Mercurial > repos > devteam > bwa
annotate bwa.xml @ 9:a628f5606f68 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit a161a3a7e9149a5ba63fe20f435cd2f275dce4c8
author | iuc |
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date | Fri, 22 Dec 2017 15:02:36 -0500 |
parents | cbc665adcde4 |
children | 29299da15326 |
rev | line source |
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0
c9c78719ef26
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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changeset
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1 <?xml version="1.0"?> |
8
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
4
diff
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2 <tool id="bwa" name="Map with BWA" version="@VERSION@.3"> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
4
diff
changeset
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3 <description>- map short reads (< 100 bp) against reference genome</description> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
4
diff
changeset
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4 <macros> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
4
diff
changeset
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5 <import>read_group_macros.xml</import> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
4
diff
changeset
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6 <import>bwa_macros.xml</import> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
4
diff
changeset
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7 <token name="@command_options@"> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
4
diff
changeset
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8 #if str( $analysis_type.analysis_type_selector ) == "full": |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
4
diff
changeset
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9 -n ${analysis_type.n} |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
4
diff
changeset
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10 -o ${analysis_type.o} |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
4
diff
changeset
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11 -e ${analysis_type.e} |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
4
diff
changeset
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12 -i ${analysis_type.i} |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
4
diff
changeset
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13 -d ${analysis_type.d} |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
4
diff
changeset
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14 -l ${analysis_type.l} |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
4
diff
changeset
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15 -k ${analysis_type.k} |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
4
diff
changeset
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16 -m ${analysis_type.m} |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
4
diff
changeset
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17 -M ${analysis_type.M} |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
4
diff
changeset
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18 -O ${analysis_type.O} |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
4
diff
changeset
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19 -E ${analysis_type.E} |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
4
diff
changeset
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20 -R ${analysis_type.R} |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
4
diff
changeset
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21 -q ${analysis_type.q} |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
4
diff
changeset
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22 #if str( $analysis_type.B ): |
0
c9c78719ef26
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
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23 -B ${analysis_type.B} |
8
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
4
diff
changeset
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24 #end if |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
4
diff
changeset
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25 #if str( $analysis_type.L ): |
0
c9c78719ef26
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
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26 -L ${analysis_type.L} |
c9c78719ef26
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
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27 #end if |
8
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
4
diff
changeset
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28 #end if |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
4
diff
changeset
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29 </token> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
4
diff
changeset
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30 <token name="@read_group_options@"> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
4
diff
changeset
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31 #if $use_rg: |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
4
diff
changeset
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32 @set_rg_string@ |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
4
diff
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33 -r '$rg_string' |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
4
diff
changeset
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34 #end if |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
4
diff
changeset
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35 </token> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
4
diff
changeset
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36 <xml name="advanced_pe_options"> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
4
diff
changeset
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37 <param name="adv_pe_options_selector" type="select" label="Set advanced paired end options?" |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
4
diff
changeset
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38 help="Provides additional controls"> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
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diff
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39 <option value="set">Set</option> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
4
diff
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40 <option value="do_not_set" selected="True">Do not set</option> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
4
diff
changeset
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41 </param> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
4
diff
changeset
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42 <when value="set"> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
4
diff
changeset
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43 <param name="a" type="integer" value="500" |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
4
diff
changeset
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44 label="Maximum insert size for a read pair to be considered being mapped properly." |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
4
diff
changeset
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45 help="sampe -a; This option is only used when there are not enough good alignment to infer the distribution of insert sizes; default=500"/> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
4
diff
changeset
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46 <param name="o" type="integer" value="100000" |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
4
diff
changeset
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47 label="Maximum occurrences of a read for pairing. A read with more occurrences will be treated as a single-end read." |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
4
diff
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48 help="sampe -o; Reducing this parameter helps faster pairing; default=100000"/> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
4
diff
changeset
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49 <param name="n" type="integer" value="3" |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
4
diff
changeset
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50 label="Maximum number of alignments to output in the XA tag for reads paired properly." |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
4
diff
changeset
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51 help="sampe -n; If a read has more than this many hits, the XA tag will not be written; default=3"/> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
4
diff
changeset
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52 <param name="N" type="integer" value="10" |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
4
diff
changeset
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53 label="Maximum number of alignments to output in the XA tag for disconcordant read pairs (excluding singletons)." |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
4
diff
changeset
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54 help="sampe -N; If a read has more than this many hits, the XA tag will not be written; default=10"/> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
4
diff
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55 <param name="c" type="float" value="0.00005" label="Prior of chimeric rate (lower bound)" |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
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56 help="sampe -c"/> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
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diff
changeset
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57 </when> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
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diff
