Mercurial > repos > iuc > bedtools
comparison closestBed.xml @ 26:95a3b2c25bd1 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b75b9e79cf3186a22dc2e1e9d27c1a080b891b59
| author | iuc |
|---|---|
| date | Thu, 26 Apr 2018 17:02:46 -0400 |
| parents | b73962f8fcbf |
| children | 4f7a5ccd2ae9 |
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| 25:e36671a0f646 | 26:95a3b2c25bd1 |
|---|---|
| 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" |