Mercurial > repos > iuc > gemini_db_info
annotate gemini_db_info.xml @ 3:4c5f4e9b1931 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 1f7418d74c6fcd61a050106ca5f9b66ab9a4c33d
author | iuc |
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date | Wed, 17 Oct 2018 13:25:30 -0400 |
parents | dc56b2d9d27c |
children | f3cc64057b4e |
rev | line source |
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dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
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1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0"> |
dc56b2d9d27c
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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2 <description>List the gemini database tables and columns</description> |
dc56b2d9d27c
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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3 <macros> |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
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4 <import>gemini_macros.xml</import> |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
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5 <token name="@BINARY@">db_info</token> |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
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6 </macros> |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
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7 <expand macro="requirements" /> |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
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8 <expand macro="stdio" /> |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
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9 <expand macro="version_command" /> |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
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10 <command> |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
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11 <![CDATA[ |
dc56b2d9d27c
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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12 gemini @BINARY@ |
dc56b2d9d27c
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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13 "${ infile }" | tr -s ' ' '\t' |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
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14 > "${ outfile }" |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
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15 ]]> |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
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16 </command> |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
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17 <inputs> |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
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18 <expand macro="infile" /> |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
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19 </inputs> |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
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20 <outputs> |
dc56b2d9d27c
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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21 <data name="outfile" format="tabular" /> |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
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22 </outputs> |
dc56b2d9d27c
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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23 <tests> |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
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24 <test> |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
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25 <param name="infile" value="gemini_comphets_input.db" ftype="gemini.sqlite" /> |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
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26 <output name="outfile" file="gemini_dbinfo_result.tabular" /> |
dc56b2d9d27c
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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27 </test> |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
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28 </tests> |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
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29 <help><![CDATA[ |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
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30 **What it does** |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
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31 |
dc56b2d9d27c
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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32 Because of the sheer number of annotations that are stored in gemini, there are admittedly too many columns to remember by rote. |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
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33 If you can’t recall the name of particular column, just use the db_info tool. |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
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34 It will report all of the tables and all of the columns / types in each table:: |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
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35 |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
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36 table_name column_name type |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
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37 variants chrom text |
dc56b2d9d27c
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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38 variants start integer |
dc56b2d9d27c
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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39 variants end integer |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
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40 variants variant_id integer |
dc56b2d9d27c
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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41 variants anno_id integer |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
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42 variants ref text |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
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43 variants alt text |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
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44 variants qual float |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
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45 variants filter text |
dc56b2d9d27c
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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46 variants type text |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
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47 variants sub_type text |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
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48 variants gts blob |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
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49 variants gt_types blob |
dc56b2d9d27c
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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50 variants gt_phases blob |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
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51 variants gt_depths blob |
dc56b2d9d27c
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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52 variants call_rate float |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
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53 variants in_dbsnp bool |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
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54 variants rs_ids text |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
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55 variants in_omim bool |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
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56 variants clin_sigs text |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
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57 variants cyto_band text |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
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58 variants rmsk text |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
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59 variants in_cpg_island bool |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
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60 variants in_segdup bool |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
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61 variants is_conserved bool |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
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62 variants num_hom_ref integer |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
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63 variants num_het integer |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
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64 variants num_hom_alt integer |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
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65 variants num_unknown integer |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
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66 variants aaf float |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
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67 variants hwe float |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
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68 variants inbreeding_coeff float |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
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69 variants pi float |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
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70 variants recomb_rate float |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
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71 variants gene text |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
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72 variants transcript text |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
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73 variants is_exonic bool |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
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74 variants is_coding bool |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
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75 variants is_lof bool |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
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76 variants exon text |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
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77 variants codon_change text |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
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78 variants aa_change text |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
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79 ... ... ... |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
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80 |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
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81 For more columns see https://gemini.readthedocs.org/en/latest/content/tools.html#db-info-list-the-gemini-database-tables-and-columns |
dc56b2d9d27c
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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82 |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
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83 ]]></help> |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
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84 <expand macro="citations"/> |
dc56b2d9d27c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff
changeset
|
85 </tool> |