Mercurial > repos > gga > genenotebook_genenotebook_build
annotate genenotebook_build.xml @ 7:dfb2bc3aedbd draft
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 91ccbf9f293fe6b183302841aa49e061c4ab3157
author | gga |
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date | Thu, 01 Feb 2024 12:45:00 +0000 |
parents | bd94e502872a |
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rev | line source |
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22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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1 <?xml version="1.0"?> |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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2 <tool id="genenotebook_build" name="Build a GeneNoteBook" version="@WRAPPER_VERSION@" profile="21.05"> |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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3 <description></description> |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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4 <macros> |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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5 <import>macros.xml</import> |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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6 </macros> |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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7 <expand macro="requirements" /> |
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5a6050937cb9
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit ec3c633a0751bb9e253bcd77fea425180c9a0014
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8 <command detect_errors="exit_code"><![CDATA[ |
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22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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9 @START_GNB@ |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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10 |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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11 #for genome in $genomes: |
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f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
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12 genoboo add genome @CONNECT_INFO@ --name '${genome.name}' ${genome.public} '${genome.genome}'; |
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22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
gga
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13 |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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14 #for annot in $genome.annots: |
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bd94e502872a
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit bd0a923142aeba63c9314632659a3095dfbedfa8
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15 genoboo add annotation @CONNECT_INFO@ --name '${genome.name}' --annot '${annot.annot}' |
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f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
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16 #if $annot.prot_naming.method == 'regex' |
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
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17 #if $annot.prot_naming.re_protein: |
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
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18 --re_protein '$annot.prot_naming.re_protein' |
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
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19 #end if |
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
gga
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20 #if $annot.prot_naming.re_protein_capture: |
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
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21 --re_protein_capture '$annot.prot_naming.re_protein_capture' |
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
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22 #end if |
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
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23 #elif $annot.prot_naming.method == "attr" |
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
gga
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24 #if $annot.prot_naming.protein_id_attr: |
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
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25 --attr_protein '$annot.prot_naming.attr_protein' |
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
gga
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26 #end if |
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
gga
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27 #end if |
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
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28 '${annot.annotation}'; |
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22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
gga
parents:
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29 #if $annot.interproscan: |
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f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
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30 genoboo add interproscan @CONNECT_INFO@ --format |
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22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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31 #if $annot.interproscan.is_of_type('gff3'): |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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32 gff3 |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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33 #else: |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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34 tsv |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
gga
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35 #end if |
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bd94e502872a
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit bd0a923142aeba63c9314632659a3095dfbedfa8
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36 --annot '${annot.annot}' |
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22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
gga
parents:
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37 '${annot.interproscan}'; |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
gga
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38 #end if |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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39 |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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40 #if $annot.eggnog: |
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bd94e502872a
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit bd0a923142aeba63c9314632659a3095dfbedfa8
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41 genoboo add eggnog @CONNECT_INFO@ --annot '${annot.annot}' '${annot.eggnog}'; |
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22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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42 #end if |
1
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
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43 |
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ace14a8ac6e4