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58 <when value="do_not_set"> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
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diff
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59 <!-- do nothing --> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
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diff
changeset
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60 </when> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
4
diff
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61 </xml> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
4
diff
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62 <xml name="advanced_se_options"> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
4
diff
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63 <param name="adv_se_options_selector" type="select" label="Set advanced single end options?" |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
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diff
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64 help="Provides additional controls"> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
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diff
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65 <option value="set">Set</option> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
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diff
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66 <option value="do_not_set" selected="True">Do not set</option> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
4
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67 </param> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
4
diff
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68 <when value="set"> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
4
diff
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69 <param name="n" type="integer" value="3" label="Maximum number of alignments to output in the XA tag." |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
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70 help="-n; If a read has more than this many hits, the XA tag will not be written; default=3"/> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
4
diff
changeset
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71 </when> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
4
diff
changeset
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72 <when value="do_not_set"> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
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73 <!-- do nothing --> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
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74 </when> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
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diff
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75 </xml> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
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76 </macros> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
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77 <expand macro="requirements"/> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
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78 <expand macro="stdio"/> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
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79 <command> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
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80 <![CDATA[ |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents:
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81 @set_reference_fasta_filename@ |
0
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82 |
8
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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83 ## setup vars for rg handling... |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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84 @define_read_group_helpers@ |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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85 #if str( $input_type.input_type_selector ) == "paired": |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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86 #set $rg_auto_name = $read_group_name_default($input_type.fastq_input1, $input_type.fastq_input2) |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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87 #elif str( $input_type.input_type_selector ) in ["single_bam", "paired_bam"]: |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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88 #set $rg_auto_name = $read_group_name_default($input_type.bam_input) |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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89 #else |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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90 #set $rg_auto_name = $read_group_name_default($input_type.fastq_input1) |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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91 #end if |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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92 @set_use_rg_var@ |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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93 @set_read_group_vars@ |
0
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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94 |
8
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95 ## Begin bwa command line |
0
c9c78719ef26
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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96 |
c9c78719ef26
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97 ####### Fastq paired |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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98 |
8
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99 #if str( $input_type.input_type_selector ) == "paired" or str( $input_type.input_type_selector ) == "paired_collection": |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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100 bwa aln |
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101 -t "\${GALAXY_SLOTS:-1}" |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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102 @command_options@ |
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103 '$reference_fasta_filename' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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104 #if str( $input_type.input_type_selector ) == "paired_collection": |
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105 '${input_type.fastq_input1.forward}' |
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106 #else |
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107 '${input_type.fastq_input1}' |
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108 #end if |
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109 > first.sai && |
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110 |
8
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111 bwa aln |
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112 -t "\${GALAXY_SLOTS:-1}" |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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113 @command_options@ |
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114 '${reference_fasta_filename}' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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115 #if str( $input_type.input_type_selector ) == "paired_collection": |
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116 '${input_type.fastq_input1.reverse}' |
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117 #else |
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118 '${input_type.fastq_input2}' |
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119 #end if |
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120 > second.sai && |
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121 |
8
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122 bwa sampe |
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123 #if str( $input_type.adv_pe_options.adv_pe_options_selector) == "True": |
0
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124 -a ${$input_type.adv_pe_options.a} |
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125 -o ${$input_type.adv_pe_options.o} |
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126 -n ${$input_type.adv_pe_options.n} |
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127 -N ${$input_type.adv_pe_options.N} |
8
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128 #end if |
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129 @read_group_options@ |
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130 #if str( $input_type.input_type_selector ) == "paired_collection": |
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131 '${reference_fasta_filename}' first.sai second.sai '${input_type.fastq_input1.forward}' '${input_type.fastq_input1.reverse}' |
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132 #else: |
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133 '${reference_fasta_filename}' first.sai second.sai '${input_type.fastq_input1}' '${input_type.fastq_input2}' |
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134 #end if |
0
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135 |
8
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136 ## Fastq single |
0
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137 |
8
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138 #elif str( $input_type.input_type_selector ) == "single": |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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139 bwa aln |
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140 -t "\${GALAXY_SLOTS:-1}" |
0
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141 |
