Mercurial > repos > iuc > trinity
diff trinity.xml @ 34:8f1c3df4dd49 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit ec26c475a013d89b0f973f29250d660e79d4751f
| author | iuc |
|---|---|
| date | Wed, 20 Sep 2023 14:54:54 +0000 |
| parents | 9fa24d5aac68 |
| children |
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--- 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>