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 81226a2f347b2dc273546311e7269c07f0b0f485
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44 #if $annot.hectar: |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit bd0a923142aeba63c9314632659a3095dfbedfa8
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45 genoboo add hectar @CONNECT_INFO@ --annot '${annot.annot}' '${annot.hectar}'; |
4
ace14a8ac6e4
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 81226a2f347b2dc273546311e7269c07f0b0f485
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46 #end if |
ace14a8ac6e4
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 81226a2f347b2dc273546311e7269c07f0b0f485
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47 |
2
5a6050937cb9
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit ec3c633a0751bb9e253bcd77fea425180c9a0014
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48 #if $annot.blast_cond.blast_choice == "blast": |
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f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
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49 genoboo add blast @CONNECT_INFO@ |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit bd0a923142aeba63c9314632659a3095dfbedfa8
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50 --annot '${annot.annot}' |
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f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
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51 --format 'xml' |
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
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52 --algorithm '${annot.blast_cond.algorithm}' |
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
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53 --matrix '${annot.blast_cond.matrix}' |
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
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54 --database '${annot.blast_cond.database}' |
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
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55 '${annot.blast_cond.blast}'; |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit ec3c633a0751bb9e253bcd77fea425180c9a0014
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56 #elif $annot.blast_cond.blast_choice == "diamond": |
5a6050937cb9
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit ec3c633a0751bb9e253bcd77fea425180c9a0014
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57 genoboo add diamond @CONNECT_INFO@ |
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bd94e502872a
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit bd0a923142aeba63c9314632659a3095dfbedfa8
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58 --annot '${annot.annot}' |
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5a6050937cb9
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit ec3c633a0751bb9e253bcd77fea425180c9a0014
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59 --format 'xml' |
5a6050937cb9
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit ec3c633a0751bb9e253bcd77fea425180c9a0014
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60 --algorithm '${annot.blast_cond.algorithm}' |
5a6050937cb9
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit ec3c633a0751bb9e253bcd77fea425180c9a0014
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61 --matrix '${annot.blast_cond.matrix}' |
5a6050937cb9
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit ec3c633a0751bb9e253bcd77fea425180c9a0014
gga
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62 --database '${annot.blast_cond.database}' |
5a6050937cb9
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit ec3c633a0751bb9e253bcd77fea425180c9a0014
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63 '${annot.blast_cond.diamond}'; |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
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64 #end if |
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
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65 |
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
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66 #for exp in $annot.expression: |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 81226a2f347b2dc273546311e7269c07f0b0f485
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67 genoboo add expression @CONNECT_INFO@ |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit bd0a923142aeba63c9314632659a3095dfbedfa8
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68 --annot '${annot.annot}' |
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ace14a8ac6e4
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 81226a2f347b2dc273546311e7269c07f0b0f485
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69 --sample-description '' |
ace14a8ac6e4
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 81226a2f347b2dc273546311e7269c07f0b0f485
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70 ${exp.public} |
ace14a8ac6e4
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 81226a2f347b2dc273546311e7269c07f0b0f485
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71 #for replica in $exp.expression_replicas: |
ace14a8ac6e4
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 81226a2f347b2dc273546311e7269c07f0b0f485
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72 --replicas '${replica.replicas}' |
ace14a8ac6e4
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 81226a2f347b2dc273546311e7269c07f0b0f485
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73 --replica-names '${replica.replica_names}' |
ace14a8ac6e4
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 81226a2f347b2dc273546311e7269c07f0b0f485
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74 #end for |
ace14a8ac6e4
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 81226a2f347b2dc273546311e7269c07f0b0f485
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75 -- |
ace14a8ac6e4
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 81226a2f347b2dc273546311e7269c07f0b0f485
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76 '${exp.counts}'; |
1
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
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77 #end for |
0
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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78 #end for |
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79 #end for |
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80 |
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81 @ZIP_GNB@ |
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82 ]]></command> |
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83 <inputs> |
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84 <param name="existing" type="data" format="genenotebook" optional="true" label="Load data in an existing GeneNoteBook database" help="Leave empty to start a new database from scratch" /> |
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85 <repeat name="genomes" title="Genomes"> |
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86 <param argument="--name" label="Name" type="text" help="Reference genome name" /> |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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87 <param name="genome" label="Genome sequence" type="data" format="fasta" /> |
1
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88 <param name="public" label="Public access" type="boolean" truevalue="--public" falsevalue="" value="false" /> |
