Mercurial > repos > iuc > dram_neighborhoods
comparison dram_neighborhoods.xml @ 0:fc93558da540 draft
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 |
parents | |
children | d1f8d32bbe3b |
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1 <tool id="dram_neighborhoods" name="DRAM find neighborhoods" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> | |
2 <description>around genes of interest</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements"/> | |
7 <command detect_errors="exit_code"><![CDATA[ | |
8 DRAM.py neighborhoods | |
9 --input_file '$input_file' | |
10 --output_dir 'output_dir' | |
11 #if $advanced.genes: | |
12 --genes '$advanced.genes' | |
13 #end if | |
14 #if $advanced.identifiers: | |
15 --identifiers '$advanced.identifiers' | |
16 #end if | |
17 #if $advanced.custom_distillate: | |
18 --custom_distillate '$advanced.custom_distillate' | |
19 #end if | |
20 ## Broken in 3.5.1 - https://github.com/WrightonLabCSU/DRAM/issues/194 | |
21 ##if $advanced.categories: | |
22 ## --categories '$advanced.categories' | |
23 ##end if | |
24 #if $advanced.genes_loc: | |
25 --genes_loc '$advanced.genes_loc' | |
26 #end if | |
27 #if $advanced.scaffolds_loc: | |
28 --scaffolds_loc '$advanced.scaffolds_loc' | |
29 #end if | |
30 #if $advanced.distance_genes > 0: | |
31 --distance_genes $advanced.distance_genes | |
32 #end if | |
33 #if $advanced.distance_bp > 0: | |
34 --distance_bp $advanced.distance_bp | |
35 #end if | |
36 && test -f 'output_dir/neighborhood_annotations.tsv' && mv 'output_dir/neighborhood_annotations.tsv' '$output_neighborhood_annotations' || echo 'No neighborhood_annotations.tsv output produced' | |
37 #if $advanced.genes_loc: | |
38 && test -f 'output_dir/neighborhood_genes.dat' && mv 'output_dir/neighborhood_genes.dat' '$output_neighborhood_genes' || echo 'No neighborhood_genes.dat output produced' | |
39 #end if | |
40 #if $advanced.scaffolds_loc: | |
41 && test -f 'output_dir/neighborhood_scaffolds.fna' && mv 'output_dir/neighborhood_scaffolds.fna' '$output_neighborhood_scaffolds' || echo 'No neighborhood_scaffolds.fna output produced' | |
42 #end if | |
43 ]]></command> | |
44 <inputs> | |
45 <expand macro="input_file_param"/> | |
46 <section name="advanced" title="Advanced options" expanded="false"> | |
47 <expand macro="genes_param"/> | |
48 <expand macro="identifiers_param"/> | |
49 <expand macro="custom_distillate_param"/> | |
50 <!-- Broken in 3.5.1 - see above --> | |
51 <!-- <expand macro="categories_param"/> --> | |
52 <param argument="--genes_loc" type="data" format="fasta" optional="true" label="File containing genes to filter to neighborhoods" help="Optional, leave blank to ignore"/> | |
53 <param argument="--scaffolds_loc" type="data" format="fasta" optional="true" label="File containing scaffolds to filter to neighborhoods" help="Optional, leave blank to ignore"/> | |
54 <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"/> | |
55 <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"/> | |
56 </section> | |
57 </inputs> | |
58 <outputs> | |
59 <data name="output_neighborhood_annotations" format="tabular" label="${tool.name} on ${on_string}: neighborhood annotations"/> | |
60 <data name="output_neighborhood_genes" format="fasta" label="${tool.name} on ${on_string}: neighborhood genes"> | |
61 <filter>advanced['genes_loc']</filter> | |
62 </data> | |
63 <data name="output_neighborhood_scaffolds" format="fasta" label="${tool.name} on ${on_string}: neighborhood scaffolds"> | |
64 <filter>advanced['scaffolds_loc']</filter> | |
65 </data> | |
66 </outputs> | |
67 <tests> | |
68 <test expect_num_outputs="1"> | |
69 <param name="input_file" ftype="tabular" value="annotated1.tabular"/> | |
70 <param name="distance_genes" value="10"/> | |
71 <output name="output_neighborhood_annotations"> | |
72 <assert_contents> | |
73 <has_size value="2046495" delta="1000"/> | |
74 </assert_contents> | |
75 <assert_contents> | |
76 <has_text text="neighborhood_number"/> | |
77 </assert_contents> | |
78 </output> | |
79 </test> | |
80 <test expect_num_outputs="3"> | |
81 <param name="input_file" ftype="tabular" value="annotated1.tabular"/> | |
82 <param name="distance_genes" value="10"/> | |
83 <param name="custom_distillate" ftype="tabular" value="distill_custom.tabular"/> | |
84 <param name="genes_loc" ftype="fasta" value="neighborhoods_genes_loc1.fna"/> | |
85 <param name="scaffolds_loc" ftype="fasta" value="neighborhoods_scaffolds_loc1.fasta"/> | |
86 <output name="output_neighborhood_annotations"> | |
87 <assert_contents> | |
88 <has_size value="2046495" delta="10000"/> | |
89 </assert_contents> | |
90 <assert_contents> | |
91 <has_text text="neighborhood_number"/> | |
92 </assert_contents> | |
93 </output> | |
94 <output name="output_neighborhood_genes" ftype="fasta" value="neighborhoods_output1.fasta"/> | |
95 <output name="output_neighborhood_scaffolds" ftype="fasta" value="neighborhoods_output1.fasta"> | |
96 </output> | |
97 </test> | |
98 </tests> | |
99 <help> | |
100 **What it does** | |
101 | |
102 @WHATITDOESHEADER@ | |
103 | |
104 This tool accepts a tabular file with all gene annotations from Pfam, UniProt, dbCAN and MEROPS databases produced by the | |
105 DRAM annotate tool and finds neighborhoods around genes of interest. | |
106 | |
107 @CUSTOMDISTILLATEFILES@ | |
108 | |
109 **Options** | |
110 | |
111 * **Space-separated list of genes to keep** - genee names from DRAM around which to find neighborhoods | |
112 * **Database identifiers** - database identifiers assigned by DRAM around which to find neighborhoods | |
113 * **File containing genes to filter to neighborhoods** - file containing genes to filter to neighborhoods | |
114 * **File containing scaffolds to filter to neighborhoods** - file containing scaffolds to filter to neighborhoods | |
115 * **Number of genes away from center to include in neighborhoods** - number of genes away from center to include in neighborhoods | |
116 * **Number of base pairs away from center to include in neighborhoods** - number of base pairs away from center to include in neighborhoods | |
117 | |
118 @WHATITDOESFOOTER@ | |
119 </help> | |
120 <expand macro="citations"/> | |
121 </tool> |