changeset 34:8f1c3df4dd49 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit ec26c475a013d89b0f973f29250d660e79d4751f

--- a/trinity.xml	Tue Aug 08 09:10:25 2023 +0000
+++ b/trinity.xml	Wed Sep 20 14:54:54 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="trinity" name="Trinity" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
+<tool id="trinity" name="Trinity" version="@TOOL_VERSION@+galaxy1" profile="21.05">
     <description>de novo assembly of RNA-Seq data</description>
     <macros>
         <import>macros.xml</import>
@@ -14,12 +14,11 @@
             GALAXY_MEMORY_GB=\$((GALAXY_MEMORY_MB / 1024)) ;
         fi ;
 
-        if [ ! -z "\$TRINITY_SCRATCH_DIR" ] ; then
-            workdir=`pwd` ;
-            scratchfolder=\$(mktemp -d -p "\$TRINITY_SCRATCH_DIR");
-            emptyfolder=\$(mktemp -d -p "\$TRINITY_SCRATCH_DIR");
-            cd "\$scratchfolder" ;
-        fi ;
+        TRINITY_SCRATCH_DIR=\${TRINITY_SCRATCH_DIR:-\${TMPDIR:-\$_GALAXY_JOB_TMP_DIR}}
+        workdir=\$(pwd)
+        scratchfolder=\$(mktemp -d -p "\$TRINITY_SCRATCH_DIR");
+        emptyfolder=\$(mktemp -d -p "\$TRINITY_SCRATCH_DIR");
+        cd "\$scratchfolder" ;
 
         #if $additional_params.guided.is_guided == "yes":
             ln -s '${$additional_params.guided.genome_guided_bam}' 'localbam.bam' &&
@@ -148,22 +147,16 @@
         ## CPU and butterfly options.
         --CPU \${GALAXY_SLOTS:-4} --max_memory \${GALAXY_MEMORY_GB:-1}G --bflyHeapSpaceMax \${GALAXY_MEMORY_GB:-1}G --bfly_opts '-V 10 --stderr'
 
-        ## > $trinity_log 2>&1
-
         &&
 
         ## Trinity can create millions of files in the same directory, so the cleaning task makes use of rsync
         ## for ensuring better performances.
         ## see: https://web.archive.org/web/20130929001850/http://linuxnote.net/jianingy/en/linux/a-fast-way-to-remove-huge-number-of-files.html
-        if [ ! -z "\$TRINITY_SCRATCH_DIR" ] ; then
-            mkdir -p "\$workdir/trinity_out_dir";
-            cp -p trinity_out_dir/Trinity* "\$workdir/trinity_out_dir";
-            cd "\$TRINITY_SCRATCH_DIR";
-            rsync -a --delete "\$emptyfolder/" "\$scratchfolder/";
-            rmdir "\$emptyfolder" "\$scratchfolder/";
-            cd "\$workdir";
-        fi ;
-
+        rsync -a --delete "\$emptyfolder/" "\$scratchfolder/" --exclude=trinity_out_dir.Trinity.fasta --exclude=trinity_out_dir.Trinity.fasta.gene_trans_map;
+        mv "\$scratchfolder/trinity_out_dir.Trinity.fasta" '$assembled_transcripts';
+        mv "\$scratchfolder/trinity_out_dir.Trinity.fasta.gene_trans_map" '$gene_to_trans';
+        cd "\$workdir";
+        rmdir "\$emptyfolder" "\$scratchfolder"
     ]]></command>
     <inputs>
         <conditional name="pool">
@@ -235,8 +228,8 @@
         </section>
     </inputs>
     <outputs>
-        <data name="assembled_transcripts" format="fasta" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir.Trinity.fasta"/>
-        <data name="gene_to_trans" format="tabular" label="${tool.name} on ${on_string}: Gene to transcripts map" from_work_dir="trinity_out_dir.Trinity.fasta.gene_trans_map"/>
+        <data name="assembled_transcripts" format="fasta" label="${tool.name} on ${on_string}: Assembled Transcripts"/>
+        <data name="gene_to_trans" format="tabular" label="${tool.name} on ${on_string}: Gene to transcripts map"/>
     </outputs>
     <tests>
         <test>