Mercurial > repos > iuc > dram_merge_annotations
diff dram_merge_annotations.xml @ 1:96c0067106ec draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit e0934fc66bfd742731505cacd18cbf53b26d4f2a
| author | iuc |
|---|---|
| date | Tue, 11 Jul 2023 23:46:55 +0000 |
| parents | 2675f8d7b2a5 |
| children | 866be6c60810 |
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--- a/dram_merge_annotations.xml Sat Dec 10 21:14:28 2022 +0000 +++ b/dram_merge_annotations.xml Tue Jul 11 23:46:55 2023 +0000 @@ -1,4 +1,4 @@ -<tool id="dram_merge_annotations" name="DRAM merge multiple annotations" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> +<tool id="dram_merge_annotations" name="DRAM merge multiple annotations" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> <description>into a single set</description> <macros> <import>macros.xml</import> @@ -38,17 +38,17 @@ DRAM.py merge_annotations --input_dirs 'input_dir*' --output_dir 'output_dir' -&& test -f 'output_dir/genes.faa' && mv 'output_dir/genes.faa' '$output_genes_faa' || echo 'No genes.faa output produced' -&& test -f 'output_dir/genes.fna' && mv 'output_dir/genes.fna' '$output_genes_fna' || echo 'No genes.fna output produced' -&& test -f 'output_dir/genes.gff' && mv 'output_dir/genes.gff' '$output_genes_gff' || echo 'No genes.gff output produced' -&& test -f 'output_dir/scaffolds.fna' && mv 'output_dir/scaffolds.fna' '$output_scaffolds_fna' || echo 'No scaffolds.fna output produced' +&& (test -f 'output_dir/genes.faa' && mv 'output_dir/genes.faa' '$output_genes_faa' || echo 'No genes.faa output produced') +&& (test -f 'output_dir/genes.fna' && mv 'output_dir/genes.fna' '$output_genes_fna' || echo 'No genes.fna output produced') +&& (test -f 'output_dir/genes.gff' && mv 'output_dir/genes.gff' '$output_genes_gff' || echo 'No genes.gff output produced') +&& (test -f 'output_dir/scaffolds.fna' && mv 'output_dir/scaffolds.fna' '$output_scaffolds_fna' || echo 'No scaffolds.fna output produced') #if $rrnas_collection: - && test -f 'output_dir/rrnas.tsv' && mv 'output_dir/rrnas.tsv' '$output_rrnas' || echo 'No rrnas.tsv output produced' + && (test -f 'output_dir/rrnas.tsv' && mv 'output_dir/rrnas.tsv' '$output_rrnas' || echo 'No rrnas.tsv output produced') #end if #if $trnas_collection: - && test -f 'output_dir/trnas.tsv' && mv 'output_dir/trnas.tsv' '$output_trnas' || echo 'No trnas.tsv output produced' + && (test -f 'output_dir/trnas.tsv' && mv 'output_dir/trnas.tsv' '$output_trnas' || echo 'No trnas.tsv output produced') #end if -&& test -f 'output_dir/annotations.tsv' && mv 'output_dir/annotations.tsv' '$output_annotations' || echo 'No annotations.tsv output produced' +&& (test -f 'output_dir/annotations.tsv' && mv 'output_dir/annotations.tsv' '$output_annotations' || echo 'No annotations.tsv output produced') ]]></command> <inputs> <param name="annotations_collection" type="data_collection" format="tabular" collection_type="list" label="Collection of annotation files"/>