+#end if
+--out '$output'
+--threads \${GALAXY_SLOTS:-8}
+--tempStoreDir '.'
+    ]]></command>
+    <inputs>
+        <expand macro="input_daa_param"/>
+        <section name="advanced_options" title="Advanced options" expanded="false">
+            <param argument="--metaDataFile" type="data" format="tabular" multiple="true" optional="true" label="Files containing metadata to be included in the output files"/>
+            <conditional name="paired_reads_cond">
+                <param name="paired_reads" type="select" label="DAA file was created using paired reads?">
+                    <option value="no" selected="true">no</option>
+                    <option value="yes">Yes</option>
+                </param>
+                <when value="no"/>
+                <when value="yes">
+                    <param argument="--pairedSuffixLength" type="integer" value="0" label="Length of name suffix used to distinguish read names" help="Use 0 if read and mate have the same name"/>
+                </when>
+            </conditional>
+            <expand macro="long_reads_param"/>
+            <expand macro="max_matches_per_read_param"/>
+            <expand macro="classify_param"/>
+            <expand macro="blast_params"/>
+            <expand macro="min_max_params"/>
+            <expand macro="lca_params"/>
+            <expand macro="read_assignment_mode_param"/>
+            <expand macro="con_file_param"/>
+            <expand macro="mapdb_param"/>
+            <expand macro="only_named_classifications_param"/>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="output" format="rma6"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="in" ftype="daa" value="input.daa"/>
+            <output name="output" ftype="rma6">
+                <assert_contents>
+                    <has_size value="1487"/>
+                </assert_contents>
+            </output>
+       </test>
+        <test>
+            <param name="in" ftype="daa" value="input.daa"/>
+            <param name="longReads" value="true"/>
+            <param name="minScore" value="25.0"/>
+            <param name="maxExpected" value="0.05"/>
+            <param name="lcaAlgorithm" value="weighted"/>
+            <output name="output" ftype="rma6">
+                <assert_contents>
+                    <has_size value="1445"/>
+                </assert_contents>
+            </output>
+       </test>
+    </tests>
+    <help>
+**What it does**
+
+Computes a MEGAN RMA (RealMedia Audio) file from a DIOMAND DAA file, a proprietary file format developed by PowerISO Computing
+for disk image files.  MEGAN uses an update of the original RMA file format known as RMA6.
+    </help>
+    <expand macro="citations"/>
+</tool>