8
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142 @command_options@ |
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143 |
8
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144 '${reference_fasta_filename}' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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145 '${input_type.fastq_input1}' |
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146 > first.sai && |
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147 |
8
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148 bwa samse |
0
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149 |
8
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150 #if str( $input_type.adv_se_options.adv_se_options_selector) == "True": |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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151 -n ${$input_type.adv_se_options.n} |
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152 #end if |
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153 @read_group_options@ |
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154 '${reference_fasta_filename}' first.sai '${input_type.fastq_input1}' |
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155 |
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156 ####### BAM paired |
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157 |
8
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158 #elif str( $input_type.input_type_selector ) == "paired_bam": |
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159 bwa aln |
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160 -t "\${GALAXY_SLOTS:-1}" |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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161 -b |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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162 -1 |
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iuc
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163 @command_options@ |
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164 '${reference_fasta_filename}' |
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165 '${input_type.bam_input}' |
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166 > first.sai && |
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167 |
8
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168 bwa aln |
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169 -t "\${GALAXY_SLOTS:-1}" |
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170 -b |
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171 -2 |
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172 @command_options@ |
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173 '${reference_fasta_filename}' |
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174 '${input_type.bam_input}' |
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175 > second.sai && |
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176 |
8
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177 bwa sampe |
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178 |
8
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179 #if str( $input_type.adv_bam_pe_options.adv_pe_options_selector) == "True": |
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180 -a ${$input_type.adv_bam_pe_options.a} |
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181 -o ${$input_type.adv_bam_pe_options.o} |
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182 -n ${$input_type.adv_bam_pe_options.n} |
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183 -N ${$input_type.adv_bam_pe_options.N} |
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184 #end if |
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185 @read_group_options@ |
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186 '${reference_fasta_filename}' first.sai second.sai '${input_type.bam_input}' '${input_type.bam_input}' |
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187 |
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188 ####### Fastq single ------------ to do next |
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189 |
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190 #elif str( $input_type.input_type_selector ) == "single_bam": |
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191 bwa aln |
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192 -t "\${GALAXY_SLOTS:-1}" |
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193 -b |
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194 -0 |
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195 |
8
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196 @command_options@ |
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197 |
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198 '${reference_fasta_filename}' |
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199 '${input_type.bam_input}' |
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200 > first.sai && |
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201 |
8
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202 bwa samse |
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203 |
8
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204 #if str( $input_type.adv_bam_se_options.adv_se_options_selector) == "True": |
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205 -n ${$input_type.adv_bam_se_options.n} |
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206 #end if |
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207 @read_group_options@ |
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208 '${reference_fasta_filename}' first.sai '${input_type.bam_input}' |
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209 #end if |
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210 |
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211 | samtools sort -@\${GALAXY_SLOTS:-2} -O bam -o '$bam_output' |
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212 ]]> |
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213 </command> |
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214 |
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215 <inputs> |
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216 <expand macro="reference_source_conditional"/> |
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217 <conditional name="input_type"> |
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218 <param name="input_type_selector" type="select" label="Select input type" |
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219 help="Select between fastq and bam datasets and between paired and single end data"> |
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220 <option value="paired">Paired fastq</option> |
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221 <option value="paired_collection">Paired fastq collection</option> |
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222 <option value="single">Single fastq</option> |
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223 <option value="paired_bam">Paired BAM</option> |
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224 <option value="single_bam">Single BAM</option> |
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225 </param> |
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226 <when value="paired"> |
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227 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta" |
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228 label="Select first set of reads" help="Specify dataset with forward reads"/> |
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229 <param name="fastq_input2" type="data" format="fastqsanger,fastqsanger.gz,fasta" |
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230 label="Select second set of reads" help="Specify dataset with reverse reads"/> |
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231 <conditional name="adv_pe_options"> |
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232 <expand macro="advanced_pe_options"/> |
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233 </conditional> |
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234 </when> |
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235 <when value="paired_collection"> |
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236 <param name="fastq_input1" format="fastqsanger,fastqsanger.gz" type="data_collection" collection_type="paired" label="Select a paired collection" |
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237 help="See help section for an explanation of dataset collections"/> |
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238 <conditional name="adv_pe_options"> |
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239 <expand macro="advanced_pe_options"/> |
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240 </conditional> |
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241 </when> |
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242 <when value="single"> |
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243 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta" |
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244 label="Select fastq dataset" help="Specify dataset with single reads"/> |
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245 <conditional name="adv_se_options"> |
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246 <expand macro="advanced_se_options"/> |
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247 </conditional> |
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248 </when> |
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249 <!-- the difference between single and paired bams is in the <command> tag portion and realated to -0, -1, and -2 options --> |
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250 <when value="paired_bam"> |
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251 <param name="bam_input" type="data" format="bam" label="Select BAM dataset" |
