Mercurial > repos > iuc > gemini_query
annotate gemini_macros.xml @ 6:840fb4850be3 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 251c6024b4ff643a63e17fbfe2590998c2bae3a7"
author | iuc |
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date | Fri, 24 Jan 2020 17:31:00 -0500 |
parents | cd00221d67cb |
children | 77a1e60fd1de |
rev | line source |
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0
ab195e756e5e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
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1 <macros> |
4
7ca6716748c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
3
diff
changeset
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2 <!-- gemini version to be used --> |
5
cd00221d67cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
4
diff
changeset
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3 <token name="@VERSION@">0.20.1</token> |
4
7ca6716748c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
3
diff
changeset
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4 <!-- minimal annotation files version required by this version of gemini --> |
5
cd00221d67cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
4
diff
changeset
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5 <token name="@DB_VERSION@">200</token> |
4
7ca6716748c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
3
diff
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6 |
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ab195e756e5e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
7 <xml name="requirements"> |
ab195e756e5e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
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8 <requirements> |
4
7ca6716748c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
3
diff
changeset
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9 <requirement type="package" version="@VERSION@">gemini</requirement> |
0
ab195e756e5e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
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10 <yield /> |
ab195e756e5e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
11 </requirements> |
ab195e756e5e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
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12 </xml> |
ab195e756e5e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
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13 |
ab195e756e5e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
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14 <xml name="version_command"> |
ab195e756e5e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
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15 <version_command>gemini --version</version_command> |
ab195e756e5e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
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16 </xml> |
ab195e756e5e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
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17 |
ab195e756e5e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
18 <xml name="stdio"> |
ab195e756e5e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
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19 <stdio> |
ab195e756e5e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
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20 <exit_code range="1:" /> |
ab195e756e5e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
21 <exit_code range=":-1" /> |
ab195e756e5e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
22 <regex match="Error:" /> |
ab195e756e5e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
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23 <regex match="Exception:" /> |
5
cd00221d67cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
4
diff
changeset
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24 <yield /> |
0
ab195e756e5e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
25 </stdio> |
ab195e756e5e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
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26 </xml> |
ab195e756e5e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
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27 |
5
cd00221d67cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
4
diff
changeset
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28 <xml name="citations"> |
cd00221d67cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
4
diff
changeset
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29 <citations> |
cd00221d67cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
4
diff
changeset
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30 <citation type="doi">10.1371/journal.pcbi.1003153</citation> |
cd00221d67cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
4
diff
changeset
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31 <yield /> |
cd00221d67cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
4
diff
changeset
|
32 </citations> |
cd00221d67cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
4
diff
changeset
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33 </xml> |
cd00221d67cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
4
diff
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34 |
0
ab195e756e5e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
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35 <xml name="annotation_dir"> |
4
7ca6716748c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
3
diff
changeset
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36 <param name="annotation_databases" type="select" label="Choose a gemini annotation source"> |
7ca6716748c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
3
diff
changeset
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37 <options from_data_table="gemini_versioned_databases"> |
0
ab195e756e5e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
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38 <filter type="sort_by" column="0" /> |
4
7ca6716748c2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
3
diff
changeset
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39 <filter type="static_value" column="2" value="@DB_VERSION@" /> |
0
ab195e756e5e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
40 </options> |
ab195e756e5e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
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41 </param> |
ab195e756e5e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
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42 </xml> |
ab195e756e5e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
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43 |
5
cd00221d67cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
4
diff
changeset
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44 <xml name="infile"> |
cd00221d67cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
4
diff
changeset
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45 <param name="infile" type="data" format="gemini.sqlite" label="GEMINI database" help="Only files with version @VERSION@ are accepted." > |
cd00221d67cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
4
diff
changeset
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46 <options options_filter_attribute="metadata.gemini_version" > |
cd00221d67cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
4
diff
changeset
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47 <filter type="add_value" value="@VERSION@" /> |
cd00221d67cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
4
diff
changeset
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48 </options> |
0
ab195e756e5e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
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49 </param> |
ab195e756e5e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
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50 </xml> |
5
cd00221d67cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
4
diff
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51 |
cd00221d67cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
