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comparison dram_strainer.xml @ 0:e945bfed58b9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
author iuc
date Sat, 10 Dec 2022 21:13:43 +0000
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children 8a30a4bd0aaa
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1 <tool id="dram_strainer" name="DRAM strain annotations" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>down to 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 strainer
9 --input_annotations '$input_annotations'
10 --input_fasta '$input_fasta'
11 --output_fasta '$output_fasta'
12 #if $advanced.fastas:
13 --fastas '$advanced.fastas'
14 #end if
15 #if $advanced.scaffolds:
16 --scaffolds '$advanced.scaffolds'
17 #end if
18 #if $advanced.genes:
19 --genes '$advanced.genes'
20 #end if
21 #if $advanced.identifiers:
22 --identifiers '$advanced.identifiers'
23 #end if
24 ## Broken in 3.5.1 - https://github.com/WrightonLabCSU/DRAM/issues/194
25 ##if $advanced.categories:
26 ## --categories '$advanced.categories'
27 ##end if
28 #if $advanced.custom_distillate:
29 --custom_distillate '$advanced.custom_distillate'
30 #end if
31 ]]></command>
32 <inputs>
33 <param argument="--input_annotations" type="data" format="tabular" label="Annotations file" help="Produced by the DRAM annotate tool"/>
34 <param argument="--input_fasta" type="data" format="fasta,fasta.gz" label="FASTA file to filter"/>
35 <section name="advanced" title="Advanced options" expanded="false">
36 <param argument="--fastas" type="text" value="" label="Space-separated list of fastas to keep" help="Optional, leave blank to ignore">
37 <expand macro="sanitizer"/>
38 </param>
39 <param argument="--scaffolds" type="text" value="" label="Space-separated list of scaffolds to keep" help="Optional, leave blank to ignore">
40 <expand macro="sanitizer"/>
41 </param>
42 <expand macro="genes_param"/>
43 <expand macro="identifiers_param"/>
44 <expand macro="custom_distillate_param"/>
45 <!-- Broken in 3.5.1, see above -->
46 <!-- <expand macro="categories_param"/> -->
47 </section>
48 </inputs>
49 <outputs>
50 <data name="output_fasta" format="fasta"/>
51 </outputs>
52 <tests>
53 <test expect_num_outputs="1">
54 <param name="input_annotations" ftype="tabular" value="annotated1.tabular"/>
55 <param name="input_fasta" ftype="fasta.gz" value="strainer_input_fasta1.fasta.gz"/>
56 <param name="fastas" value="dataset_"/>
57 <param name="scaffolds" value="scaffold_"/>
58 <param name="identifiers" value="K15023"/>
59 <param name="custom_distillate" ftype="tabular" value="distill_custom.tabular"/>
60 <output name="output_fasta" ftype="fasta" value="strainer_output1.fasta"/>
61 </test>
62 </tests>
63 <help>
64 **What it does**
65
66 @WHATITDOESHEADER@
67
68 This tool accepts a tabular file with all gene annotations from Pfam, UniProt, dbCAN and MEROPS databases produced by the
69 DRAM annotate tool and strains them, further analyzing genes of interest by making trees of functional models.
70
71 @CUSTOMDISTILLATEFILES@
72
73 **Options**
74
75 * **Space-separated list of fastas to keep** - space-separated list of fastas to keep
76 * **Space-separated list of scaffolds to keep** - space-separated list of scaffolds to keep
77 * **Space-separated list of genes to keep** - space-separated list of genes to keep
78 * **Database identifiers** - database identifiers to keep
79
80 @WHATITDOESFOOTER@
81 </help>
82 <expand macro="citations"/>
83 </tool>