Mercurial > repos > iuc > bedtools
comparison makeWindowsBed.xml @ 17:44867b59dbf2 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
| author | iuc |
|---|---|
| date | Tue, 05 Sep 2017 15:40:14 -0400 |
| parents | 7308cc546a36 |
| children | a8eabd2838f6 |
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| 16:e0cec48a4695 | 17:44867b59dbf2 |
|---|---|
| 1 <tool id="bedtools_makewindowsbed" name="MakeWindowsBed" version="@WRAPPER_VERSION@.0"> | 1 <tool id="bedtools_makewindowsbed" name="MakeWindowsBed" version="@WRAPPER_VERSION@.1"> |
| 2 <description>make interval windows across a genome</description> | 2 <description>make interval windows across a genome</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" /> |
| 7 <expand macro="stdio" /> | 7 <expand macro="stdio" /> |
| 8 <command> | 8 <command> |
| 9 <![CDATA[ | 9 <![CDATA[ |
| 10 bedtools makewindows | 10 bedtools makewindows |
| 11 #if $type.type_select == 'genome': | 11 #if $type.type_select == 'genome': |
| 12 -g '$type.genome' | 12 @GENOME_FILE_MAKEWINDOWS@ |
| 13 #else: | 13 #else: |
| 14 -b '$type.input' | 14 -b '$type.input' |
| 15 #end if | 15 #end if |
| 16 #if $action.action_select == 'windowsize': | 16 #if $action.action_select == 'windowsize': |
| 17 -w $action.windowsize | 17 -w $action.windowsize |
| 34 </param> | 34 </param> |
| 35 <when value="bed"> | 35 <when value="bed"> |
| 36 <param name="input" format="bed,vcf,gff,gff3" type="data" label="BED/VCF/GFF file"/> | 36 <param name="input" format="bed,vcf,gff,gff3" type="data" label="BED/VCF/GFF file"/> |
| 37 </when> | 37 </when> |
| 38 <when value="genome"> | 38 <when value="genome"> |
| 39 <expand macro="genome" /> | 39 <expand macro="input_conditional_genome_file" /> |
| 40 </when> | 40 </when> |
| 41 </conditional> | 41 </conditional> |
| 42 <conditional name="action"> | 42 <conditional name="action"> |
| 43 <param name="action_select" type="select" label="Work with"> | 43 <param name="action_select" type="select" label="Work with"> |
| 44 <option value="windowsize" selected="True">Set WindowSize</option> | 44 <option value="windowsize" selected="True">Set WindowSize</option> |
| 79 <data name="output" format="bed" /> | 79 <data name="output" format="bed" /> |
| 80 </outputs> | 80 </outputs> |
| 81 <tests> | 81 <tests> |
| 82 <test> | 82 <test> |
| 83 <param name="type_select" value="genome" /> | 83 <param name="type_select" value="genome" /> |
| 84 <param name="genome_file_opts_selector" value="hist" /> | |
| 84 <param name="genome" value="mm9_chr1.len" ftype="tabular" /> | 85 <param name="genome" value="mm9_chr1.len" ftype="tabular" /> |
| 85 <param name="action_select" value="windowsize" /> | 86 <param name="action_select" value="windowsize" /> |
| 86 <param name="windowsize" value="1000000" /> | 87 <param name="windowsize" value="1000000" /> |
| 87 <output name="output" file="makeWindowBed_result1.bed" ftype="bed" /> | 88 <output name="output" file="makeWindowBed_result1.bed" ftype="bed" /> |
| 88 </test> | 89 </test> |
| 89 <test> | 90 <test> |
| 90 <param name="type_select" value="genome" /> | 91 <param name="type_select" value="genome" /> |
| 92 <param name="genome_file_opts_selector" value="hist" /> | |
| 91 <param name="genome" value="mm9_chr1.len" ftype="tabular" /> | 93 <param name="genome" value="mm9_chr1.len" ftype="tabular" /> |
| 92 <param name="action_select" value="windowsize" /> | 94 <param name="action_select" value="windowsize" /> |
| 93 <param name="windowsize" value="1000000" /> | 95 <param name="windowsize" value="1000000" /> |
| 94 <param name="step_size_select" value="yes" /> | 96 <param name="step_size_select" value="yes" /> |
| 95 <param name="step_size" value="50000" /> | 97 <param name="step_size" value="50000" /> |
| 96 <output name="output" file="makeWindowBed_result2.bed" ftype="bed" /> | 98 <output name="output" file="makeWindowBed_result2.bed" ftype="bed" /> |
| 97 </test> | 99 </test> |
| 98 <test> | 100 <test> |
| 99 <param name="type_select" value="genome" /> | 101 <param name="type_select" value="genome" /> |
| 102 <param name="genome_file_opts_selector" value="hist" /> | |
| 100 <param name="genome" value="mm9_chr1.len" ftype="tabular" /> | 103 <param name="genome" value="mm9_chr1.len" ftype="tabular" /> |
| 101 <param name="action_select" value="number" /> | 104 <param name="action_select" value="number" /> |
| 102 <param name="number" value="100" /> | 105 <param name="number" value="100" /> |
| 103 <param name="step_size" value="10000" /> | 106 <param name="step_size" value="10000" /> |
| 104 <output name="output" file="makeWindowBed_result3.bed" ftype="bed" /> | 107 <output name="output" file="makeWindowBed_result3.bed" ftype="bed" /> |