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comparison dram_merge_annotations.xml @ 1:96c0067106ec draft

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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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0:2675f8d7b2a5 1:96c0067106ec
1 <tool id="dram_merge_annotations" name="DRAM merge multiple annotations" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 1 <tool id="dram_merge_annotations" name="DRAM merge multiple annotations" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
2 <description>into a single set</description> 2 <description>into a single set</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
36 #end for 36 #end for
37 37
38 DRAM.py merge_annotations 38 DRAM.py merge_annotations
39 --input_dirs 'input_dir*' 39 --input_dirs 'input_dir*'
40 --output_dir 'output_dir' 40 --output_dir 'output_dir'
41 && test -f 'output_dir/genes.faa' && mv 'output_dir/genes.faa' '$output_genes_faa' || echo 'No genes.faa output produced' 41 && (test -f 'output_dir/genes.faa' && mv 'output_dir/genes.faa' '$output_genes_faa' || echo 'No genes.faa output produced')
42 && test -f 'output_dir/genes.fna' && mv 'output_dir/genes.fna' '$output_genes_fna' || echo 'No genes.fna output produced' 42 && (test -f 'output_dir/genes.fna' && mv 'output_dir/genes.fna' '$output_genes_fna' || echo 'No genes.fna output produced')
43 && test -f 'output_dir/genes.gff' && mv 'output_dir/genes.gff' '$output_genes_gff' || echo 'No genes.gff output produced' 43 && (test -f 'output_dir/genes.gff' && mv 'output_dir/genes.gff' '$output_genes_gff' || echo 'No genes.gff output produced')
44 && test -f 'output_dir/scaffolds.fna' && mv 'output_dir/scaffolds.fna' '$output_scaffolds_fna' || echo 'No scaffolds.fna output produced' 44 && (test -f 'output_dir/scaffolds.fna' && mv 'output_dir/scaffolds.fna' '$output_scaffolds_fna' || echo 'No scaffolds.fna output produced')
45 #if $rrnas_collection: 45 #if $rrnas_collection:
46 && test -f 'output_dir/rrnas.tsv' && mv 'output_dir/rrnas.tsv' '$output_rrnas' || echo 'No rrnas.tsv output produced' 46 && (test -f 'output_dir/rrnas.tsv' && mv 'output_dir/rrnas.tsv' '$output_rrnas' || echo 'No rrnas.tsv output produced')
47 #end if 47 #end if
48 #if $trnas_collection: 48 #if $trnas_collection:
49 && test -f 'output_dir/trnas.tsv' && mv 'output_dir/trnas.tsv' '$output_trnas' || echo 'No trnas.tsv output produced' 49 && (test -f 'output_dir/trnas.tsv' && mv 'output_dir/trnas.tsv' '$output_trnas' || echo 'No trnas.tsv output produced')
50 #end if 50 #end if
51 && test -f 'output_dir/annotations.tsv' && mv 'output_dir/annotations.tsv' '$output_annotations' || echo 'No annotations.tsv output produced' 51 && (test -f 'output_dir/annotations.tsv' && mv 'output_dir/annotations.tsv' '$output_annotations' || echo 'No annotations.tsv output produced')
52 ]]></command> 52 ]]></command>
53 <inputs> 53 <inputs>
54 <param name="annotations_collection" type="data_collection" format="tabular" collection_type="list" label="Collection of annotation files"/> 54 <param name="annotations_collection" type="data_collection" format="tabular" collection_type="list" label="Collection of annotation files"/>
55 <param name="genbank_collection" type="data_collection" format="genbank" collection_type="list" label="Collection of genbank files"/> 55 <param name="genbank_collection" type="data_collection" format="genbank" collection_type="list" label="Collection of genbank files"/>
56 <param name="trnas_collection" type="data_collection" format="tabular" collection_type="list" optional="true" label="Collection of trna files"/> 56 <param name="trnas_collection" type="data_collection" format="tabular" collection_type="list" optional="true" label="Collection of trna files"/>