Mercurial > repos > iuc > bbtools_bbmap
annotate bbmap.xml @ 6:858a65b52cf9 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ef7069328751b534fd4c90115e5afc59b82d8a95
| author | iuc |
|---|---|
| date | Tue, 05 Jul 2022 13:06:30 +0000 |
| parents | 81cbb6a4c1ca |
| children | 9ed6579f52f3 |
| rev | line source |
|---|---|
|
5
81cbb6a4c1ca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 08ae36bc77634de84d9613a71552a3e64a71a3f7"
iuc
parents:
4
diff
changeset
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1 <tool id="bbtools_bbmap" name="BBTools: BBMap" version="@WRAPPER_VERSION@+galaxy4" profile="@PROFILE@"> |
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0
07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff
changeset
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2 <description>short-read aligner</description> |
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07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff
changeset
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3 <macros> |
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07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff
changeset
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4 <import>macros.xml</import> |
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07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff
changeset
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5 </macros> |
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07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff
changeset
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6 <expand macro="requirements"/> |
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07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff
changeset
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7 <command detect_errors="exit_code"><![CDATA[ |
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07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff
changeset
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8 #import os |
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07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff
changeset
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9 #import re |
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07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff
changeset
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10 |
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07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff
changeset
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11 #if str($ref_source_cond.ref_source) == 'cached' |
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07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff
changeset
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12 #set ref = str($ref_source_cond.reference.fields.path) |
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07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff
changeset
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13 #else: |
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07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff
changeset
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14 #set ref = $ref_source_cond.reference |
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07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff
changeset
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15 #end if |
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07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff
changeset
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16 |
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07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff
changeset
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17 #if str($input_type_cond.input_type) in ['single', 'pair']: |
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07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff
changeset
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18 #set read1 = $input_type_cond.read1 |
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07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff
changeset
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19 ## bbmap uses the file extension to determine the input format. |
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3
8157a81f511c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 425671870866660485ef6a35c94d3736f5c1df97"
iuc
parents:
2
diff
changeset
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20 #set ext = '.fastq' |
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0
07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff
changeset
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21 #if $read1.ext.endswith('.gz'): |
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07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff
changeset
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22 #set ext = $ext + '.gz' |
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07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff
changeset
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23 #end if |
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3
8157a81f511c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 425671870866660485ef6a35c94d3736f5c1df97"
iuc
parents:
2
diff
changeset
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24 #set read1_file = 'forward' + $ext |
|
0
07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff
changeset
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25 ln -s '${read1}' '${read1_file}' && |
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07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff
changeset
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26 #if str($input_type_cond.input_type) == 'pair': |
|
07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff
changeset
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27 #set read2 = $input_type_cond.read2 |
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3
8157a81f511c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 425671870866660485ef6a35c94d3736f5c1df97"
iuc
parents:
2
diff
changeset
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28 #set read2_file = 'reverse' + $ext |
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0
07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff
changeset
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29 ln -s '${read2}' '${read2_file}' && |
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07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff
changeset
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30 #end if |
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07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff
changeset
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31 #else: |
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07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff
changeset
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32 #set read1 = $input_type_cond.reads_collection['forward'] |
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5
81cbb6a4c1ca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 08ae36bc77634de84d9613a71552a3e64a71a3f7"
iuc
parents:
4
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33 #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.element_identifier)) |
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0
07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff
changeset
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34 ## bbmap uses the file extension to determine the input format. |
|
07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff
changeset
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35 #set ext = $read1_identifier + '.fastq' |
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07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff
changeset
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36 #if $read1.ext.endswith('.gz'): |
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07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff
changeset
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37 #set ext = $ext + '.gz' |
|
07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff
changeset
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38 #end if |
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07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff
changeset
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39 #set read1_file = $read1_identifier + $ext |