0
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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89 <repeat name="annots" title="Annotations"> |
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90 <param name="annotation" label="Annotation" type="data" format="gff3" /> |
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91 <param argument="--annot" label="Annotation name" type="text" help="Annotation name" /> |
1
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92 <conditional name="prot_naming"> |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
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93 <param name="method" type="select" label="Protein naming method"> |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
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94 <option value="none">No specific names for proteins</option> |
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95 <option value="regex">Based on mRNA name with regular expression</option> |
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96 <option value="attr">From GFF attribute</option> |
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97 </param> |
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98 <when value="none" /> |
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99 <when value="regex"> |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
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100 <param argument="--re_protein_capture" label="Regex protein capture" type="text" help="Regular expression to capture groups in mRNA name to use in 'Regex protein'" value="^(.*?)-R([A-Z]+)$"> |
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101 <expand macro="sanitized"/> |
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102 </param> |
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103 <param argument="--re_protein" label="Regex protein" type="text" help="Replacement string for the protein name using capturing groups defined in 'Regex protein capture'" value="$1-P$2"> |
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104 <expand macro="sanitized"/> |
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105 </param> |
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106 </when> |
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107 <when value="attr"> |
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108 <param argument="--attr_protein" label="Protein id attribute" type="text" help="Attribute containing the protein uniquename. It is searched at the mRNA level, and if not found at CDS level." value="protein_id"/> |
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109 </when> |
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110 </conditional> |
0
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111 <param name="interproscan" label="InterProScan results" optional="true" type="data" format="tsv,gff3" /> |
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112 <param name="eggnog" label="EggNOG-Mapper results" optional="true" type="data" format="tsv" /> |
4
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113 <param name="hectar" label="Hectar results" optional="true" type="data" format="tsv" /> |
1
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114 |
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115 <conditional name="blast_cond"> |
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116 <param name="blast_choice" type="select" label="Import Blast or Diamond results"> |
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117 <option value="no" selected="true">No</option> |
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118 <option value="blast">Blast</option> |
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119 <option value="diamond">Diamond</option> |
1
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120 </param> |
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121 <when value="no" /> |
2
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122 <when value="blast"> |
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123 <param name="blast" label="Blast results (xml)" optional="false" type="data" format="xml" /> |
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124 <param argument="--algorithm" label="Algorithm" optional="false" type="text" help="e.g. blastx, blastp" /> |
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125 <param argument="--matrix" label="Matrix" optional="false" type="text" help="e.g. BLOSUM90, BLOSUM80, PAM100" /> |
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126 <param argument="--database" label="database" optional="false" type="text" help="e.g. Non-reundant protein sequences (nr)" /> |
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127 </when> |
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128 <when value="diamond"> |
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129 <param name="diamond" label="Diamond results (xml)" optional="false" type="data" format="xml" /> |
1
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130 <param argument="--algorithm" label="Algorithm" optional="false" type="text" help="e.g. blastx, blastp" /> |
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131 <param argument="--matrix" label="Matrix" optional="false" type="text" help="e.g. BLOSUM90, BLOSUM80, PAM100" /> |
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132 <param argument="--database" label="database" optional="false" type="text" help="e.g. Non-reundant protein sequences (nr)" /> |
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133 </when> |
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134 </conditional> |
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135 |
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136 <repeat name="expression" title="Expression data"> |
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137 <param name="counts" label="Expression data tabular file" help="One line per mRNA, first column is mRNA ID, each other columns is an experimental condition. TPM values preferably." optional="false" type="data" format="tsv" /> |
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138 <param name="public" label="Public access" type="boolean" truevalue="--public" falsevalue="" value="false" /> |
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139 <repeat name="expression_replicas" title="Expression replicas"> |
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140 <param argument="--replica-names" label="Name of a replica group" type="text"/> |
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141 <param argument="--replicas" label="Comma-separated list of columns of replicas (e.g. 1,2,3)" type="text" help="Comma-separated list of column positions, which are part of the same replica group. Columns not mentionned in any replica group will be considered to be a single replica experiment." /> |
ace14a8ac6e4
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 81226a2f347b2dc273546311e7269c07f0b0f485
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142 </repeat> |
1
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143 </repeat> |
0
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144 </repeat> |
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145 </repeat> |
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146 </inputs> |
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147 <outputs> |
