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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
author | iuc |
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date | Sat, 10 Dec 2022 21:14:08 +0000 |
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children | d1f8d32bbe3b |
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<tool id="dram_neighborhoods" name="DRAM find neighborhoods" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>around genes of interest</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ DRAM.py neighborhoods --input_file '$input_file' --output_dir 'output_dir' #if $advanced.genes: --genes '$advanced.genes' #end if #if $advanced.identifiers: --identifiers '$advanced.identifiers' #end if #if $advanced.custom_distillate: --custom_distillate '$advanced.custom_distillate' #end if ## Broken in 3.5.1 - https://github.com/WrightonLabCSU/DRAM/issues/194 ##if $advanced.categories: ## --categories '$advanced.categories' ##end if #if $advanced.genes_loc: --genes_loc '$advanced.genes_loc' #end if #if $advanced.scaffolds_loc: --scaffolds_loc '$advanced.scaffolds_loc' #end if #if $advanced.distance_genes > 0: --distance_genes $advanced.distance_genes #end if #if $advanced.distance_bp > 0: --distance_bp $advanced.distance_bp #end if && test -f 'output_dir/neighborhood_annotations.tsv' && mv 'output_dir/neighborhood_annotations.tsv' '$output_neighborhood_annotations' || echo 'No neighborhood_annotations.tsv output produced' #if $advanced.genes_loc: && test -f 'output_dir/neighborhood_genes.dat' && mv 'output_dir/neighborhood_genes.dat' '$output_neighborhood_genes' || echo 'No neighborhood_genes.dat output produced' #end if #if $advanced.scaffolds_loc: && test -f 'output_dir/neighborhood_scaffolds.fna' && mv 'output_dir/neighborhood_scaffolds.fna' '$output_neighborhood_scaffolds' || echo 'No neighborhood_scaffolds.fna output produced' #end if ]]></command> <inputs> <expand macro="input_file_param"/> <section name="advanced" title="Advanced options" expanded="false"> <expand macro="genes_param"/> <expand macro="identifiers_param"/> <expand macro="custom_distillate_param"/> <!-- Broken in 3.5.1 - see above --> <!-- <expand macro="categories_param"/> --> <param argument="--genes_loc" type="data" format="fasta" optional="true" label="File containing genes to filter to neighborhoods" help="Optional, leave blank to ignore"/> <param argument="--scaffolds_loc" type="data" format="fasta" optional="true" label="File containing scaffolds to filter to neighborhoods" help="Optional, leave blank to ignore"/> <param argument="--distance_genes" type="integer" value="0" min="0" label="Number of genes away from center to include in neighborhoods" help="Optional, set to 0 to ignore, but must provide distance away in genes, bp or both"/> <param argument="--distance_bp" type="integer" value="0" min="0" label="Number of base pairs away from center to include in neighborhoods" help="Optional, set to 0 to ignore, but must provide distance away in bp, genes or both"/> </section> </inputs> <outputs> <data name="output_neighborhood_annotations" format="tabular" label="${tool.name} on ${on_string}: neighborhood annotations"/> <data name="output_neighborhood_genes" format="fasta" label="${tool.name} on ${on_string}: neighborhood genes"> <filter>advanced['genes_loc']</filter> </data> <data name="output_neighborhood_scaffolds" format="fasta" label="${tool.name} on ${on_string}: neighborhood scaffolds"> <filter>advanced['scaffolds_loc']</filter> </data> </outputs> <tests> <test expect_num_outputs="1"> <param name="input_file" ftype="tabular" value="annotated1.tabular"/> <param name="distance_genes" value="10"/> <output name="output_neighborhood_annotations"> <assert_contents> <has_size value="2046495" delta="1000"/> </assert_contents> <assert_contents> <has_text text="neighborhood_number"/> </assert_contents> </output> </test> <test expect_num_outputs="3"> <param name="input_file" ftype="tabular" value="annotated1.tabular"/> <param name="distance_genes" value="10"/> <param name="custom_distillate" ftype="tabular" value="distill_custom.tabular"/> <param name="genes_loc" ftype="fasta" value="neighborhoods_genes_loc1.fna"/> <param name="scaffolds_loc" ftype="fasta" value="neighborhoods_scaffolds_loc1.fasta"/> <output name="output_neighborhood_annotations"> <assert_contents> <has_size value="2046495" delta="10000"/> </assert_contents> <assert_contents> <has_text text="neighborhood_number"/> </assert_contents> </output> <output name="output_neighborhood_genes" ftype="fasta" value="neighborhoods_output1.fasta"/> <output name="output_neighborhood_scaffolds" ftype="fasta" value="neighborhoods_output1.fasta"> </output> </test> </tests> <help> **What it does** @WHATITDOESHEADER@ This tool accepts a tabular file with all gene annotations from Pfam, UniProt, dbCAN and MEROPS databases produced by the DRAM annotate tool and finds neighborhoods around genes of interest. @CUSTOMDISTILLATEFILES@ **Options** * **Space-separated list of genes to keep** - genee names from DRAM around which to find neighborhoods * **Database identifiers** - database identifiers assigned by DRAM around which to find neighborhoods * **File containing genes to filter to neighborhoods** - file containing genes to filter to neighborhoods * **File containing scaffolds to filter to neighborhoods** - file containing scaffolds to filter to neighborhoods * **Number of genes away from center to include in neighborhoods** - number of genes away from center to include in neighborhoods * **Number of base pairs away from center to include in neighborhoods** - number of base pairs away from center to include in neighborhoods @WHATITDOESFOOTER@ </help> <expand macro="citations"/> </tool>