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07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff
changeset
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40 ln -s '${read1}' '${read1_file}' && |
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07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff
changeset
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41 #set read2 = $input_type_cond.reads_collection['reverse'] |
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5
81cbb6a4c1ca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 08ae36bc77634de84d9613a71552a3e64a71a3f7"
iuc
parents:
4
diff
changeset
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42 #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.element_identifier)) |
|
0
07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff
changeset
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43 #set read2_file = $read2_identifier + $ext |
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07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff
changeset
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44 ln -s '${read2}' '${read2_file}' && |
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07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff
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45 #end if |
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07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff
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46 |
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4
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
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47 bbmap.sh |
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6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
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48 |
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6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
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49 #### Indexing Parameters |
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6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
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50 nodisk=f |
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6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
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51 ref='${ref}' |
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6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
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52 k=13 |
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6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
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53 usemodulo=f |
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6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
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54 rebuild=f |
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6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
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55 |
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6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
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56 #### Input Parameters |
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0
07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff
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57 #if str($input_type_cond.input_type) == 'single': |
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07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff
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58 in='${read1_file}' |
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07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff
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59 #else: |
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4
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
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60 in='${read1_file}' in2='${read2_file}' |
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0
07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff
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61 #end if |
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4
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
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62 fastareadlen=500 |
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6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
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63 unpigz=f |
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6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
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64 touppercase=t |
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6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
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65 |
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6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
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66 #### Sampling Parameters |
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6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
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67 reads=-1 |
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6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
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68 samplerate=1 |
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6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
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69 skipreads=0 |
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6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
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70 |
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6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
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71 #### Mapping Parameters |
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6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
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72 maxindel=$mapping_options.maxindel |
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6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
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73 strictmaxindel='$mapping_options.strictmaxindel' |
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6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
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74 tipsearch=$mapping_options.tipsearch |
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6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
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75 minid=$mapping_options.minid |
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6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
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76 minhits=$mapping_options.minhits |
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6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
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77 local='$mapping_options.local' |
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6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
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78 perfectmode='$mapping_options.perfectmode' |
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6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
79 semiperfectmode='$mapping_options.semiperfectmode' |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
80 threads=\${GALAXY_SLOTS:-4} |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
81 ambiguous='$mapping_options.ambiguous' |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
82 samestrandpairs='$mapping_options.samestrandpairs' |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
83 requirecorrectstrand='$mapping_options.requirecorrectstrand' |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
84 killbadpairs='$mapping_options.killbadpairs' |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
85 pairedonly='$mapping_options.pairedonly' |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
86 rcomp='$mapping_options.rcomp' |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
87 rcompmate='$mapping_options.rcompmate' |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
88 pairlen=$mapping_options.pairlen |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
89 rescuedist=$mapping_options.rescuedist |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