4
diff
changeset
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52 <xml name="add_header_column"> |
cd00221d67cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
4
diff
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53 <param argument="--header" name="header" type="boolean" truevalue="--header" falsevalue="" checked="True" |
cd00221d67cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
4
diff
changeset
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54 label="Add a header of column names to the output" /> |
0
ab195e756e5e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
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55 </xml> |
ab195e756e5e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
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56 |
5
cd00221d67cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
4
diff
changeset
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57 <xml name="column_filter" token_help="" token_minimalset="variant_id, gene"> |
0
ab195e756e5e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
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58 <conditional name="report"> |
5
cd00221d67cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
4
diff
changeset
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59 <param name="report_selector" type="select" |
cd00221d67cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
4
diff
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60 label="Set of columns to include in the variant report table" |
cd00221d67cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
4
diff
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61 help="@HELP@"> |
cd00221d67cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
4
diff
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62 <option value="minimal">Minimal (report only a preconfigured minimal set of columns)</option> |
cd00221d67cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
4
diff
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63 <option value="full">Full (report all columns defined in the GEMINI database variants table)</option> |
cd00221d67cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
4
diff
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64 <option value="custom">Custom (report user-specified columns)</option> |
0
ab195e756e5e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
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65 </param> |
5
cd00221d67cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
4
diff
changeset
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66 <when value="full" /> |
cd00221d67cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
4
diff
changeset
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67 <when value="minimal"> |
cd00221d67cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
4
diff
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68 <param name="columns" type="hidden" value="@MINIMALSET@" /> |
cd00221d67cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
4
diff
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69 <param name="extra_cols" type="hidden" value="" /> |
cd00221d67cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
4
diff
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70 </when> |
cd00221d67cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
4
diff
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71 <when value="custom"> |
cd00221d67cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
4
diff
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72 <param name="columns" type="select" display="checkboxes" multiple="true" optional="true" |
cd00221d67cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
4
diff
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73 label="Choose columns to include in the report" help="(--columns)"> |
0
ab195e756e5e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
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74 <option value="gene">gene</option> |
ab195e756e5e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
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75 <option value="chrom">chrom</option> |
ab195e756e5e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
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76 <option value="start">start</option> |
ab195e756e5e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
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77 <option value="end">end</option> |
ab195e756e5e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
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78 <option value="ref">ref</option> |
ab195e756e5e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
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79 <option value="alt">alt</option> |
ab195e756e5e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
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80 <option value="impact">impact</option> |
ab195e756e5e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
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81 <option value="impact_severity">impact_severity</option> |
5
cd00221d67cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
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diff
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82 <option value="max_aaf_all">alternative allele frequency (max_aaf_all)</option> |
0
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83 </param> |
5
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84 <param name="extra_cols" type="text" |
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85 label="Additional columns (comma-separated)" |
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86 help="Column must be specified by the exact name they have in the GEMINI database, e.g., is_exonic or num_hom_alt, but, for genotype columns, GEMINI wildcard syntax is supported. The order of columns in the list is maintained in the output."> |
cd00221d67cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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87 <expand macro="sanitize_query" /> |
cd00221d67cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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88 </param> |
0
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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89 </when> |
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90 </conditional> |
ab195e756e5e
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91 </xml> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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92 |
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93 <xml name="filter" token_argument="--filter"> |
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94 <param argument="@ARGUMENT@" name="filter" type="text" |
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95 label="Additional constraints expressed in SQL syntax" |
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96 help="Constraints defined here will become the WHERE clause of the SQL query issued to the GEMINI database. E.g. alt='G' or impact_severity = 'HIGH'."> |
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97 <expand macro="sanitize_query" /> |
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98 </param> |
0
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99 </xml> |
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100 |
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101 <xml name="sanitize_query"> |
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102 <sanitizer invalid_char=""> |
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103 <valid initial="string.printable"> |
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104 <remove value="'" /> |
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105 </valid> |
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106 <mapping initial="none"> |
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107 <add source="'" target="'"'"'" /> |
