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comparison mash_screen.xml @ 9:a33df3111153 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 38a8594d05b6a2fc57db891858b789735dc4a8c3
author iuc
date Thu, 11 Sep 2025 10:21:48 +0000
parents d608e90fb3f0
children
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8:d608e90fb3f0 9:a33df3111153
1 <tool id="mash_screen" name="mash screen" version="@TOOL_VERSION@+galaxy3" profile="19.01"> 1 <tool id="mash_screen" name="mash screen" version="@TOOL_VERSION@+galaxy4" profile="@PROFILE@">
2 <description>determines how well query sequences are contained within a pool of sequences</description> 2 <description>Determine sequence conservation</description>
3 <xrefs>
4 <xref type="bio.tools">mash</xref>
5 </xrefs>
6 <macros> 3 <macros>
7 <import>macros.xml</import> 4 <import>macros.xml</import>
8 </macros> 5 </macros>
9 <expand macro="requirements" /> 6 <expand macro="xref"/>
10 <expand macro="version_command" /> 7 <expand macro="requirements"/>
8 <expand macro="version_command"/>
11 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
12 #if str( $queries_input_source.queries_input_source_selector ) == "tool_data_table": 10 #if str( $queries_input_source.queries_input_source_selector ) == "tool_data_table":
13 ln -s '$queries_input_source.queries.fields.path' queries.msh && 11 ln -s '$queries_input_source.queries.fields.path' queries.msh &&
14 #elif str( $queries_input_source.queries_input_source_selector ) == 'history': 12 #elif str( $queries_input_source.queries_input_source_selector ) == 'history':
15 ln -s '$queries_input_source.queries' queries.msh && 13 ln -s '$queries_input_source.queries' queries.msh &&
57 <param name="queries" type="select" label="Queries (Mash Sketch)"> 55 <param name="queries" type="select" label="Queries (Mash Sketch)">
58 <options from_data_table="mash_sketches"/> 56 <options from_data_table="mash_sketches"/>
59 </param> 57 </param>
60 </when> 58 </when>
61 <when value="history"> 59 <when value="history">
62 <param name="queries" type="data" format="msh" /> 60 <param name="queries" type="data" format="msh"/>
63 </when> 61 </when>
64 </conditional> 62 </conditional>
65 <param name="winner_takes_all" argument="-w" type="boolean" checked="true" truevalue="-w" falsevalue="" label="'Winner takes all' to remove redundancy in the result" 63 <param name="winner_takes_all" argument="-w" type="boolean" checked="true" truevalue="-w" falsevalue="" label="'Winner takes all' to remove redundancy in the result" help="If this option is not enabled, every matching strain from the same species of the reference database is reported in the result."/>
66 help="If this option is not enabled, every matching strain from the same species of the reference database is reported in the result."/> 64 <param type="float" name="minimum_identity_to_report" argument="-i" value="0." min="-1." max="1." label="Minimum identity to report"/>
67 <param type="float" name="minimum_identity_to_report" argument="-i" value="0." min="-1." max="1." label="Minimum identity 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"/>
68 <param type="float" name="maximum_p_value_to_report" argument="-v" value="1." min="0." max="1." label="Maximum p-value to report" />
69 </inputs> 66 </inputs>
70 <outputs> 67 <outputs>
71 <data name="output" format="tabular" /> 68 <data name="output" format="tabular"/>
72 </outputs> 69 </outputs>
73 <tests> 70 <tests>
74 <test> 71 <test expect_num_outputs="1">
75 <param name="queries_input_source_selector" value="history"/> 72 <conditional name="pool_input">
76 <param name="queries" value="NZ_MYON01000010.1.msh"/> 73 <param name="pool_input_selector" value="single"/>
77 <param name="pool_input_selector" value="single"/> 74 <param name="pool" value="ERR024951_seqtk_sample_1000_1.fastq"/>
78 <param name="pool" value="ERR024951_seqtk_sample_1000_1.fastq"/> 75 </conditional>
76 <conditional name="queries_input_source">
77 <param name="queries_input_source_selector" value="history"/>
78 <param name="queries" value="NZ_MYON01000010.1.msh"/>
79 </conditional>
79 <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_1.tsv"/> 80 <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_1.tsv"/>
80 </test> 81 </test>
81 <test> 82 <test expect_num_outputs="1">
82 <param name="queries_input_source_selector" value="tool_data_table"/> 83 <conditional name="pool_input">
83 <param name="queries" value="test_sketch"/> 84 <param name="pool_input_selector" value="single"/>
84 <param name="pool_input_selector" value="single"/> 85 <param name="pool" value="ERR024951_seqtk_sample_1000_2.fastq"/>
85 <param name="pool" value="ERR024951_seqtk_sample_1000_2.fastq"/> 86 </conditional>
87 <conditional name="queries_input_source">
88 <param name="queries_input_source_selector" value="tool_data_table"/>
89 <param name="queries" value="test_sketch"/>
90 </conditional>
86 <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_2.tsv"/> 91 <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_2.tsv"/>
87 </test> 92 </test>
88 <test> 93 <test expect_num_outputs="1">
89 <param name="queries_input_source_selector" value="history"/> 94 <conditional name="pool_input">
90 <param name="queries" value="NZ_MYON01000010.1.msh"/> 95 <param name="pool_input_selector" value="paired"/>
91 <param name="pool_input_selector" value="paired"/> 96 <param name="pool_1" value="ERR024951_seqtk_sample_1000_1.fastq"/>
92 <param name="pool_1" value="ERR024951_seqtk_sample_1000_1.fastq"/> 97 <param name="pool_2" value="ERR024951_seqtk_sample_1000_2.fastq"/>
93 <param name="pool_2" value="ERR024951_seqtk_sample_1000_2.fastq"/> 98 </conditional>
99 <conditional name="queries_input_source">
100 <param name="queries_input_source_selector" value="history"/>
101 <param name="queries" value="NZ_MYON01000010.1.msh"/>
102 </conditional>
94 <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_1and2.tsv"/> 103 <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_1and2.tsv"/>
95 </test> 104 </test>
96 </tests> 105 </tests>
97 <help><![CDATA[ 106 <help><![CDATA[
98 107