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comparison mash_screen.xml @ 4:d9fb7a9bce28 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 419003af9d5cdf7466b3bbc229256da4fb5852e6"
author iuc
date Wed, 26 Feb 2020 19:04:41 +0000
parents 6d63b05cfea8
children d608e90fb3f0
comparison
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3:6d63b05cfea8 4:d9fb7a9bce28
1 <tool id="mash_screen" name="mash screen" version="@TOOL_VERSION@+galaxy2" profile="19.01"> 1 <tool id="mash_screen" name="mash screen" version="@TOOL_VERSION@+galaxy3" profile="19.01">
2 <description>determines how well query sequences are contained within a pool of sequences</description> 2 <description>determines how well query sequences are contained within a pool of sequences</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" />
7 <expand macro="version_command" /> 7 <expand macro="version_command" />
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 ln -s '$queries' queries.msh && 9 #if str( $queries_input_source.queries_input_source_selector ) == "tool_data_table":
10 ln -s '$queries_input_source.queries.fields.path' queries.msh &&
11 #elif str( $queries_input_source.queries_input_source_selector ) == 'history':
12 ln -s '$queries_input_source.queries' queries.msh &&
13 #end if
10 mash screen 14 mash screen
11 $winner_takes_all 15 $winner_takes_all
12 -i $minimum_identity_to_report 16 -i $minimum_identity_to_report
13 -v $maximum_p_value_to_report 17 -v $maximum_p_value_to_report
14 queries.msh 18 queries.msh
39 </when> 43 </when>
40 <when value="paired_collection"> 44 <when value="paired_collection">
41 <param name="pool" format="@INTYPES@" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/> 45 <param name="pool" format="@INTYPES@" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
42 </when> 46 </when>
43 </conditional> 47 </conditional>
44 <param name="queries" type="data" format="msh" /> 48 <conditional name="queries_input_source">
49 <param name="queries_input_source_selector" type="select" label="Select queries from your history or use one from a tool data table?" help="">
50 <option value="tool_data_table">Queries from tool data table</option>
51 <option selected="True" value="history">Queries from history</option>
52 </param>
53 <when value="tool_data_table">
54 <param name="queries" type="select" label="Queries (Mash Sketch)">
55 <options from_data_table="mash_sketches"/>
56 </param>
57 </when>
58 <when value="history">
59 <param name="queries" type="data" format="msh" />
60 </when>
61 </conditional>
45 <param name="winner_takes_all" argument="-w" type="boolean" checked="true" truevalue="-w" falsevalue="" label="'Winner takes all' to remove redundancy in the result" 62 <param name="winner_takes_all" argument="-w" type="boolean" checked="true" truevalue="-w" falsevalue="" label="'Winner takes all' to remove redundancy in the result"
46 help="If this option is not enabled, every matching strain from the same species of the reference database is reported in the result."/> 63 help="If this option is not enabled, every matching strain from the same species of the reference database is reported in the result."/>
47 <param type="float" name="minimum_identity_to_report" argument="-i" value="0." min="-1." max="1." label="Minimum identity to report" /> 64 <param type="float" name="minimum_identity_to_report" argument="-i" value="0." min="-1." max="1." label="Minimum identity to report" />
48 <param type="float" name="maximum_p_value_to_report" argument="-v" value="1." min="0." max="1." label="Maximum p-value to report" /> 65 <param type="float" name="maximum_p_value_to_report" argument="-v" value="1." min="0." max="1." label="Maximum p-value to report" />
49 </inputs> 66 </inputs>
50 <outputs> 67 <outputs>
51 <data name="output" format="tabular" /> 68 <data name="output" format="tabular" />
52 </outputs> 69 </outputs>
53 <tests> 70 <tests>
54 <test> 71 <test>
72 <param name="queries_input_source_selector" value="history"/>
55 <param name="queries" value="NZ_MYON01000010.1.msh"/> 73 <param name="queries" value="NZ_MYON01000010.1.msh"/>
56 <param name="pool_input_selector" value="single"/> 74 <param name="pool_input_selector" value="single"/>
57 <param name="pool" value="ERR024951_seqtk_sample_1000_1.fastq"/> 75 <param name="pool" value="ERR024951_seqtk_sample_1000_1.fastq"/>
58 <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_1.tsv"/> 76 <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_1.tsv"/>
59 </test> 77 </test>
60 <test> 78 <test>
61 <param name="queries" value="NZ_MYON01000010.1.msh"/> 79 <param name="queries_input_source_selector" value="tool_data_table"/>
80 <param name="queries" value="test_sketch"/>
62 <param name="pool_input_selector" value="single"/> 81 <param name="pool_input_selector" value="single"/>
63 <param name="pool" value="ERR024951_seqtk_sample_1000_2.fastq"/> 82 <param name="pool" value="ERR024951_seqtk_sample_1000_2.fastq"/>
64 <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_2.tsv"/> 83 <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_2.tsv"/>
65 </test> 84 </test>
66 <test> 85 <test>
86 <param name="queries_input_source_selector" value="history"/>
67 <param name="queries" value="NZ_MYON01000010.1.msh"/> 87 <param name="queries" value="NZ_MYON01000010.1.msh"/>
68 <param name="pool_input_selector" value="paired"/> 88 <param name="pool_input_selector" value="paired"/>
69 <param name="pool_1" value="ERR024951_seqtk_sample_1000_1.fastq"/> 89 <param name="pool_1" value="ERR024951_seqtk_sample_1000_1.fastq"/>
70 <param name="pool_2" value="ERR024951_seqtk_sample_1000_2.fastq"/> 90 <param name="pool_2" value="ERR024951_seqtk_sample_1000_2.fastq"/>
71 <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_1and2.tsv"/> 91 <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_1and2.tsv"/>