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108 </mapping> |
0
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109 </sanitizer> |
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110 </xml> |
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111 |
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112 <xml name="lenient" token_argument="--lenient" token_truevalue="--lenient" token_help="The exact consequence of this setting depends on the type of inheritance pattern you are looking for (see the tool help below)."> |
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113 <param argument="@ARGUMENT@" name="lenient" type="boolean" truevalue="@TRUEVALUE@" falsevalue="" checked="False" |
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114 label="Include hits with less convincing inheritance patterns" |
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115 help= "@HELP@" /> |
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116 </xml> |
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117 |
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118 <xml name="unaffected"> |
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119 <param argument="--allow-unaffected" name="allow_unaffected" type="boolean" truevalue="--allow-unaffected" falsevalue="" checked="False" |
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120 label="Report candidates shared by unaffected samples" |
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121 help="Activating this option will enable the reporting of variants as candidate causative even if they are shared by unaffected samples in the family tree. The default will only report variants that are unique to affected samples."/> |
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122 </xml> |
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123 |
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124 <xml name="min_kindreds" token_label="Minimum number of families with a candidate variant for a gene to be reported" token_help="This is the number of families required to have a variant fitting the inheritance model in the same gene in order for the gene and its variants to be reported. For example, we may only be interested in candidates where at least 4 families have a variant (with a fitting inheritance pattern) in that gene."> |
cd00221d67cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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125 <param argument="--min-kindreds" name="min_kindreds" type="integer" value="1" min="1" |
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126 label="@LABEL@" |
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127 help="@HELP@" /> |
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128 </xml> |
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129 |
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130 <xml name="insert_constraint" token_max_repeat="1"> |
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131 <repeat name="constraint" title="Additional constraints on variants" default="0" max="@MAX_REPEAT@"> |
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132 <expand macro="filter" /> |
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133 <yield /> |
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134 </repeat> |
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135 </xml> |
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136 |
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137 <xml name="overwritable_where_default" token_default_where=""> |
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138 <param name="overwrite_default_filter" type="boolean" checked="false" |
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139 label="Overwrite the default constraint of this tool" |
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140 help="By default, this tool restricts its analysis to @DEFAULT_WHERE@ and this constraint is applied on top of any constraint expressed above. With this option here selected, your custom constraint, if given, will overwrite the default instead." /> |
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141 </xml> |
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142 |
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143 <xml name="gt_filter" token_default_repeat="0" token_min_repeat="0" token_max_repeat="1"> |
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144 <repeat name="filter_by_genotype" title="Genotype filter expression" default="@DEFAULT_REPEAT@" min="@MIN_REPEAT@" max="@MAX_REPEAT@"> |
cd00221d67cb
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145 <param argument="--gt-filter" name="gt_filter" type="text" value="" area="True" size="5x50" |
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146 label="Restrictions to apply to genotype values" help=""> |
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147 <expand macro="sanitize_query" /> |
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148 <validator type="expression" message="Genotype filter expression cannot be empty">value.strip()</validator> |
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149 </param> |
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150 <yield /> |
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151 </repeat> |
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152 </xml> |
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153 |
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154 <xml name="sample_filter"> |
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155 <repeat name="filter_by_sample" title="Sample filter expression" default="0" max="1"> |
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156 <param argument="--sample-filter" name="sample_filter" type="text" area="True" size="5x50" |
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157 label="SQL filter to use to filter the sample table" help=""> |
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158 <expand macro="sanitize_query" /> |
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159 <validator type="expression" message="Sample filter expression cannot be empty">value.strip()</validator> |
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160 </param> |
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161 <param argument="--in" name="in" type="select" |
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162 label="A variant must be in either all, none or any samples passing the sample-query filter" |
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163 help=""> |
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164 <option value="">Return a variant if it is found in any sample passing the sample filter. (default) </option> |
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165 <option value="--in all">Return a variant if it is found in ALL samples passing the sample filter. (all)</option> |
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166 <option value="--in none">Return a variant if it is found in NO sample passing the sample filter. (none)</option> |
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167 <option value="--in only">Return a variant if it is found in any sample passing the sample filter, and in NO sample NOT passing it. (only)</option> |
cd00221d67cb
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168 <option value="--in only all">Return a variant if is found in ALL samples passing the sample filter, and in NO sample NOT passing it. (only all)</option> |
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169 </param> |
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170 <expand macro="min_kindreds" |
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171 label="Minimum number of families in which a variant must pass the sample filter" help=""/> |
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172 <param argument="--family-wise" name="family_wise" type="boolean" truevalue="--family-wise" falsevalue="" checked="False" |
