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comparison closestBed.xml @ 42:d279800f4ff9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b75b9e79cf3186a22dc2e1e9d27c1a080b891b59
author iuc
date Thu, 26 Apr 2018 17:02:24 -0400
parents 374e84779e62
children 2f457890d8c8
comparison
equal deleted inserted replaced
41:c96688f1746d 42:d279800f4ff9
28 -b '$inputBs' 28 -b '$inputBs'
29 #end if 29 #end if
30 > '$output' 30 > '$output'
31 ]]></command> 31 ]]></command>
32 <inputs> 32 <inputs>
33 <param name="inputA" type="data" format="bed,vcf,gff,gff3" label="BED/VCF/GFF file"/> 33 <param name="inputA" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
34 <!-- overlap with file (inputB) --> 34 <!-- overlap with file (inputB) -->
35 <conditional name="overlap_with"> 35 <conditional name="overlap_with">
36 <param name="source" type="select" label="Overlap with: will you select a BED/VCF/GFF file from your history or use a built-in GFF file?" help="Built-in GFF files contain full annotation of a reference genome"> 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">
37 <option value="history" selected="true">Use a BED/VCF/GFF file from the history</option> 37 <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> 38 <option value="data_table">Use a built-in GFF file</option>
39 </param> 39 </param>
40 <when value="data_table"> 40 <when value="data_table">
41 <param name="table" type="select" label="Select reference GFF" help="If your genome of interest is not listed, contact the Galaxy team"> 41 <param name="table" type="select" label="Select reference GFF" help="If your genome of interest is not listed, contact the Galaxy team">
42 <options from_data_table="all_gff"> 42 <options from_data_table="all_gff">
44 <validator type="no_options" message="No files are available"/> 44 <validator type="no_options" message="No files are available"/>
45 </options> 45 </options>
46 </param> 46 </param>
47 </when> 47 </when>
48 <when value="history"> 48 <when value="history">
49 <param name="inputB" type="data" format="bed,gff,vcf,gff3" multiple="true" label="Select a BED/VCF/GFF file" /> 49 <param name="inputB" type="data" format="@STD_BEDTOOLS_INPUTS@" multiple="true" label="Select a @STD_BEDTOOLS_INPUT_LABEL@ file" />
50 </when> 50 </when>
51 </conditional> 51 </conditional>
52 52
53 <param name="ties" type="select" 53 <param name="ties" type="select"
54 label="How ties for closest feature should be handled" 54 label="How ties for closest feature should be handled"