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comparison mash_screen.xml @ 1:402b67d1af7d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 91435d801528addac840722e9a0092b2d342b8bb
author iuc
date Wed, 23 Jan 2019 15:59:25 -0500
parents bac720dc1948
children 7f7d8b0c8517
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0:bac720dc1948 1:402b67d1af7d
1 <tool id="mash_screen" name="mash screen" version="@TOOL_VERSION@+galaxy0" profile="19.01"> 1 <tool id="mash_screen" name="mash screen" version="@TOOL_VERSION@+galaxy1" 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 <requirements> 6 <requirements>
12 mash screen 12 mash screen
13 $winner_takes_all 13 $winner_takes_all
14 -i $minimum_identity_to_report 14 -i $minimum_identity_to_report
15 -v $maximum_p_value_to_report 15 -v $maximum_p_value_to_report
16 queries.msh 16 queries.msh
17 '${ str($pool).replace(',', '\' \'') }' 17 #if str( $pool_input.pool_input_selector ) == "paired"
18 '$pool_input.pool_1' '$pool_input.pool_2'
19 #end if
20 #if str( $pool_input.pool_input_selector ) == "paired_collection"
21 '$pool_input.pool.forward' '$pool_input.pool.reverse'
22 #end if
23 #if str( $pool_input.pool_input_selector ) == "single"
24 '$pool_input.pool'
25 #end if
18 > '$output' 26 > '$output'
19 ]]></command> 27 ]]></command>
20 <inputs> 28 <inputs>
29 <conditional name="pool_input">
30 <param name="pool_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data">
31 <option value="paired">Paired</option>
32 <option value="single">Single</option>
33 <option value="paired_collection">Paired Collection</option>
34 </param>
35 <when value="paired">
36 <param name="pool_1" type="data" format="@INTYPES@" label="Select first set of reads" help="Specify dataset with forward reads"/>
37 <param name="pool_2" type="data" format="@INTYPES@" label="Select second set of reads" help="Specify dataset with reverse reads"/>
38 </when>
39 <when value="single">
40 <param name="pool" type="data" format="@INTYPES@" label="Select fastq dataset" help="Specify dataset with single reads"/>
41 </when>
42 <when value="paired_collection">
43 <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"/>
44 </when>
45 </conditional>
21 <param name="queries" type="data" format="msh" /> 46 <param name="queries" type="data" format="msh" />
22 <param type="data" multiple="true" name="pool" format="@INTYPES@" />
23 <param type="boolean" name="winner_takes_all" argument="-w" truevalue="-w" falsevalue=""/> 47 <param type="boolean" name="winner_takes_all" argument="-w" truevalue="-w" falsevalue=""/>
24 <param type="float" name="minimum_identity_to_report" argument="-i" value="0." min="-1." max="1." /> 48 <param type="float" name="minimum_identity_to_report" argument="-i" value="0." min="-1." max="1." />
25 <param type="float" name="maximum_p_value_to_report" argument="-v" value="1." min="0." max="1."/> 49 <param type="float" name="maximum_p_value_to_report" argument="-v" value="1." min="0." max="1."/>
26 </inputs> 50 </inputs>
27 <outputs> 51 <outputs>
28 <data name="output" format="tabular" /> 52 <data name="output" format="tabular" />
29 </outputs> 53 </outputs>
30 <tests> 54 <tests>
31 <test> 55 <test>
32 <param name="queries" value="NZ_MYON01000010.1.msh"/> 56 <param name="queries" value="NZ_MYON01000010.1.msh"/>
57 <param name="pool_input_selector" value="single"/>
33 <param name="pool" value="ERR024951_seqtk_sample_1000_1.fastq"/> 58 <param name="pool" value="ERR024951_seqtk_sample_1000_1.fastq"/>
34 <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_1.tsv"/> 59 <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_1.tsv"/>
35 </test> 60 </test>
36 <test> 61 <test>
37 <param name="queries" value="NZ_MYON01000010.1.msh"/> 62 <param name="queries" value="NZ_MYON01000010.1.msh"/>
63 <param name="pool_input_selector" value="single"/>
38 <param name="pool" value="ERR024951_seqtk_sample_1000_2.fastq"/> 64 <param name="pool" value="ERR024951_seqtk_sample_1000_2.fastq"/>
39 <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_2.tsv"/> 65 <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_2.tsv"/>
40 </test> 66 </test>
41 <test> 67 <test>
42 <param name="queries" value="NZ_MYON01000010.1.msh"/> 68 <param name="queries" value="NZ_MYON01000010.1.msh"/>
43 <param name="pool" value="ERR024951_seqtk_sample_1000_1.fastq,ERR024951_seqtk_sample_1000_2.fastq"/> 69 <param name="pool_input_selector" value="paired"/>
70 <param name="pool_1" value="ERR024951_seqtk_sample_1000_1.fastq"/>
71 <param name="pool_2" value="ERR024951_seqtk_sample_1000_2.fastq"/>
44 <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_1and2.tsv"/> 72 <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_1and2.tsv"/>
45 </test> 73 </test>
46 </tests> 74 </tests>
47 <help><![CDATA[ 75 <help><![CDATA[
48 Description: 76 Description:
67 number={1}, 95 number={1},
68 pages={132}, 96 pages={132},
69 year={2016}, 97 year={2016},
70 publisher={BioMed Central} 98 publisher={BioMed Central}
71 } 99 }
72 </citation> 100 </citation>
73 </citations> 101 </citations>
74 </tool> 102 </tool>