Mercurial > repos > iuc > gemini
annotate gemini_windower.xml @ 17:65f742e605ec draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 344140b8df53b8b7024618bb04594607a045c03a
| author | iuc |
|---|---|
| date | Mon, 04 May 2015 22:46:38 -0400 |
| parents | 53a5647e5271 |
| children | ce61d4876838 |
| rev | line source |
|---|---|
| 0 | 1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0"> |
| 2 <description>Conducting analyses on genome "windows"</description> | |
| 3 <macros> | |
| 4 <import>gemini_macros.xml</import> | |
| 5 <token name="@BINARY@">windower</token> | |
| 6 </macros> | |
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17
65f742e605ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
11
diff
changeset
|
7 <expand macro="requirements" /> |
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65f742e605ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
11
diff
changeset
|
8 <expand macro="stdio" /> |
|
65f742e605ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
11
diff
changeset
|
9 <expand macro="version_command" /> |
| 0 | 10 <command> |
| 11 <![CDATA[ | |
| 12 gemini @BINARY@ | |
| 13 -w $w | |
| 14 -s $s | |
| 15 -t $window_analysis | |
| 16 -o $operation | |
| 17 "${ infile }" | |
| 18 > "${ outfile }" | |
| 19 ]]> | |
| 20 </command> | |
| 21 <inputs> | |
| 11 | 22 <expand macro="infile" /> |
| 0 | 23 |
| 24 <param name="window_analysis" type="select" label="The type of window analysis requested?" help="(-t)"> | |
| 25 <option value="nucl_div">(nucl_div)</option> | |
| 26 <option value="hwe">(hwe)</option> | |
| 27 </param> | |
| 28 | |
| 29 <param name="operation" type="select" label="The operation that should be applied to the -t values" help="(-o)"> | |
| 30 <option value="mean">mean</option> | |
| 31 <option value="median">median</option> | |
| 32 <option value="min">min</option> | |
| 33 <option value="max">max</option> | |
| 34 <option value="collapse">collapse</option> | |
| 35 </param> | |
| 36 | |
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17
65f742e605ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
11
diff
changeset
|
37 <param name="w" type="integer" value="10000" size="10" label="The window size in bp" |
| 0 | 38 help="(-w)"> |
| 39 <validator type="in_range" min="0"/> | |
| 40 </param> | |
| 41 | |
|
17
65f742e605ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
11
diff
changeset
|
42 <param name="s" type="integer" value="1000" size="10" label="The step size for the windows in bp" |
| 0 | 43 help="(-s)"> |
| 44 <validator type="in_range" min="0"/> | |
| 45 </param> | |
| 46 | |
| 47 </inputs> | |
| 48 | |
| 49 <outputs> | |
| 11 | 50 <data name="outfile" format="tabular" /> |
| 0 | 51 </outputs> |
| 52 <tests> | |
| 53 <test> | |
| 54 </test> | |
| 55 </tests> | |
| 56 <help> | |
| 57 **What it does** | |
| 58 | |
| 59 It computs variation metrics across genomic windows (both fixed and sliding). | |
| 60 | |
| 61 @CITATION@ | |
| 62 </help> | |
| 63 <expand macro="citations"/> | |
| 64 </tool> |