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148 <data format="genenotebook" name="gnb_db" label="GeneNoteBook on ${on_string}"/> |
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149 </outputs> |
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150 <tests> |
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151 <test> |
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152 <repeat name="genomes"> |
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153 <param name="name" value="Test org" /> |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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154 <param name="genome" value="genome.fa" /> |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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155 </repeat> |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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156 <output name="gnb_db" file="output/genome.tar.bz2" compare="sim_size" /> |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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157 <assert_stdout> |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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158 <has_text text="addGenome succesfully inserted 1 elements" /> |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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159 </assert_stdout> |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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160 </test> |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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161 <test> |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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162 <repeat name="genomes"> |
1
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
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0
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163 <param name="name" value="Test org" /> |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
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0
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164 <param name="public" value="true" /> |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
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165 <param name="genome" value="genome.fa" /> |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
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166 </repeat> |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
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0
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167 <output name="gnb_db" file="output/genome.tar.bz2" compare="sim_size" /> |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
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168 <assert_stdout> |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
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169 <has_text text="addGenome succesfully inserted 1 elements" /> |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
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170 </assert_stdout> |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
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171 </test> |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
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172 <test> |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
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0
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173 <repeat name="genomes"> |
0
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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174 <param name="name" value="Test org 2" /> |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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175 <param name="genome" value="genome.fa" /> |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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176 <repeat name="annots"> |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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177 <param name="annotation" value="annot.gff" /> |
5
bd94e502872a
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit bd0a923142aeba63c9314632659a3095dfbedfa8
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178 <param name="annot" value="My annotation" /> |
0
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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179 </repeat> |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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180 </repeat> |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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181 <output name="gnb_db" file="output/genome_annot.tar.bz2" compare="sim_size" /> |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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182 <assert_stdout> |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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183 <has_text text="addGenome succesfully inserted 1 elements" /> |
1
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
gga
parents:
0
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184 <has_text text="addAnnotation succesfully inserted 5 elements" /> |
0
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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185 </assert_stdout> |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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186 </test> |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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187 <test> |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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188 <repeat name="genomes"> |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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189 <param name="name" value="Test org 2" /> |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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190 <param name="genome" value="genome.fa" /> |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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191 <repeat name="annots"> |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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192 <param name="annotation" value="annot.gff" /> |
5
bd94e502872a
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit bd0a923142aeba63c9314632659a3095dfbedfa8
gga
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4
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193 <param name="annot" value="My annotation" /> |
0
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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194 <param name="interproscan" value="interproscan.tsv" ftype="tsv" /> |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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195 </repeat> |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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196 </repeat> |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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197 <output name="gnb_db" file="output/genome_annot_ips.tar.bz2" compare="sim_size" /> |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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198 <assert_stdout> |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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199 <has_text text="addGenome succesfully inserted 1 elements" /> |