90 rescuemismatches=$mapping_options.rescuemismatches |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
91 averagepairdist=$mapping_options.averagepairdist |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
92 deterministic='$mapping_options.deterministic' |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
93 bandwidthratio='$mapping_options.bandwidthratio' |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
94 bandwidth='$mapping_options.bandwidth' |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
95 usejni='f' |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
96 maxsites2=$mapping_options.maxsites2 |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
97 ignorefrequentkmers='$mapping_options.ignorefrequentkmers' |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
98 excludefraction=$mapping_options.excludefraction |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
99 greedy='$mapping_options.greedy' |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
100 kfilter=$mapping_options.kfilter |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
101 |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
102 #### Quality and Trimming Parameters |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
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103 qin='auto' |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
104 qout='auto' |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
105 qtrim='$qt_options.qtrim' |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
106 untrim='$qt_options.untrim' |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
107 trimq=$qt_options.trimq |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
108 mintrimlength=$qt_options.mintrimlength |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
109 fakefastaquality=$qt_options.fakefastaquality |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
110 ignorebadquality='$qt_options.ignorebadquality' |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
111 usequality='$qt_options.usequality' |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
112 minaveragequality=$qt_options.minaveragequality |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
113 maqb=$qt_options.maqb |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
114 |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
115 #### Post-Filtering options |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
116 idfilter=$pf_options.idfilter |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
117 subfilter=$pf_options.subfilter |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
118 insfilter=$pf_options.insfilter |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
119 delfilter=$pf_options.delfilter |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
120 indelfilter=$pf_options.indelfilter |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
121 editfilter=$pf_options.editfilter |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
122 inslenfilter=$pf_options.inslenfilter |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
123 dellenfilter=$pf_options.dellenfilter |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
124 nfilter=$pf_options.nfilter |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
125 |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
126 #### Output parameters |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
127 secondary='$output_options.secondary' |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
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|
128 maxsites=$output_options.maxsites |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
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129 sssr=$output_options.sssr |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
130 ssao='$output_options.ssao' |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
131 quickmatch='$output_options.quickmatch' |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
132 trimreaddescriptions='$output_options.trimreaddescriptions' |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
133 machineout='$output_options.machineout' |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
134 printunmappedcount='$output_options.printunmappedcount' |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
135 renamebyinsert='$output_options.renamebyinsert' |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
136 #if str($output_options.output_sort) == 'coordinate': |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
137 out='all_reads.bam' |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
138 outu='unmapped_reads.bam' |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
139 outm='mapped_reads.bam' |
|
6
858a65b52cf9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ef7069328751b534fd4c90115e5afc59b82d8a95
iuc
parents:
5
diff
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|
140 && samtools sort --no-PG -@\${GALAXY_SLOTS:-4} -T "\${TMPDIR:-.}" -O bam -o '$output_all_reads' 'all_reads.bam' |
|
858a65b52cf9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ef7069328751b534fd4c90115e5afc59b82d8a95
iuc
parents:
5
diff
changeset
|
141 && samtools sort --no-PG -@\${GALAXY_SLOTS:-4} -T "\${TMPDIR:-.}" -O bam -o '$output_unmapped_reads' 'unmapped_reads.bam' |
|
858a65b52cf9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ef7069328751b534fd4c90115e5afc59b82d8a95
iuc
parents:
5
diff
changeset
|
142 && samtools sort --no-PG -@\${GALAXY_SLOTS:-4} -T "\${TMPDIR:-.}" -O bam -o '$output_mapped_reads' 'mapped_reads.bam' |
|
4
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
143 #elif str($output_options.output_sort) == 'name': |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
144 out='all_reads.bam' |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
145 outu='unmapped_reads.bam' |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
146 outm='mapped_reads.bam' |
|
6
858a65b52cf9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ef7069328751b534fd4c90115e5afc59b82d8a95
iuc
parents:
5
diff
changeset
|
147 && samtools sort --no-PG -n -@\${GALAXY_SLOTS:-4} -T '\${TMPDIR:-.}' -O bam -o '$output_all_reads' 'all_reads.bam' |
|
858a65b52cf9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ef7069328751b534fd4c90115e5afc59b82d8a95
iuc
parents:
5
diff
changeset
|
148 && samtools sort --no-PG -n -@\${GALAXY_SLOTS:-4} -T '\${TMPDIR:-.}' -O bam -o '$output_unmapped_reads' 'unmapped_reads.bam' |
|
858a65b52cf9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ef7069328751b534fd4c90115e5afc59b82d8a95
iuc
parents:
5
diff
changeset
|
149 && samtools sort --no-PG -n -@\${GALAXY_SLOTS:-4} -T '\${TMPDIR:-.}' -O bam -o '$output_mapped_reads' 'mapped_reads.bam' |
|
0
07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff
changeset
|
150 #else: |
|
4
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
151 out='all_reads.bam' |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
|
152 outu='unmapped_reads.bam' |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents:
3
diff
changeset
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153 outm='mapped_reads.bam' |
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154 && mv 'all_reads.bam' '$output_all_reads' |
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155 && mv 'unmapped_reads.bam' '$output_unmapped_reads' |
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156 && mv 'mapped_reads.bam' '$output_mapped_reads' |
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157 #end if |
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158 ]]></command> |
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159 <inputs> |
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160 <expand macro="input_type_cond"/> |
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161 <expand macro="reference_source_cond"/> |
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162 <section name="mapping_options" title="Mapping options"> |
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163 <param argument="maxindel" type="integer" value="16000" label="Maximum indel length" help="Don't look for indels longer than this (lower is faster)"/> |
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164 <param argument="strictmaxindel" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Do not allow indels longer than the specified maximum indel length?" help="By default these are not sought, but may be found anyway"/> |
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165 <param argument="tipsearch" type="integer" value="100" label="Look this far for read-end deletions with anchors shorter than K using brute force"/> |
