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comparison dram_strainer.xml @ 2:0fc8251d3d0b draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit 3234c3d93fa294fa9c2c5148eae4b399d42904d8
author iuc
date Fri, 23 Aug 2024 08:17:28 +0000
parents 8a30a4bd0aaa
children
comparison
equal deleted inserted replaced
1:8a30a4bd0aaa 2:0fc8251d3d0b
1 <tool id="dram_strainer" name="DRAM strain annotations" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> 1 <tool id="dram_strainer" name="DRAM strain annotations" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
2 <description>down to genes of interest</description> 2 <description>down to genes of interest</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="bio_tools"/>
6 <expand macro="requirements"/> 7 <expand macro="requirements"/>
7 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
8 DRAM.py strainer 9 DRAM.py strainer
9 --input_annotations '$input_annotations' 10 --input_tsv '$input_tsv'
10 --input_fasta '$input_fasta' 11 --input_fasta '$input_fasta'
11 --output_fasta '$output_fasta' 12 --output_fasta '$output_fasta'
12 #if $advanced.fastas: 13 #if $advanced.fastas:
13 --fastas '$advanced.fastas' 14 --fastas '$advanced.fastas'
14 #end if 15 #end if
19 --genes '$advanced.genes' 20 --genes '$advanced.genes'
20 #end if 21 #end if
21 #if $advanced.identifiers: 22 #if $advanced.identifiers:
22 --identifiers '$advanced.identifiers' 23 --identifiers '$advanced.identifiers'
23 #end if 24 #end if
24 ## Broken in 3.5.1 - https://github.com/WrightonLabCSU/DRAM/issues/194 25 #if $advanced.categories:
25 ##if $advanced.categories: 26 --categories '$advanced.categories'
26 ## --categories '$advanced.categories' 27 #end if
27 ##end if
28 #if $advanced.custom_distillate: 28 #if $advanced.custom_distillate:
29 --custom_distillate '$advanced.custom_distillate' 29 --custom_distillate '$advanced.custom_distillate'
30 #end if 30 #end if
31 ]]></command> 31 ]]></command>
32 <inputs> 32 <inputs>
33 <param argument="--input_annotations" type="data" format="tabular" label="Annotations file" help="Produced by the DRAM annotate tool"/> 33 <param argument="--input_tsv" 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"/> 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"> 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"> 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"/> 37 <expand macro="sanitizer"/>
38 </param> 38 </param>
40 <expand macro="sanitizer"/> 40 <expand macro="sanitizer"/>
41 </param> 41 </param>
42 <expand macro="genes_param"/> 42 <expand macro="genes_param"/>
43 <expand macro="identifiers_param"/> 43 <expand macro="identifiers_param"/>
44 <expand macro="custom_distillate_param"/> 44 <expand macro="custom_distillate_param"/>
45 <!-- Broken in 3.5.1, see above --> 45 <expand macro="categories_param"/>
46 <!-- <expand macro="categories_param"/> -->
47 </section> 46 </section>
48 </inputs> 47 </inputs>
49 <outputs> 48 <outputs>
50 <data name="output_fasta" format="fasta"/> 49 <data name="output_fasta" format="fasta"/>
51 </outputs> 50 </outputs>
52 <tests> 51 <tests>
53 <test expect_num_outputs="1"> 52 <test expect_num_outputs="1">
54 <param name="input_annotations" ftype="tabular" value="annotated1.tabular"/> 53 <param name="input_tsv" value="annotated1.tabular" ftype="tabular"/>
55 <param name="input_fasta" ftype="fasta.gz" value="strainer_input_fasta1.fasta.gz"/> 54 <param name="input_fasta" value="strainer_input_fasta1.fasta.gz" ftype="fasta.gz"/>
56 <param name="fastas" value="dataset_"/> 55 <param name="fastas" value="dataset_"/>
57 <param name="scaffolds" value="scaffold_"/> 56 <param name="scaffolds" value="scaffold_"/>
58 <param name="identifiers" value="K15023"/> 57 <param name="identifiers" value="K15023"/>
59 <param name="custom_distillate" ftype="tabular" value="distill_custom.tabular"/> 58 <param name="custom_distillate" value="distill_custom.tabular" ftype="tabular"/>
60 <output name="output_fasta" ftype="fasta" value="strainer_output1.fasta"/> 59 <output name="output_fasta" ftype="fasta" value="strainer_output1.fasta"/>
61 </test> 60 </test>
62 </tests> 61 </tests>
63 <help> 62 <help>
64 **What it does** 63 **What it does**