1
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
gga
parents:
0
diff
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|
200 <has_text text="addAnnotation succesfully inserted 5 elements" /> |
2
5a6050937cb9
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit ec3c633a0751bb9e253bcd77fea425180c9a0014
gga
parents:
1
diff
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|
201 <has_text text="addInterproscan succesfully inserted 3 elements" /> |
0
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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202 </assert_stdout> |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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203 </test> |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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204 <test> |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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205 <param name="existing" value="output/genome.tar.bz2" /> |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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206 <repeat name="genomes"> |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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207 <param name="name" value="Test org 2" /> |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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208 <param name="genome" value="genome.fa" /> |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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209 </repeat> |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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210 <output name="gnb_db" file="output/genome_reload.tar.bz2" compare="sim_size" /> |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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211 <assert_stdout> |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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212 <has_text text="addGenome succesfully inserted 1 elements" /> |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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213 </assert_stdout> |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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214 </test> |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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215 <test> |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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216 <repeat name="genomes"> |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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217 <param name="name" value="Test org 2" /> |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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218 <param name="genome" value="genome.fa" /> |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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219 <repeat name="annots"> |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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220 <param name="annotation" value="annot.gff" /> |
5
bd94e502872a
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit bd0a923142aeba63c9314632659a3095dfbedfa8
gga
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4
diff
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221 <param name="annot" value="My annotation" /> |
0
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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222 <param name="interproscan" value="interproscan.tsv" ftype="tsv" /> |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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223 <param name="eggnog" value="eggnog.tsv" ftype="tsv" /> |
4
ace14a8ac6e4
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 81226a2f347b2dc273546311e7269c07f0b0f485
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3
diff
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224 <param name="hectar" value="hectar.tsv" ftype="tsv" /> |
0
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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225 </repeat> |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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226 </repeat> |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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227 <output name="gnb_db" file="output/genome_annot_ips_en.tar.bz2" compare="sim_size" delta="15000" /> |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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228 <assert_stdout> |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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229 <has_text text="addGenome succesfully inserted 1 elements" /> |
1
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
gga
parents:
0
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|
230 <has_text text="addAnnotation succesfully inserted 5 elements" /> |
2
5a6050937cb9
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit ec3c633a0751bb9e253bcd77fea425180c9a0014
gga
parents:
1
diff
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231 <has_text text="addInterproscan succesfully inserted 3 elements" /> |
1
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
gga
parents:
0
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|
232 <has_text text="addEggnog succesfully inserted 4 elements" /> |
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
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0
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233 </assert_stdout> |
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
gga
parents:
0
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234 </test> |
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
gga
parents:
0
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changeset
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235 <test> |
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
gga
parents:
0
diff
changeset
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236 <repeat name="genomes"> |
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
gga
parents:
0
diff
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237 <param name="name" value="Test org 2" /> |
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
gga
parents:
0
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238 <param name="genome" value="genome.fa" /> |
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
gga
parents:
0
diff
changeset
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239 <repeat name="annots"> |
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
gga
parents:
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240 <param name="annotation" value="annot.gff" /> |
5
bd94e502872a
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit bd0a923142aeba63c9314632659a3095dfbedfa8
gga
parents:
4
diff
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241 <param name="annot" value="My annotation" /> |
1
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
gga
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242 |
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
gga
parents:
0
diff
changeset
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243 <conditional name="prot_naming"> |
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
gga
parents:
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244 <param name="method" value="regex"/> |