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166 <param argument="minid" type="float" value="0.76" label="Approximate minimum alignment identity to look for" help="Higher is faster and less sensitive"/> |
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167 <param argument="minhits" type="integer" value="1" label="Minimum number of seed hits required for candidate sites" help="Higher is faster"/> |
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168 <param argument="local" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Use local (rather than global) alignments?"/> |
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169 <param argument="perfectmode" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Allow only perfect mappings?"/> |
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170 <param argument="semiperfectmode" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Allow only perfect and semiperfect (perfect except for N's in the reference) mappings?"/> |
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171 <param name="ambiguous" type="select" label="Specify behavior on ambiguously-mapped reads with multiple top-scoring mapping locations"> |
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172 <option value="best" selected="true">Use the first best site</option> |
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173 <option value="toss">Consider unmapped</option> |
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174 <option value="random">Select one top-scoring site randomly</option> |
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175 <option value="all">Retain all top-scoring sites</option> |
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176 </param> |
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177 <param argument="samestrandpairs" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Map paired reads to the same strand?" help="No value will map to opposite strands"/> |
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178 <param argument="requirecorrectstrand" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Forbid pairing of reads without correct strand orientation?" help="Select No for long-mate-pair libraries"/> |
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179 <param argument="killbadpairs" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Mark the read with the lower mapping quality as unmapped if a read pair is mapped with an inappropriate insert size or orientation?"/> |
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180 <param argument="pairedonly" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Treat unpaired reads as unmapped?"/> |
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181 <param argument="rcomp" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Reverse complement both reads prior to mapping (for LMP outward-facing libraries)?"/> |
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182 <param argument="rcompmate" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Reverse complement read2 prior to mapping?"/> |
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183 <param argument="pairlen" type="integer" value="32000" label="Maximum allowed distance between paired reads"/> |
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184 <param argument="rescuedist" type="integer" value="1200" label="Maximum average insert size for trying to rescue paired reads" help="Lower is faster"/> |
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185 <param argument="rescuemismatches" type="integer" value="32" label="Maximum mismatches allowed in a rescued read" help="Lower is faster"/> |
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186 <param argument="averagepairdist" type="integer" value="100" label="Initial average distance between paired reads" help="Varies dynamically; does not need to be specified"/> |
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187 <param argument="deterministic" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Run in deterministic mode?" help="BBMap is deterministic without this flag if using single-ended reads?"/> |
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188 <param argument="bandwidthratio" type="integer" value="0" label="Restrict alignment band to this fraction of read length" help="Zero value ignores"/> |
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189 <param argument="bandwidth" type="integer" value="0" label="Set the bandwidth directly to this fraction of read length" help="Faster but less accurate"/> |
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190 <param argument="maxsites2" type="integer" value="800" label="Maximum number of alignments per read to output"/> |
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191 <param argument="ignorefrequentkmers" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Discard low-information kmers that occur often?"/> |
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192 <param argument="excludefraction" type="float" value="0.03" label="Fraction of kmers to ignore" help="For example, 0.03 will ignore the most common 3% of kmers"/> |
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193 <param argument="greedy" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Use a greedy algorithm to discard the least-useful kmers on a per-read basis?"/> |
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194 <param argument="kfilter" type="integer" value="0" label="Potential mapping sites must have at least this many consecutive exact matches" help="Zero value ignores"/> |
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195 </section> |
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196 <section name="qt_options" title="Quality and trimming options"> |
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197 <param name="qtrim" type="select" label="Select option for quality trimming ends before mapping"> |
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198 <option value="f" selected="true">No trimming</option> |
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199 <option value="l">Trim left</option> |
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200 <option value="r">Trim right</option> |
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201 <option value="lr">Trim both</option> |
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202 </param> |
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203 <param argument="untrim" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Undo trimming after mapping?" help="Untrimmed bases will be soft-clipped in cigar strings"/> |
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204 <param argument="trimq" type="integer" value="6" label="Trim regions with average quality below this value"/> |
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205 <param argument="mintrimlength" type="integer" value="60" label="Don't trim reads to be shorter than this value"/> |
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206 <param argument="fakefastaquality" type="integer" value="-1" max="50" label="Set to a positive number 1-50 to generate fake quality strings for fasta input reads"/> |
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207 <param argument="ignorebadquality" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Keep going, rather than crashing, if a read has out-of-range quality values?"/> |
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208 <param argument="usequality" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Use quality scores when determining which read kmers to use as seeds?"/> |
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209 <param argument="minaveragequality" type="integer" value="0" label="Do not map reads with average quality below this value"/> |
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210 <param argument="maqb" type="integer" value="0" label="Calculate maq from this many initial bases" help="Zero value ignores"/> |
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211 </section> |
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212 <section name="output_options" title="Output options"> |
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213 <param argument="secondary" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Output secondary alignments?"/> |
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214 <param argument="maxsites" type="integer" value="5" label="Maximum number of total alignments to output per read" help="Relevant only when outputting secondary alignments"/> |
