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comparison mash_screen.xml @ 4:033da434cfaf draft

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planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/mash commit 54c5ec0b3958115ccb9071184268bfe4f7425baa-dirty
author dfornika
date Mon, 28 Jan 2019 22:00:44 -0500
parents 351388dbbc0a
children cf0d6a872bd4
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3:351388dbbc0a 4:033da434cfaf
1 <tool id="mash_screen" name="mash screen" version="@TOOL_VERSION@+galaxy0">fastq_ 1 <tool id="mash_screen" name="mash screen" version="@TOOL_VERSION@+galaxy0">
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>
24 '$pool_input.pool' 24 '$pool_input.pool'
25 #end if 25 #end if
26 > '$output' 26 > '$output'
27 ]]></command> 27 ]]></command>
28 <inputs> 28 <inputs>
29 <conditional name="pool_input"> 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"> 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> 31 <option value="paired">Paired</option>
32 <option value="single">Single</option> 32 <option value="single">Single</option>
33 <option value="paired_collection">Paired Collection</option> 33 <option value="paired_collection">Paired Collection</option>
34 </param> 34 </param>
35 <when value="paired"> 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"/> 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"/> 37 <param name="pool_2" type="data" format="@INTYPES@" label="Select second set of reads" help="Specify dataset with reverse reads"/>
38 </when> 38 </when>
39 <when value="single"> 39 <when value="single">
40 <param name="pool" type="data" format="@INTYPES@" label="Select fastq dataset" help="Specify dataset with single reads"/> 40 <param name="pool" type="data" format="@INTYPES@" label="Select fastq dataset" help="Specify dataset with single reads"/>
41 </when> 41 </when>
42 <when value="paired_collection"> 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"/> 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> 44 </when>
45 </conditional> 45 </conditional>
46 <param name="queries" type="data" format="binary" /> 46 <param name="queries" type="data" format="binary" />
47 <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=""/>
48 <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." />
49 <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."/>
67 <test> 67 <test>
68 <param name="queries" value="NZ_MYON01000010.1.msh"/> 68 <param name="queries" value="NZ_MYON01000010.1.msh"/>
69 <param name="pool_input_selector" value="paired"/> 69 <param name="pool_input_selector" value="paired"/>
70 <param name="pool_1" value="ERR024951_seqtk_sample_1000_1.fastq"/> 70 <param name="pool_1" value="ERR024951_seqtk_sample_1000_1.fastq"/>
71 <param name="pool_2" value="ERR024951_seqtk_sample_1000_2.fastq"/> 71 <param name="pool_2" value="ERR024951_seqtk_sample_1000_2.fastq"/>
72 <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_1and2.tsv"/>
73 </test>
74 <test>
75 <param name="queries" value="NZ_MYON01000010.1.msh"/>
76 <param name="pool_input_selector" value="paired_collection"/>
77 <param name="pool">
78 <collection type="paired">
79 <element name="forward" value="ERR024951_seqtk_sample_1000_1.fastq"/>
80 <element name="reverse" value="ERR024951_seqtk_sample_1000_2.fastq"/>
81 </collection>
82 </param>
72 <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_1and2.tsv"/> 83 <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_1and2.tsv"/>
73 </test> 84 </test>
74 </tests> 85 </tests>
75 <help><![CDATA[ 86 <help><![CDATA[
76 Description: 87 Description: