Mercurial > repos > lparsons > cutadapt
annotate macros.xml @ 19:49370cb85f0f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 6318c53e772ed592862729f3048ed9bd3a711969
| author | iuc |
|---|---|
| date | Tue, 18 Dec 2018 14:09:53 -0500 |
| parents | 8f1df515eb87 |
| children | e4691e1589d3 |
| rev | line source |
|---|---|
|
11
8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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1 <macros> |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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2 |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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3 <token name="@read1_options@"><![CDATA[ |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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4 |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
|
5 ## Read1 trimming |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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6 |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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7 #for $a in $library.r1.adapters |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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8 #if $a.adapter_source.adapter_source_list == 'builtin': |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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9 -a "${a.adapter_source.adapter.fields.name}"='${a.adapter_source.adapter}' |
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19
49370cb85f0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 6318c53e772ed592862729f3048ed9bd3a711969
iuc
parents:
16
diff
changeset
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10 #else if $a.adapter_source.adapter_source_list == 'file': |
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49370cb85f0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 6318c53e772ed592862729f3048ed9bd3a711969
iuc
parents:
16
diff
changeset
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11 -a file:'${a.adapter_source.adapter_file}' |
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11
8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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12 #else if str($a.adapter_source.adapter_name) != "": |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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13 -a '${a.adapter_source.adapter_name}'='${a.adapter_source.adapter}' |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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14 #else |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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15 -a '${a.adapter_source.adapter}' |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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16 #end if |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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17 #end for |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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18 #for $aa in $library.r1.anywhere_adapters |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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19 #if $aa.anywhere_adapter_source.anywhere_adapter_source_list == 'builtin': |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
|
20 -b ${aa.anywhere_adapter_source.anywhere_adapter.fields.name}"='${aa.anywhere_adapter_source.anywhere_adapter}' |
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19
49370cb85f0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 6318c53e772ed592862729f3048ed9bd3a711969
iuc
parents:
16
diff
changeset
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21 #else if $aa.anywhere_adapter_source.anywhere_adapter_source_list == 'file': |
|
49370cb85f0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 6318c53e772ed592862729f3048ed9bd3a711969
iuc
parents:
16
diff
changeset
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22 -b file:'${aa.anywhere_adapter_source.anywhere_adapter_file}' |
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11
8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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23 #else if str($aa.anywhere_adapter_source.anywhere_adapter_name) != "": |
|
8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
|
24 -b '${aa.anywhere_adapter_source.anywhere_adapter_name}'='${aa.anywhere_adapter_source.anywhere_adapter}' |
|
8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
|
25 #else |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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26 -b '${aa.anywhere_adapter_source.anywhere_adapter}' |
|
8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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27 #end if |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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28 #end for |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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29 #for $fa in $library.r1.front_adapters |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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30 #if $fa.front_adapter_source.front_adapter_source_list == 'builtin': |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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31 -g "${fa.front_adapter_source.front_adapter.fields.name}"='${fa.front_adapter_source.front_adapter}' |
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19
49370cb85f0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 6318c53e772ed592862729f3048ed9bd3a711969
iuc
parents:
16
diff
changeset
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32 #else if $fa.front_adapter_source.front_adapter_source_list == 'file': |
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49370cb85f0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 6318c53e772ed592862729f3048ed9bd3a711969
iuc
parents:
16
diff
changeset
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33 -g file:'${fa.front_adapter_source.front_adapter_file}' |
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11
8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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34 #else if str($fa.front_adapter_source.front_adapter_name) != "": |
|
8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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35 -g '${fa.front_adapter_source.front_adapter_name}'='${fa.front_adapter_source.front_adapter}' |
|
8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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36 #else |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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37 -g '${fa.front_adapter_source.front_adapter}' |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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38 #end if |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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39 #end for |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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40 |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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41 #if str($library.r1.cut) != '0': |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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42 -u $library.r1.cut |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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43 #end if |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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44 |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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45 ## Additional Outputs |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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46 |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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47 #if $output_options.info_file: |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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48 --info-file=$info_file |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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49 #end if |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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50 #if $output_options.rest_file: |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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51 --rest-file=$rest_output |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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52 #end if |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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53 #if $output_options.wildcard_file: |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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54 --wildcard-file=$wild_output |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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55 #end if |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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56 #if $output_options.too_short_file: |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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57 --too-short-output=$too_short_output |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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58 #end if |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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59 #if $output_options.too_long_file: |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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60 --too-long-output=$too_long_output |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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61 #end if |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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62 #if $output_options.untrimmed_file: |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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63 --untrimmed-output=$untrimmed_output |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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64 #end if |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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65 |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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66 ]]></token> |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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67 |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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68 <token name="@read2_options@"><![CDATA[ |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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69 |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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70 ## Read2 trimming |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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71 |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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72 #for $a in $library.r2.adapters2 |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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73 #if $a.adapter_source2.adapter_source_list2 == 'builtin': |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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74 -A "${a.adapter_source2.adapter2.fields.name}"='${a.adapter_source2.adapter2}' |
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19
49370cb85f0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 6318c53e772ed592862729f3048ed9bd3a711969
iuc
parents:
16
diff
changeset
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75 #else if $a.adapter_source2.adapter_source_list2 == 'file': |
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49370cb85f0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 6318c53e772ed592862729f3048ed9bd3a711969
iuc
parents:
16
diff
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76 -A file:'${a.adapter_source2.adapter_file2}' |
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11
8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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77 #else if str($a.adapter_source2.adapter_name2) != "": |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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78 -A '${a.adapter_source2.adapter_name2}'='${a.adapter_source2.adapter2}' |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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79 #else |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
changeset
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80 -A '${a.adapter_source2.adapter2}' |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff
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81 #end if |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
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82 #end for |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
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83 #for $aa in $library.r2.anywhere_adapters2 |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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84 #if $aa.anywhere_adapter_source2.anywhere_adapter_source_list2 == 'builtin': |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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85 -B "${aa.anywhere_adapter_source2.anywhere_adapter2.fields.name}"='${aa.anywhere_adapter_source2.anywhere_adapter2}' |
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19
49370cb85f0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 6318c53e772ed592862729f3048ed9bd3a711969
iuc
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86 #else if $aa.anywhere_adapter_source2.anywhere_adapter_source_list2 == 'file': |
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49370cb85f0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 6318c53e772ed592862729f3048ed9bd3a711969
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87 -B file:'${aa.anywhere_adapter_source2.anywhere_adapter_file2}' |
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11
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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88 #else if str($aa.anywhere_adapter_source2.anywhere_adapter_name2) != "": |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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89 -B '${aa.anywhere_adapter_source2.anywhere_adapter_name2}'='${aa.anywhere_adapter_source2.anywhere_adapter2}' |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
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90 #else |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
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91 -B '${aa.anywhere_adapter_source2.anywhere_adapter2}' |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
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92 #end if |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
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93 #end for |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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94 #for $fa in $library.r2.front_adapters2 |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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95 #if $fa.front_adapter_source2.front_adapter_source_list2 == 'builtin': |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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96 -G "${fa.front_adapter_source2.front_adapter2.fields.name}"='${fa.front_adapter_source2.front_adapter2}' |
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19
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97 #else if $fa.front_adapter_source2.front_adapter_source_list2 == 'file': |
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49370cb85f0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 6318c53e772ed592862729f3048ed9bd3a711969
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98 -G file:'${fa.front_adapter_source2.front_adapter_file2}' |
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11
8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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99 #else if str($fa.front_adapter_source2.front_adapter_name2) != "": |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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100 -G '${fa.front_adapter_source2.front_adapter_name2}'='${fa.front_adapter_source2.front_adapter2}' |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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101 #else |
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8665bcc8b847
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102 -G '${fa.front_adapter_source2.front_adapter2}' |
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8665bcc8b847
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103 #end if |
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8665bcc8b847
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104 #end for |
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8665bcc8b847
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105 |
|
8665bcc8b847
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106 #if str($library.r2.cut2) != '0': |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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107 -U $library.r2.cut2 |
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108 #end if |
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109 |
|
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110 ## Additional Outputs - Read 2 |
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111 |
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112 #if $output_options.too_short_file: |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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113 --too-short-paired-output=$too_short_paired_output |
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8665bcc8b847
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114 #end if |