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215 <param argument="sssr" type="float" value="0.95" label="Output only secondary alignments with score of at least this fraction of primary"/> |
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216 <param argument="ssao" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Only output secondary alignments for ambiguously-mapped reads?"/> |
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217 <param argument="quickmatch" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Generate cigar strings more quickly?"/> |
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218 <param argument="trimreaddescriptions" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Truncate read and ref names at the first whitespace, assuming that the remainder is a comment or description?"/> |
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219 <param argument="machineout" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Output statistics in machine-friendly (key=value) format?"/> |
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220 <param argument="printunmappedcount" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Output the total number of unmapped reads and bases?" help="If input is paired, the number will be of pairs for which both reads are unmapped"/> |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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221 <param argument="renamebyinsert" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Rename reads based on their mapped insert size?"/> |
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6d44c9f1a42b
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222 <param name="output_sort" type="select" label="BAM sorting mode" help="The 'Not sorted' option can significantly extend the run time of the tool (it runs using a single thread)"> |
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6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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223 <option value="coordinate" selected="True">Sort by chromosomal coordinates</option> |
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6d44c9f1a42b
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224 <option value="name">Sort by read names</option> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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225 <option value="unsorted">Not sorted (sorted as input)</option> |
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226 </param> |
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227 </section> |
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228 <section name="pf_options" title="Post-filtering options"> |
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6d44c9f1a42b
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229 <param argument="idfilter" type="integer" value="0" min="0" max="1" label="Specify exact minimum identity allowed for alignments to be output" help="Independent of approximate minimum alignment identity to look for"/> |
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6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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230 <param argument="subfilter" type="integer" value="-1" label="Ban alignments with more than this many substitutions" help="Negative value ignores"/> |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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231 <param argument="insfilter" type="integer" value="-1" label="Ban alignments with more than this many insertions" help="Negative value ignores"/> |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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232 <param argument="delfilter" type="integer" value="-1" label="Ban alignments with more than this many deletions" help="Negative value ignores"/> |
|
6d44c9f1a42b
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233 <param argument="indelfilter" type="integer" value="-1" label="Ban alignments with more than this many indels" help="Negative value ignores"/> |
|
6d44c9f1a42b
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234 <param argument="editfilter" type="integer" value="-1" label="Ban alignments with more than this many edits" help="Negative value ignores"/> |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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235 <param argument="inslenfilter" type="integer" value="-1" label="Ban alignments with an insertion longer than this" help="Negative value ignores"/> |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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236 <param argument="dellenfilter" type="integer" value="-1" label="Ban alignments with a deletion longer than this" help="Negative value ignores"/> |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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237 <param argument="nfilter" type="integer" value="-1" label="Ban alignments with more than this many ns (includes nocall, noref, and off scaffold ends)" help="Negative value ignores"/> |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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238 </section> |
|
0
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239 </inputs> |
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07a6e49c7d74
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240 <outputs> |
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241 <data format="bam" name="output_all_reads" label="${tool.name} on ${on_string} (all reads)"> |
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6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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242 <expand macro="dbKeyActionsBBMap"/> |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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243 <change_format> |
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6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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244 <when input="output_options.output_sort" value="name" format="qname_sorted.bam"/> |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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245 <when input="output_options.output_sort" value="unsorted" format="qname_input_sorted.bam"/> |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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246 </change_format> |
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6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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247 </data> |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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248 <data format="bam" name="output_unmapped_reads" label="${tool.name} on ${on_string} (unmapped reads)"> |
|
0
07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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249 <expand macro="dbKeyActionsBBMap"/> |
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07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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250 <change_format> |
|
4
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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251 <when input="output_options.output_sort" value="name" format="qname_sorted.bam"/> |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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252 <when input="output_options.output_sort" value="unsorted" format="qname_input_sorted.bam"/> |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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253 </change_format> |
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6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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254 </data> |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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255 <data format="bam" name="output_mapped_reads" label="${tool.name} on ${on_string} (mapped reads)"> |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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256 <expand macro="dbKeyActionsBBMap"/> |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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257 <change_format> |
