Mercurial > repos > iuc > gemini_actionable_mutations
annotate gemini_macros.xml @ 5:643a9ad97f08 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
author | iuc |
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date | Fri, 11 Jan 2019 17:49:17 -0500 |
parents | 712aa8283200 |
children | db47f4939381 |
rev | line source |
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0
b6fb24500a86
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
712aa8283200
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
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diff
changeset
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2 <!-- gemini version to be used --> |
5
643a9ad97f08
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
712aa8283200
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
643a9ad97f08
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
712aa8283200
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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b6fb24500a86
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
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7 <xml name="requirements"> |
b6fb24500a86
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
712aa8283200
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
b6fb24500a86
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 /> |
b6fb24500a86
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
11 </requirements> |
b6fb24500a86
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> |
b6fb24500a86
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
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13 |
b6fb24500a86
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"> |
b6fb24500a86
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> |
b6fb24500a86
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> |
b6fb24500a86
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
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17 |
b6fb24500a86
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
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18 <xml name="stdio"> |
b6fb24500a86
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> |
b6fb24500a86
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:" /> |
b6fb24500a86
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
21 <exit_code range=":-1" /> |
b6fb24500a86
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
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22 <regex match="Error:" /> |
b6fb24500a86
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
643a9ad97f08
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
b6fb24500a86
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
25 </stdio> |
b6fb24500a86
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
26 </xml> |
b6fb24500a86
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
643a9ad97f08
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"> |
643a9ad97f08
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> |
643a9ad97f08
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> |
643a9ad97f08
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 /> |
643a9ad97f08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
4
diff
changeset
|
32 </citations> |
643a9ad97f08
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> |
643a9ad97f08
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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34 |
0
b6fb24500a86
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
712aa8283200
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"> |
712aa8283200
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
b6fb24500a86
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
712aa8283200
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
b6fb24500a86
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
40 </options> |
b6fb24500a86
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> |
b6fb24500a86
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
42 </xml> |
b6fb24500a86
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
643a9ad97f08
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"> |
643a9ad97f08
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." > |
643a9ad97f08
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" > |
643a9ad97f08
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@" /> |
643a9ad97f08
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
b6fb24500a86
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> |
b6fb24500a86
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
643a9ad97f08
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 |
643a9ad97f08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
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diff
changeset
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52 <xml name="add_header_column"> |
643a9ad97f08
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" |
643a9ad97f08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
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54 label="Add a header of column names to the output" /> |
0
b6fb24500a86
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> |
b6fb24500a86
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
643a9ad97f08
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
b6fb24500a86
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
643a9ad97f08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
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diff
changeset
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59 <param name="report_selector" type="select" |
643a9ad97f08
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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60 label="Set of columns to include in the variant report table" |
643a9ad97f08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
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61 help="@HELP@"> |
643a9ad97f08
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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62 <option value="minimal">Minimal (report only a preconfigured minimal set of columns)</option> |
643a9ad97f08
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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63 <option value="full">Full (report all columns defined in the GEMINI database variants table)</option> |
643a9ad97f08
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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64 <option value="custom">Custom (report user-specified columns)</option> |
0
b6fb24500a86
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
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65 </param> |
5
643a9ad97f08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
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diff
changeset
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66 <when value="full" /> |
643a9ad97f08
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"> |
643a9ad97f08
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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68 <param name="columns" type="hidden" value="@MINIMALSET@" /> |
643a9ad97f08
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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69 <param name="extra_cols" type="hidden" value="" /> |
643a9ad97f08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
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diff
changeset
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70 </when> |
643a9ad97f08
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"> |
643a9ad97f08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
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72 <param name="columns" type="select" display="checkboxes" multiple="true" optional="true" |
643a9ad97f08
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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73 label="Choose columns to include in the report" help="(--columns)"> |
0
b6fb24500a86
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
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changeset
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74 <option value="gene">gene</option> |
b6fb24500a86
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> |
b6fb24500a86
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
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changeset
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76 <option value="start">start</option> |
b6fb24500a86
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
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changeset
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77 <option value="end">end</option> |
b6fb24500a86
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
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changeset
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78 <option value="ref">ref</option> |
b6fb24500a86
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> |
b6fb24500a86
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
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changeset
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80 <option value="impact">impact</option> |
b6fb24500a86
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
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changeset
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81 <option value="impact_severity">impact_severity</option> |
5
643a9ad97f08
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> |
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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."> |
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87 <expand macro="sanitize_query" /> |
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88 </param> |
0
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89 </when> |
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90 </conditional> |
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91 </xml> |
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92 |
5
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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> |
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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."> |
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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@"> |
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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> |
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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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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 |
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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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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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244 #if str($r.start).strip(): |
643a9ad97f08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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245 #silent $r_elements.append("start >= %d" % int($r.start)) |
643a9ad97f08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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246 #end if |
643a9ad97f08
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(): |
643a9ad97f08
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)) |
643a9ad97f08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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249 #end if |
643a9ad97f08
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)) |
643a9ad97f08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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251 #end for |
643a9ad97f08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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252 ]]> |
643a9ad97f08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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253 </token> |
0
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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> |