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173 label="Apply the sample-filter on a family-wise basis" help="If a variant passes the sample filter in at least the minimum number of families specified above it is retained." /> |
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174 </repeat> |
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175 </xml> |
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176 |
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177 <xml name="region_filter"> |
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178 <repeat name="regions" title="Region Filter" default="0" min="0" |
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179 help="Filter variant sites by their position in the genome. If multiple Region Filters are specified, all variants that fall in ONE of the regions are reported."> |
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180 <param name="chrom" type="text" label="Chromosome"> |
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181 <validator type="expression" message="A chromosome identifier is required when specifying a region filter">value.strip()</validator> |
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182 </param> |
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183 <param name="start" type="text" label="Region Start"> |
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184 <validator type="expression" message="an integer number is required">not value or value.isdigit()</validator> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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185 </param> |
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186 <param name="stop" type="text" label="Region End"> |
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187 <validator type="expression" message="an integer number is required">not value or value.isdigit()</validator> |
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188 </param> |
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189 </repeat> |
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190 </xml> |
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191 |
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192 <token name="@PROVIDE_ANNO_DATA@"><![CDATA[ |
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193 mkdir gemini && |
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194 ln -s '${annotation_databases.fields.path}/gemini/data' gemini/data && |
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195 export GEMINI_CONFIG='${annotation_databases.fields.path}' && |
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196 ]]></token> |
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197 |
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198 <token name="@MULTILN_SQL_EXPR_TO_CMDLN@"> |
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199 #set $sql_expr = str($multiline_sql_expr).strip() |
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200 #if str($sql_expr): |
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201 #set $sql_expr = $sql_expr.replace('\r\n', '\n') |
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202 #set $sql_expr = $sql_expr.replace('\r', '\n') |
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203 #set $sql_expr = $sql_expr.replace('\\\n', ' ') |
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204 $cmdln_param '$sql_expr' |
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205 #end if |
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206 </token> |
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207 |
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208 <token name="@SET_COLS@"> |
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209 #if str($report.report_selector) == 'full': |
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210 #set cols = "*" |
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211 #else: |
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212 #if $report.columns and str($report.columns) != '': |
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213 #set $cols = str($report.columns) |
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214 #else |
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215 #set $cols = '' |
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216 #end if |
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217 #if str($report.extra_cols).strip(): |
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218 #if $cols: |
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219 #set $cols = $cols + ', ' + str($report.extra_cols) |
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220 #else: |
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221 #set $cols = str($report.extra_cols) |
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222 #end if |
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223 #end if |
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224 #if not $cols: |
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225 #set $cols = "variant_id, gene" |
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226 #end if |
0
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227 #end if |
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228 </token> |
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229 |
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230 <token name="@COLUMN_SELECT@"> |
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231 @SET_COLS@ |
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232 #if $cols != "*" |
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233 --columns '$cols' |
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234 #end if |
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235 </token> |
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236 |
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237 <token name="@PARSE_REGION_ELEMENTS@"><![CDATA[ |
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238 #set $region_elements = [] |
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239 #for $r in $regions: |
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240 ## The actual chromosome name needs to be single-quoted |
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241 ## in SQL, so we need to quote the single quotes like the |
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242 ## sanitize_query macro would if the whole was a parameter. |
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243 #set $r_elements = ["chrom = '\"'\"'%s'\"'\"'" % str($r.chrom).strip()] |
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244 #if str($r.start).strip(): |
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245 #silent $r_elements.append("start >= %d" % int($r.start)) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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246 #end if |
cd00221d67cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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247 #if str($r.stop).strip(): |
cd00221d67cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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248 #silent $r_elements.append("end <= %d" % int($r.stop)) |
cd00221d67cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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249 #end if |
cd00221d67cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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250 #silent $region_elements.append("(%s)" % " AND ".join($r_elements)) |
cd00221d67cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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251 #end for |
cd00221d67cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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252 ]]> |
cd00221d67cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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253 </token> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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254 </macros> |