diff macros.xml @ 1:d5124d5c8131 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"

--- a/macros.xml	Mon Sep 28 07:45:41 2020 +0000
+++ b/macros.xml	Thu Oct 29 20:51:54 2020 +0000
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">0.8.3</token>
-    <token name="@DESCRIPTION@"></token>
+    <token name="@TOOL_VERSION@">0.8.5</token>
+    <token name="@VERSION_SUFFIX@">0</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">delly</requirement>
@@ -18,6 +18,32 @@
     </xml>
 	
     <!--
+        command 
+    -->
+
+    <token name="@BAM@"><![CDATA[
+#for $i, $current in enumerate($samples)
+    ln -s '${current}' 'sample_${i}.bam' &&
+    ln -s '${current.metadata.bam_index}' 'sample_${i}.bam.bai' &&
+#end for
+    ]]></token>
+    <token name="@DUMP@"><![CDATA[
+#if 'dump' in $oo.out
+    && test -f 'dump.tsv.gz' && bgzip -d 'dump.tsv.gz' || echo 'No dump file.'
+#end if
+    ]]></token>
+    <token name="@LOG@"><![CDATA[
+#if 'log' in $oo.out
+    |& tee '$out_log'
+#end if
+    ]]></token>
+    <token name="@VCF@"><![CDATA[
+#if 'vcf' in $oo.out
+    && test -f 'result.bcf' && bcftools view 'result.bcf' > 'result.vcf' || echo 'No results.'
+#end if
+    ]]></token>
+
+    <!--
         input 
     -->
 
@@ -33,11 +59,20 @@
     <xml name="minclip">
         <param argument="--minclip" type="integer" value="25" label="Set minimum clipping length"/>
     </xml>
-    <xml name="maxreadsep">
-        <param argument="--maxreadsep" type="integer" value="40" label="Set maximum read separation"/>
+    <xml name="maxreadsep" token_default="40">
+        <param argument="--maxreadsep" type="integer" value="@DEFAULT@" label="Set maximum read separation"/>
+    </xml>
+    <xml name="maxsize" token_default="1000000">
+        <param argument="--maxsize" type="integer" value="@DEFAULT@" label="Set maximum SV size"/>
     </xml>
-    <xml name="minrefsep">
-        <param argument="--minrefsep" type="integer" value="25" label="Set minimum reference separation"/>
+    <xml name="mincliquesize">
+        <param name="mincliquesize" type="integer" value="2" label="Set minimum min. PE/SR clique size" help="(--min-clique-size)"/>
+    </xml>
+    <xml name="minrefsep" token_default="25">
+        <param argument="--minrefsep" type="integer" value="@DEFAULT@" label="Set minimum reference separation"/>
+    </xml>
+    <xml name="minsize">
+        <param argument="--minsize" type="integer" value="0" label="Set minimum SV size"/>
     </xml>
     <xml name="samples" token_format="bam" token_multiple="true" token_label="Select sample file(s)">
         <param name="samples" type="data" format="@FORMAT@" multiple="@MULTIPLE@" label="@LABEL@"/>
@@ -76,7 +111,7 @@
         </data>
     </xml>
     <xml name="log">
-        <data name="out_log" format="txt" from_work_dir="log.txt" label="${tool.name} on ${on_string}: Log">
+        <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log">
             <filter>'log' in oo['out']</filter>
         </data>
     </xml>
@@ -89,6 +124,6 @@
 Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome.
     ]]></token>
     <token name="@REFERENCES@"><![CDATA[
-More information are available on `github <https://github.com/dellytools/delly>`_.
+More information are available on `GitHub <https://github.com/dellytools/delly>`_.
     ]]></token>
 </macros>
\ No newline at end of file