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6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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258 <when input="output_options.output_sort" value="name" format="qname_sorted.bam"/> |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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259 <when input="output_options.output_sort" value="unsorted" format="qname_input_sorted.bam"/> |
|
0
07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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260 </change_format> |
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07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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261 </data> |
|
07a6e49c7d74
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262 </outputs> |
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07a6e49c7d74
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263 <tests> |
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07a6e49c7d74
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264 <!-- Single file, cached reference, output coordinate sorted --> |
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4
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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265 <test expect_num_outputs="3"> |
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0
07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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266 <param name="input_type" value="single"/> |
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07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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267 <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz"/> |
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4
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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268 <param name="output_sort" value="coordinate"/> |
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6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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269 <output name="output_all_reads" ftype="bam"> |
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6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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270 <metadata name="dbkey" value="89"/> |
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6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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271 <assert_contents> |
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6
858a65b52cf9
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272 <has_size value="9639" delta="300"/> |
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4
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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273 </assert_contents> |
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6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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274 </output> |
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6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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275 <output name="output_unmapped_reads" ftype="bam"> |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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276 <metadata name="dbkey" value="89"/> |
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6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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277 <assert_contents> |
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6
858a65b52cf9
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278 <has_size value="9639" delta="300"/> |
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4
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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279 </assert_contents> |
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6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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280 </output> |
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6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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281 <output name="output_mapped_reads" ftype="bam"> |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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282 <metadata name="dbkey" value="89"/> |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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283 <assert_contents> |
|
6
858a65b52cf9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ef7069328751b534fd4c90115e5afc59b82d8a95
iuc
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284 <has_size value="851" delta="100"/> |
|
4
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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285 </assert_contents> |
|
0
07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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286 </output> |
|
07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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287 </test> |
|
07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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288 <!-- Paired reads in separate datasets, cached reference, output name sorted --> |
|
4
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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289 <test expect_num_outputs="3"> |
|
0
07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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290 <param name="input_type" value="pair"/> |
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07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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291 <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz"/> |
|
07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
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|
292 <param name="read2" value="13-1941-6_S4_L001_R2_600000.fastq.gz"/> |
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07a6e49c7d74
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293 <param name="output_sort" value="name"/> |
|
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6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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294 <output name="output_all_reads" ftype="qname_sorted.bam"> |
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6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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295 <metadata name="dbkey" value="89"/> |
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6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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296 <assert_contents> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ef7069328751b534fd4c90115e5afc59b82d8a95
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297 <has_size value="17540" delta="600"/> |
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4
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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298 </assert_contents> |
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6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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299 </output> |
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6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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300 <output name="output_unmapped_reads" ftype="qname_sorted.bam"> |
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6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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301 <metadata name="dbkey" value="89"/> |
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6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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302 <assert_contents> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ef7069328751b534fd4c90115e5afc59b82d8a95
iuc
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303 <has_size value="17540" delta="600"/> |
|
4
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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304 </assert_contents> |
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6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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305 </output> |
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6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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306 <output name="output_mapped_reads" ftype="qname_sorted.bam"> |