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115 #if $output_options.too_long_file: |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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116 --too-long-paired-output=$too_long_paired_output |
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8665bcc8b847
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117 #end if |
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118 #if $output_options.untrimmed_file: |
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8665bcc8b847
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119 --untrimmed-paired-output=$untrimmed_paired_output |
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8665bcc8b847
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120 #end if |
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121 |
|
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122 ]]></token> |
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123 |
|
8665bcc8b847
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124 <xml name="single_end_options" > |
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125 |
|
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126 <section name="r1" title="Read 1 Options" expanded="True"> |
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8665bcc8b847
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127 |
|
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128 <repeat name="adapters" title="3' (End) Adapters" help="Sequence of an adapter ligated to the 3' end (paired data: of the first read). The adapter and subsequent bases are trimmed. If a '$' character is appended ('anchoring'), the adapter is only found if it is a suffix of the read. To search for a linked adapter, separate the 2 sequences with 3 dots (ADAPTER1...ADAPTER2), see Help below."> |
|
8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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129 <conditional name="adapter_source"> |
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130 <param name="adapter_source_list" type="select" label="Source" > |
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8665bcc8b847
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131 <option value="builtin" selected="True">Standard (select from the list below)</option> |
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8665bcc8b847
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132 <option value="user">Enter custom sequence</option> |
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19
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133 <option value="file">File From History</option> |
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134 </param> |
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135 |
|
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136 <when value="user"> |
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16
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137 <param name="adapter_name" type="text" value="" optional="True" label="Enter custom 3' adapter name (Optional if Multiple output is 'No')" /> |
|
11
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138 <param name="adapter" argument="-a" type="text" value="AATTGGCC" label="Enter custom 3' adapter sequence" /> |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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139 </when> |
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140 |
|
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141 <when value="builtin"> |
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142 <param name="adapter" argument="-a" type="select" label="Choose 3' adapter"> |
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8665bcc8b847
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143 <options from_data_table="adapters"> |
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144 <filter type="sort_by" column="1" /> |
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145 </options> |
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146 </param> |
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147 </when> |
|
19
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148 |
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149 <when value="file"> |
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150 <param name="adapter_file" argument="-a" format="fasta" type="data" help="Should be of datatype FASTA" label="Choose file containing 3' adapters" /> |
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49370cb85f0f
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151 </when> |
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11
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152 </conditional> |
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153 </repeat> |
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154 |
|
8665bcc8b847
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155 <repeat name="front_adapters" title="5' (Front) Adapters" help="Sequence of an adapter ligated to the 5' end (paired data: of the first read). The adapter and any preceding bases are trimmed. Partial matches at the 5' end are allowed. If a '^' character is prepended ('anchoring'), the adapter is only found if it is a prefix of the read. To search for a linked adapter, separate the 2 sequences with 3 dots (ADAPTER1...ADAPTER2), see Help below."> |
|
8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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156 <conditional name="front_adapter_source"> |
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8665bcc8b847
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157 <param name="front_adapter_source_list" type="select" label="Source"> |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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158 <option value="builtin" selected="True">Standard (select from the list below)</option> |
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8665bcc8b847
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159 <option value="user">Enter custom sequence</option> |
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19
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160 <option value="file">File From History</option> |
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iuc
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161 </param> |
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162 |
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163 <when value="user"> |
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164 <param name="front_adapter_name" type="text" value="" optional="True" label="Enter custom 5' adapter name (Optional if Multiple output is 'No')" /> |
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165 <param name="front_adapter" argument="-g" type="text" value="AATTGGCC" label="Enter custom 5' adapter sequence" /> |
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166 </when> |
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167 <when value="builtin"> |
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168 <param name="front_adapter" argument="-g" type="select" label="Choose 5' adapter"> |
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169 <options from_data_table="adapters"> |
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170 <filter type="sort_by" column="1" /> |
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171 </options> |
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172 </param> |
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173 </when> |
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174 <when value="file"> |
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175 <param name="front_adapter_file" argument="-g" format="fasta" type="data" help="Should be of datatype "FASTA"" label="Choose file containing 5' adapters" /> |
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176 </when> |
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177 </conditional> |
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178 </repeat> |
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179 |
|
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180 <repeat name="anywhere_adapters" title="5' or 3' (Anywhere) Adapters" help="Sequence of an adapter that may be ligated to the 5' or 3' end (paired data: of the first read). Both types of matches as described under 3' und 5' Adapters are allowed. If the first base of the read is part of the match, the behavior is as with 5' Adapters, otherwise as with 3' Adapters. This option is mostly for rescuing failed library preparations - do not use if you know which end your adapter was ligated to!"> |
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181 <conditional name="anywhere_adapter_source"> |
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182 <param name="anywhere_adapter_source_list" type="select" label="Source"> |
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183 <option value="builtin" selected="True">Standard (select from the list below)</option> |
