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comparison closestBed.xml @ 34:dde39ba9c031 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
author iuc
date Mon, 29 Apr 2019 05:55:48 -0400
parents 4f7a5ccd2ae9
children 3e38c9b3214f
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equal deleted inserted replaced
33:87ee588b3d45 34:dde39ba9c031
1 <tool id="bedtools_closestbed" name="bedtools ClosestBed" version="@WRAPPER_VERSION@"> 1 <tool id="bedtools_closestbed" name="bedtools ClosestBed" version="@TOOL_VERSION@">
2 <description>find the closest, potentially non-overlapping interval</description> 2 <description>find the closest, potentially non-overlapping interval</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" />
22 #end if 22 #end if
23 -a '$inputA' 23 -a '$inputA'
24 #if str($overlap_with.source) == "data_table": 24 #if str($overlap_with.source) == "data_table":
25 -b '$overlap_with.table.fields.path' 25 -b '$overlap_with.table.fields.path'
26 #else 26 #else
27 #set inputBs = "' '".join([str( $file ) for $file in $overlap_with.inputB]) 27 -b
28 -b '$inputBs' 28 #for $file in $overlap_with.inputB:
29 '$file'
30 #end for
29 #end if 31 #end if
30 > '$output' 32 > '$output'
31 ]]></command> 33 ]]></command>
32 <inputs> 34 <inputs>
33 <param name="inputA" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/> 35 <param name="inputA" argument="-a" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
34 <!-- overlap with file (inputB) --> 36 <!-- overlap with file (inputB) -->
35 <conditional name="overlap_with"> 37 <conditional name="overlap_with">
36 <param name="source" type="select" label="Overlap with: will you select a @STD_BEDTOOLS_INPUT_LABEL@ file from your history or use a built-in GFF file?" help="Built-in GFF files contain full annotation of a reference genome"> 38 <param name="source" type="select" label="Overlap with: will you select a @STD_BEDTOOLS_INPUT_LABEL@ file from your history or use a built-in GFF file?" help="Built-in GFF files contain full annotation of a reference genome">
37 <option value="history" selected="true">Use a @STD_BEDTOOLS_INPUT_LABEL@ file from the history</option> 39 <option value="history" selected="true">Use a @STD_BEDTOOLS_INPUT_LABEL@ file from the history</option>
38 <option value="data_table">Use a built-in GFF file</option> 40 <option value="data_table">Use a built-in GFF file</option>
44 <validator type="no_options" message="No files are available"/> 46 <validator type="no_options" message="No files are available"/>
45 </options> 47 </options>
46 </param> 48 </param>
47 </when> 49 </when>
48 <when value="history"> 50 <when value="history">
49 <param name="inputB" type="data" format="@STD_BEDTOOLS_INPUTS@" multiple="true" label="Select a @STD_BEDTOOLS_INPUT_LABEL@ file" /> 51 <param name="inputB" argument="-b" type="data" format="@STD_BEDTOOLS_INPUTS@" multiple="true" label="Select a @STD_BEDTOOLS_INPUT_LABEL@ file" />
50 </when> 52 </when>
51 </conditional> 53 </conditional>
52 54
53 <param name="ties" type="select" 55 <param name="ties" type="select"
54 label="How ties for closest feature should be handled" 56 label="How ties for closest feature should be handled"
98 <option value="all">Report closest records among all databases. (-all)</option> 100 <option value="all">Report closest records among all databases. (-all)</option>
99 </param> 101 </param>
100 </inputs> 102 </inputs>
101 <outputs> 103 <outputs>
102 <!-- Would like to use a nicer name, but since there are possibly many inputB datasets, falling back to ${on_string} --> 104 <!-- Would like to use a nicer name, but since there are possibly many inputB datasets, falling back to ${on_string} -->
103 <!-- <data format_source="inputA" name="output" metadata_source="inputA" label="Closest regions from ${inputB[0].name} to ${inputA.name}"/> --> 105 <!-- <data name="output" format_source="inputA" metadata_source="inputA" label="Closest regions from ${inputB[0].name} to ${inputA.name}"/> -->
104 <data name="output" format_source="inputA" metadata_source="inputA" label="Closest regions from ${on_string}" /> 106 <data name="output" format_source="inputA" metadata_source="inputA" label="Closest regions from ${on_string}" />
105 </outputs> 107 </outputs>
106 <tests> 108 <tests>
107 <test> 109 <test>
108 <param name="inputA" value="closestBedA.bed" ftype="bed" /> 110 <param name="inputA" value="closestBedA.bed" ftype="bed" />