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252 help="Specify BAM dataset with paired reads"/> |
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253 <conditional name="adv_bam_pe_options"> |
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254 <expand macro="advanced_pe_options"/> |
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255 </conditional> |
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256 </when> |
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257 <when value="single_bam"> |
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258 <param name="bam_input" type="data" format="bam" label="Select BAM dataset" |
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259 help="Specify BAM dataset with single reads"/> |
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260 <conditional name="adv_bam_se_options"> |
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261 <expand macro="advanced_se_options"/> |
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262 </conditional> |
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263 </when> |
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264 </conditional> |
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265 <expand macro="read_group_conditional"/> |
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266 <conditional name="analysis_type"> |
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267 <param name="analysis_type_selector" type="select" label="Select analysis mode"> |
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268 <option value="illumina">1.Simple Illumina mode</option> |
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269 <option value="full">2.Full list of options</option> |
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270 </param> |
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271 <when value="illumina"> |
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272 <!-- do nothing --> |
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273 </when> |
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274 <when value="full"> |
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275 <param name="n" type="text" value="0.04" |
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276 label="maximum edit distance if the value is integer, or the fraction of missing alignments given 2% uniform base error rate if float. In the latter case, the maximum edit distance is automatically chosen for different read lengths." |
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277 help="aln -n; default=0.04"/> |
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278 <param name="o" type="integer" value="1" label="maximum number or gap openings" |
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279 help="aln -o; default=1"/> |
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280 <param name="e" type="integer" value="-1" label="maximum number of gap extensions" |
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281 help="aln -e; -1 disables long gaps and invokes k-difference mode; default=-1"/> |
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282 <param name="i" type="integer" value="5" |
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283 label="do not put an indel within this many bp towards the ends" help="aln -i; default=5"/> |
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284 <param name="d" type="integer" value="10" label="maximum occurrences for extending a long deletion" |
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285 help="aln -d; default=10"/> |
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286 <param name="l" type="integer" value="32" label="seed length" help="aln -l; default=32"/> |
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287 <param name="k" type="integer" value="2" label="maximum differences in the seed" |
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288 help="aln -k; default=2"/> |
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289 <param name="m" type="integer" value="2000000" label="maximum entries in the queue" |
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290 help="aln -m; default=2000000"/> |
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291 <param name="M" type="integer" value="3" label="mismatch penalty" help="aln -M; default=3"/> |
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292 <param name="O" type="integer" value="11" label="gap open penalty" help="aln -O; default=11"/> |
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293 <param name="E" type="integer" value="4" label="gap extension penalty" help="aln -E; default=4"/> |
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294 <param name="R" type="integer" value="30" |
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295 label="stop searching when there are more than this value of equally best hits" |
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296 help="aln -R; default=30"/> |
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297 <param name="q" type="integer" value="0" label="quality threshold for read trimming down to 35bp" |
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298 help="aln -q; default=0"/> |
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299 <param name="B" type="integer" optional="True" label="length of barcode" |
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300 help="aln -B; optional parameter"/> |
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301 <param name="L" type="float" optional="True" label="log-scaled gap penalty for long deletions" |
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302 help="aln -L; optional parameter"/> |
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303 </when> |
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304 </conditional> |
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305 </inputs> |
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306 <outputs> |
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307 <data format="bam" name="bam_output" label="${tool.name} on ${on_string} (mapped reads in BAM format)"> |
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308 <expand macro="dbKeyActionsBwa"/> |
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309 </data> |
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310 </outputs> |
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311 <tests> |
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312 <test> |
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313 <param name="reference_source_selector" value="history"/> |
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314 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> |
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315 <param name="input_type_selector" value="single"/> |
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316 <param name="fastq_input1" ftype="fasta" value="bwa-mem-fasta1.fa"/> |
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317 <param name="analysis_type_selector" value="illumina"/> |
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318 <output name="bam_output" ftype="bam" file="bwa-aln-test1-fasta.bam" lines_diff="2"/> |
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319 </test> |
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320 <test> |
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321 <param name="reference_source_selector" value="history"/> |
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322 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> |
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323 <param name="input_type_selector" value="paired"/> |
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324 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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325 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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326 <param name="analysis_type_selector" value="illumina"/> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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327 <output name="bam_output" ftype="bam" file="bwa-aln-test1.bam" lines_diff="2"/> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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328 </test> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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329 <test> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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330 <param name="reference_source_selector" value="history"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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331 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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332 <param name="input_type_selector" value="paired"/> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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333 <param name="fastq_input1" ftype="fastqsanger.gz" value="bwa-mem-fastq1.fq.gz"/> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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334 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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335 <param name="analysis_type_selector" value="illumina"/> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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336 <output name="bam_output" ftype="bam" file="bwa-aln-test1.bam" lines_diff="2"/> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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337 </test> |
cbc665adcde4
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338 <test> |