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
gga
parents:
0
diff
changeset
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245 <param name="re_protein_capture" value="^(.*?)-T([0-9]+)$" /> |
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
gga
parents:
0
diff
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246 <param name="re_protein" value="$1-P$2" /> |
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
gga
parents:
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247 </conditional> |
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
gga
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248 |
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
gga
parents:
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diff
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249 <conditional name="blast_cond"> |
2
5a6050937cb9
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit ec3c633a0751bb9e253bcd77fea425180c9a0014
gga
parents:
1
diff
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250 <param name="blast_choice" value="blast"/> |
1
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
gga
parents:
0
diff
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251 <param name="blast" value="blast.xml" ftype="xml" /> |
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
gga
parents:
0
diff
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252 <param name="algorithm" value="blastx" /> |
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
gga
parents:
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253 <param name="matrix" value="BLOSUM80" /> |
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
gga
parents:
0
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254 <param name="database" value="Non-reundant garbage (nrg)" /> |
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
gga
parents:
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255 </conditional> |
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
gga
parents:
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256 |
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
gga
parents:
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diff
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257 <repeat name="expression"> |
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
gga
parents:
0
diff
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258 <param name="counts" value="exp.tsv" ftype="tsv" /> |
4
ace14a8ac6e4
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 81226a2f347b2dc273546311e7269c07f0b0f485
gga
parents:
3
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259 <param name="public" value="true" /> |
1
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
gga
parents:
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260 </repeat> |
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
gga
parents:
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diff
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261 </repeat> |
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
gga
parents:
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262 </repeat> |
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
gga
parents:
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263 <output name="gnb_db" file="output/genome_annot_ips_en_bl_exp.tar.bz2" compare="sim_size" delta="15000" /> |
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
gga
parents:
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264 <assert_stdout> |
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
gga
parents:
0
diff
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265 <has_text text="addGenome succesfully inserted 1 elements" /> |
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
gga
parents:
0
diff
changeset
|
266 <has_text text="addAnnotation succesfully inserted 5 elements" /> |
f415e44e71de
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit a04f273adbc0ebb95bf42bf5bad8b41ba7aba91d
gga
parents:
0
diff
changeset
|
267 <has_text text="addSimilarSequence succesfully inserted 1 elements" /> |
4
ace14a8ac6e4
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 81226a2f347b2dc273546311e7269c07f0b0f485
gga
parents:
3
diff
changeset
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268 <has_text text="addExpression succesfully inserted 4 elements" /> |
0
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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269 </assert_stdout> |
22f22c3e81bf
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b
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270 </test> |
2
5a6050937cb9
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit ec3c633a0751bb9e253bcd77fea425180c9a0014
gga
parents:
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271 <test> |
5a6050937cb9
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit ec3c633a0751bb9e253bcd77fea425180c9a0014
gga
parents:
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diff
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272 <repeat name="genomes"> |
5a6050937cb9
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit ec3c633a0751bb9e253bcd77fea425180c9a0014
gga
parents:
1
diff
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273 <param name="name" value="Test org 2" /> |
5a6050937cb9
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit ec3c633a0751bb9e253bcd77fea425180c9a0014
gga
parents:
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274 <param name="genome" value="genome.fa" /> |
5a6050937cb9
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit ec3c633a0751bb9e253bcd77fea425180c9a0014
gga
parents:
1
diff
changeset
|
275 <repeat name="annots"> |
5a6050937cb9
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit ec3c633a0751bb9e253bcd77fea425180c9a0014
gga
parents:
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276 <param name="annotation" value="annot.gff" /> |
5
bd94e502872a
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit bd0a923142aeba63c9314632659a3095dfbedfa8
gga
parents:
4
diff
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|
277 <param name="annot" value="My annotation" /> |
2
5a6050937cb9
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit ec3c633a0751bb9e253bcd77fea425180c9a0014
gga
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278 |
5a6050937cb9
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit ec3c633a0751bb9e253bcd77fea425180c9a0014
gga
parents:
1
diff
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279 <conditional name="prot_naming"> |
5a6050937cb9
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit ec3c633a0751bb9e253bcd77fea425180c9a0014
gga
parents:
1
diff
changeset
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280 <param name="method" value="regex"/> |
5a6050937cb9
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit ec3c633a0751bb9e253bcd77fea425180c9a0014
gga
parents:
1
diff
changeset
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281 <param name="re_protein_capture" value="^(.*?)-T([0-9]+)$" /> |
5a6050937cb9
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit ec3c633a0751bb9e253bcd77fea425180c9a0014
gga
parents:
1
diff
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282 <param name="re_protein" value="$1-P$2" /> |
5a6050937cb9
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit ec3c633a0751bb9e253bcd77fea425180c9a0014
gga
parents:
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283 </conditional> |
5a6050937cb9