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184 <option value="user">Enter custom sequence</option> |
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185 <option value="file">File From History</option> |
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186 </param> |
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187 |
|
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188 <when value="user"> |
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189 <param name="anywhere_adapter_name" type="text" value="" optional="True" label="Enter custom 5' or 3' adapter name (Optional if Multiple output is 'No')" /> |
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190 <param name="anywhere_adapter" argument="-b" type="text" value="AATTGGCC" label="Enter custom 5' or 3' adapter sequence" /> |
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191 </when> |
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192 <when value="builtin"> |
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193 <param name="anywhere_adapter" argument="-b" type="select" label="Choose 5' or 3' adapter"> |
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194 <options from_data_table="adapters"> |
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195 <filter type="sort_by" column="1" /> |
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196 </options> |
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197 </param> |
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198 </when> |
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19
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199 <when value="file"> |
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200 <param name="anywhere_adapter_file" argument="-b" format="fasta" type="data" help="Should be of datatype "FASTA"" label="Choose file containing 3' or 5' adapters" /> |
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201 </when> |
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202 </conditional> |
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203 </repeat> |
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204 |
|
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205 <param name="cut" argument="-u" type="integer" value="0" optional="True" label="Cut bases from reads before adapter trimming" help="Remove bases from each read (first read only if paired). If positive, remove bases from the beginning. If negative, remove bases from the end. This is applied *before* adapter trimming." /> |
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206 |
|
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207 </section> |
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208 |
|
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209 </xml> |
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210 |
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211 <xml name="paired_end_options" > |
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212 |
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213 <!-- Read 1 Options --> |
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214 <expand macro="single_end_options" /> |
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215 |
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216 <!-- Read 2 Options --> |
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217 <section name="r2" title="Read 2 Options" expanded="True"> |
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218 |
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219 <repeat name="adapters2" title="3' (End) Adapters" help="Sequence of an adapter ligated to the 3' end of the second read in each pair. The adapter and subsequent bases are trimmed. If a '$' character is appended ('anchoring'), the adapter is only found if it is a suffix of the read. To search for a linked adapter, separate the 2 sequences with 3 dots (ADAPTER1...ADAPTER2), see Help below."> |
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220 <conditional name="adapter_source2"> |
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221 <param name="adapter_source_list2" type="select" label="Source" > |
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222 <option value="builtin" selected="True">Standard (select from the list below)</option> |
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223 <option value="user">Enter custom sequence</option> |
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224 <option value="file">File From History</option> |
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225 </param> |
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226 |
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227 <when value="user"> |
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228 <param name="adapter_name2" type="text" value="" optional="True" label="Enter custom 3' adapter name (Optional)" /> |
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229 <param name="adapter2" argument="-A" type="text" label="Enter custom 3' adapter sequence" value="AATTGGCC" /> |
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230 </when> |
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231 |
|
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232 <when value="builtin"> |
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233 <param name="adapter2" argument="-A" type="select" label="Choose 3' adapter"> |
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234 <options from_data_table="adapters"> |
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235 <filter type="sort_by" column="1" /> |
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236 </options> |
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237 </param> |
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238 </when> |
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239 <when value="file"> |
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240 <param name="adapter_file2" argument="-a" format="fasta" type="data" help="Should be of datatype "FASTA"" label="Choose file containing 3' adapters" /> |
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241 </when> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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242 </conditional> |
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243 </repeat> |
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244 |
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245 <repeat name="front_adapters2" title="5' (Front) Adapters" help="Sequence of an adapter ligated to the 5' end of the second read in each pair. The adapter and any preceding bases are trimmed. Partial matches at the 5' end are allowed. If a '^' character is prepended ('anchoring'), the adapter is only found if it is a prefix of the read. To search for a linked adapter, separate the 2 sequences with 3 dots (ADAPTER1...ADAPTER2), see Help below."> |
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8665bcc8b847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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246 <conditional name="front_adapter_source2"> |
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247 <param name="front_adapter_source_list2" type="select" label="Source"> |
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248 <option value="builtin" selected="True">Standard (select from the list below)</option> |
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249 <option value="user">Enter custom sequence</option> |
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250 <option value="file">File From History</option> |
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251 </param> |
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252 |
|
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253 <when value="user"> |
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254 <param name="front_adapter_name2" type="text" value="" label="Enter custom 5' adapter name (Optional)" /> |
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8665bcc8b847
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255 <param name="front_adapter2" argument="-G" type="text" value="AATTGGCC" label="Enter custom 5' adapter sequence" /> |
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8665bcc8b847
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256 </when> |
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257 <when value="builtin"> |
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258 <param name="front_adapter2" argument="-G" type="select" label="Choose 5' adapter"> |
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8665bcc8b847
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259 <options from_data_table="adapters"> |
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260 <filter type="sort_by" column="1" /> |
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261 </options> |
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262 </param> |
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263 </when> |
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19