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339 <param name="reference_source_selector" value="history"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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340 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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341 <param name="input_type_selector" value="paired_bam"/> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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342 <param name="bam_input" ftype="bam" value="bwa-aln-bam-input.bam"/> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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343 <param name="analysis_type_selector" value="illumina"/> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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344 <output name="bam_output" ftype="bam" file="bwa-aln-test2.bam" lines_diff="2"/> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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345 </test> |
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346 <test> |
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347 <param name="reference_source_selector" value="history"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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348 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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349 <param name="input_type_selector" value="paired"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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350 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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351 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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352 <param name="rg_selector" value="set"/> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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353 <param name="ID" value="rg1"/> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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354 <param name="PL" value="CAPILLARY"/> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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355 <param name="analysis_type_selector" value="illumina"/> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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356 <output name="bam_output" ftype="bam" file="bwa-aln-test3.bam" lines_diff="2"/> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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357 </test> |
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358 </tests> |
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359 <help><![CDATA[ |
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c9c78719ef26
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360 **What is does** |
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361 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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362 BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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363 human genome. The bwa-aln algorithm is designed for Illumina sequence reads up to 100bp. For longer reads use |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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364 the separate BWA-MEM Galaxy tool. |
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365 |
c9c78719ef26
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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366 This Galaxy tool wraps bwa-aln, bwa-samse and -sampe modules of bwa read mapping tool: |
c9c78719ef26
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367 |
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368 - **bwa aln** - actual mapper placing reads onto the reference sequence |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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369 - **bwa samse** - post-processor converting suffix array coordinates into genome coordinates in SAM format for |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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370 single reads |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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371 - **bam sampe** - post-processor for paired reads |
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c9c78719ef26
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372 |
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373 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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374 The Galaxy implementation takes fastq or BAM (unaligned BAM) datasets as input and produces output in BAM format, |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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375 which can be further processed using various BAM utilities exiting in Galaxy (BAMTools, SAMTools, Picard). |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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376 |
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377 ----- |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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378 |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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379 **Indices: Selecting reference genomes for BWA** |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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380 |
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381 The Galaxy wrapper for BWA allows you to select between precomputed and user-defined indices for reference genomes |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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382 using the **Will you select a reference genome from your history or use a built-in index?** select box. |
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383 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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384 This select box has two options: |
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385 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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386 1. **Use a built-in genome index** - when selected (this is default), Galaxy provides the user with **Select |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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387 reference genome index** dropdown. Genomes listed in this dropdown have been pre-indexed with bwa index utility |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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388 and are ready to be mapped against. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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389 2. **Use a genome from the history and build index** - when selected, Galaxy provides the user with **Select |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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390 reference genome sequence** dropdown. This dropdown is populated by all FASTA formatted files listed in your |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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391 current history. If your genome of interest is uploaded into history it will be shown there. Selecting a genome |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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392 from this dropdown will cause Galaxy to first transparently index it using `bwa index` command, and then run |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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393 mapping with `bwa aln`. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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394 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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395 |
0
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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396 If your genome of interest is not listed here you have two choices: |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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397 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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398 1. Contact galaxy team using **Help->Support** link at the top of the interface and let us know that an index |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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399 needs to be added |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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400 2. Upload your genome of interest as a FASTA file to Galaxy history and selected **Use a genome from the history |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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401 and build index** option. |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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402 |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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403 |
c9c78719ef26
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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404 @RG@ |
c9c78719ef26
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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405 |
c9c78719ef26
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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406 @info@ |
8
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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407 ]]></help> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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408 <citations> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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409 <citation type="doi">10.1093/bioinformatics/btp324</citation> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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410 <citation type="doi">10.1093/bioinformatics/btp698</citation> |
cbc665adcde4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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411 </citations> |
0
c9c78719ef26
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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412 </tool> |