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit ec3c633a0751bb9e253bcd77fea425180c9a0014
gga
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284 |
5a6050937cb9
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit ec3c633a0751bb9e253bcd77fea425180c9a0014
gga
parents:
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285 <conditional name="blast_cond"> |
5a6050937cb9
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit ec3c633a0751bb9e253bcd77fea425180c9a0014
gga
parents:
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286 <param name="blast_choice" value="diamond"/> |
5a6050937cb9
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit ec3c633a0751bb9e253bcd77fea425180c9a0014
gga
parents:
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287 <param name="diamond" value="blast.xml" ftype="xml" /> |
5a6050937cb9
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit ec3c633a0751bb9e253bcd77fea425180c9a0014
gga
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288 <param name="algorithm" value="blastx" /> |
5a6050937cb9
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit ec3c633a0751bb9e253bcd77fea425180c9a0014
gga
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289 <param name="matrix" value="BLOSUM62" /> |
5a6050937cb9
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit ec3c633a0751bb9e253bcd77fea425180c9a0014
gga
parents:
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290 <param name="database" value="Non-reundant garbage (nrg)" /> |
5a6050937cb9
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit ec3c633a0751bb9e253bcd77fea425180c9a0014
gga
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291 </conditional> |
5a6050937cb9
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit ec3c633a0751bb9e253bcd77fea425180c9a0014
gga
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292 |
5a6050937cb9
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit ec3c633a0751bb9e253bcd77fea425180c9a0014
gga
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293 <repeat name="expression"> |
5a6050937cb9
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit ec3c633a0751bb9e253bcd77fea425180c9a0014
gga
parents:
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294 <param name="counts" value="exp.tsv" ftype="tsv" /> |
4
ace14a8ac6e4
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 81226a2f347b2dc273546311e7269c07f0b0f485
gga
parents:
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295 <repeat name="expression_replicas"> |
ace14a8ac6e4
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 81226a2f347b2dc273546311e7269c07f0b0f485
gga
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296 <param name="replicas" value="1,2" /> |
ace14a8ac6e4
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 81226a2f347b2dc273546311e7269c07f0b0f485
gga
parents:
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297 <param name="replica_names" value="ReplicaName1" /> |
ace14a8ac6e4
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 81226a2f347b2dc273546311e7269c07f0b0f485
gga
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298 </repeat> |
ace14a8ac6e4
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 81226a2f347b2dc273546311e7269c07f0b0f485
gga
parents:
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changeset
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299 <repeat name="expression_replicas"> |
ace14a8ac6e4
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 81226a2f347b2dc273546311e7269c07f0b0f485
gga
parents:
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changeset
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300 <param name="replicas" value="3,4" /> |
ace14a8ac6e4
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 81226a2f347b2dc273546311e7269c07f0b0f485
gga
parents:
3
diff
changeset
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301 <param name="replica_names" value="ReplicaName2" /> |
ace14a8ac6e4
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 81226a2f347b2dc273546311e7269c07f0b0f485
gga
parents:
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diff
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302 </repeat> |
2
5a6050937cb9
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit ec3c633a0751bb9e253bcd77fea425180c9a0014
gga
parents:
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303 </repeat> |
5a6050937cb9
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit ec3c633a0751bb9e253bcd77fea425180c9a0014
gga
parents:
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304 </repeat> |
5a6050937cb9
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit ec3c633a0751bb9e253bcd77fea425180c9a0014
gga
parents:
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305 </repeat> |
5a6050937cb9
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit ec3c633a0751bb9e253bcd77fea425180c9a0014
gga
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|
306 <output name="gnb_db" file="output/genome_annot_ips_en_bl_exp.tar.bz2" compare="sim_size" delta="15000" /> |
5a6050937cb9
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit ec3c633a0751bb9e253bcd77fea425180c9a0014
gga
parents:
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307 <assert_stdout> |
5a6050937cb9
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit ec3c633a0751bb9e253bcd77fea425180c9a0014
gga
parents:
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diff
changeset
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308 <has_text text="addGenome succesfully inserted 1 elements" /> |
5a6050937cb9
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit ec3c633a0751bb9e253bcd77fea425180c9a0014
gga
parents:
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diff
changeset
|
309 <has_text text="addAnnotation succesfully inserted 5 elements" /> |
5a6050937cb9
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit ec3c633a0751bb9e253bcd77fea425180c9a0014
gga
parents:
1
diff
changeset
|
310 <has_text text="addSimilarSequence succesfully inserted 1 elements" /> |
4
ace14a8ac6e4
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 81226a2f347b2dc273546311e7269c07f0b0f485
gga
parents:
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311 <has_text text="addExpression succesfully inserted 4 elements" /> |
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312 </assert_stdout> |
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313 </test> |
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314 </tests> |
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315 <help><![CDATA[ |
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316 Build a GeneNoteBook by loading data into a MongoDB database. The resulting dataset can then be displayed with the "GeneNoteBook viewer" interactive tool. |
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317 |
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318 The resulting GeneNoteBook will contain the default user accounts created on the first launch. You are responsible to change them if you ever want to put your result online. |
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319 |
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320 The current version is based on a forked version of GeneNoteBook including several various improvements (https://github.com/gogepp/genoboo/). |
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321 ]]></help> |
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322 <expand macro="citation" /> |
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323 </tool> |