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264 <when value="file"> |
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265 <param name="front_adapter_file2" argument="-g" format="fasta" type="data" help="Should be of datatype "FASTA"" label="Choose file containing 5' adapters" /> |
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49370cb85f0f
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266 </when> |
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267 </conditional> |
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268 </repeat> |
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269 |
|
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270 <repeat name="anywhere_adapters2" title="5' or 3' (Anywhere) Adapters" help="Sequence of an adapter that may be ligated to the 5' or 3' end of the second read in each pair. Both types of matches as described under under 3' und 5' Adapters are allowed. If the first base of the read is part of the match, the behavior is as with 5' Adapters, otherwise as with 3' Adapters. This option is mostly for rescuing failed library preparations - do not use if you know which end your adapter was ligated to!"> |
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271 <conditional name="anywhere_adapter_source2"> |
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272 <param name="anywhere_adapter_source_list2" type="select" label="Source"> |
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8665bcc8b847
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273 <option value="builtin" selected="True">Standard (select from the list below)</option> |
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8665bcc8b847
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274 <option value="user">Enter custom sequence</option> |
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275 <option value="file">File From History</option> |
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276 </param> |
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277 |
|
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278 <when value="user"> |
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279 <param name="anywhere_adapter_name2" type="text" value="" optional="True" label="Enter custom 5' or 3' adapter name (Optional)" /> |
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280 <param name="anywhere_adapter2" argument="-B" type="text" label="Enter custom 5' or 3' adapter sequence" value="AATTGGCC" /> |
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8665bcc8b847
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281 </when> |
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282 <when value="builtin"> |
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283 <param name="anywhere_adapter2" argument="-B" type="select" label="Choose 5' or 3' adapter"> |
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284 <options from_data_table="adapters"> |
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285 <filter type="sort_by" column="1" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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286 </options> |
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287 </param> |
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288 </when> |
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19
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289 <when value="file"> |
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290 <param name="anywhere_adapter_file2" argument="-b" format="fasta" type="data" help="Should be of datatype "FASTA"" label="Choose file containing 3' or 5' adapters" /> |
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291 </when> |
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11
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292 </conditional> |
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293 </repeat> |
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294 |
|
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295 <param name="cut2" argument="-U" type="integer" value="0" optional="True" label="Cut bases from the second read in each pair." help="Remove bases from the beginning or end of each read before trimming adapters. If positive, the bases are removed from the beginning of each read. If negative, the bases are removed from the end of each read." /> |
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8665bcc8b847
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296 |
|
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297 </section> |
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298 |
|
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299 </xml> |
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300 |
|
12
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301 <xml name="inherit_format_1"> |
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302 <actions> |
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303 <conditional name="library.type"> |
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304 <when value="single"> |
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305 <action type="format"> |
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306 <option type="from_param" name="library.input_1" param_attribute="ext" /> |
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307 </action> |
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308 </when> |
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309 <when value="paired"> |
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310 <action type="format"> |
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311 <option type="from_param" name="library.input_1" param_attribute="ext" /> |
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312 </action> |
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313 </when> |
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314 <when value="paired_collection"> |
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315 <action type="format"> |
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316 <option type="from_param" name="library.input_1" param_attribute="forward.ext" /> |
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317 </action> |
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318 </when> |
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319 </conditional> |
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320 </actions> |
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321 </xml> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
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322 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
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323 <xml name="inherit_format_2"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
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324 <actions> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
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325 <conditional name="library.type"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
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326 <when value="paired"> |
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78e1cf88d133
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
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327 <action type="format"> |
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78e1cf88d133
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
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328 <option type="from_param" name="library.input_2" param_attribute="ext" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
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329 </action> |
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78e1cf88d133
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
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330 </when> |
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78e1cf88d133
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
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331 <when value="paired_collection"> |
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78e1cf88d133
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
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332 <action type="format"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
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333 <option type="from_param" name="library.input_1" param_attribute="reverse.ext" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
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334 </action> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
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335 </when> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
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336 </conditional> |
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337 </actions> |
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338 </xml> |
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339 |
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340 </macros> |