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6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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307 <metadata name="dbkey" value="89"/> |
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6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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308 <assert_contents> |
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858a65b52cf9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ef7069328751b534fd4c90115e5afc59b82d8a95
iuc
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309 <has_size value="860" delta="100"/> |
|
4
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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310 </assert_contents> |
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0
07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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311 </output> |
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07a6e49c7d74
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312 </test> |
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07a6e49c7d74
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313 <!-- Collection of Paired reads, history reference, output unsorted --> |
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6d44c9f1a42b
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314 <test expect_num_outputs="3"> |
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0
07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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315 <param name="input_type" value="paired"/> |
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07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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316 <param name="reads_collection"> |
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07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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317 <collection type="paired"> |
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07a6e49c7d74
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318 <element name="forward" value="13-1941-6_S4_L001_R1_600000.fastq.gz"/> |
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07a6e49c7d74
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319 <element name="reverse" value="13-1941-6_S4_L001_R2_600000.fastq.gz"/> |
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07a6e49c7d74
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320 </collection> |
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07a6e49c7d74
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iuc
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321 </param> |
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07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
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322 <param name="ref_source" value="history"/> |
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07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
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323 <param name="reference" value="NC_002945v4.fasta" dbkey="89" ftype="fasta"/> |
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07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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324 <param name="output_sort" value="unsorted"/> |
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4
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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325 <output name="output_all_reads" ftype="qname_input_sorted.bam"> |
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6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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326 <metadata name="dbkey" value="89"/> |
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6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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327 <assert_contents> |
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6
858a65b52cf9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ef7069328751b534fd4c90115e5afc59b82d8a95
iuc
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328 <has_size value="17602" delta="600"/> |
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4
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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329 </assert_contents> |
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6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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330 </output> |
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6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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331 <output name="output_unmapped_reads" ftype="qname_input_sorted.bam"> |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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332 <metadata name="dbkey" value="89"/> |
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6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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333 <assert_contents> |
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6
858a65b52cf9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ef7069328751b534fd4c90115e5afc59b82d8a95
iuc
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334 <has_size value="17602" delta="600"/> |
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4
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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335 </assert_contents> |
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6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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336 </output> |
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6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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337 <output name="output_mapped_reads" ftype="qname_input_sorted.bam"> |
|
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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338 <metadata name="dbkey" value="89"/> |
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6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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339 <assert_contents> |
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6
858a65b52cf9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ef7069328751b534fd4c90115e5afc59b82d8a95
iuc
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340 <has_size value="878" delta="100"/> |
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4
6d44c9f1a42b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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341 </assert_contents> |
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0
07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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342 </output> |
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07a6e49c7d74
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343 </test> |
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07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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344 </tests> |
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07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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345 <help> |
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07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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346 **What it does** |
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07a6e49c7d74
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347 |
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07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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348 BBMap is a splice-aware global aligner for DNA and RNA sequencing reads. It is fast and extremely accurate, particularly |
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07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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349 with highly mutated genomes or reads with long indels, even whole-gene deletions over 100kbp long. It has no upper limit |
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07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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350 to genome size or number of contigs and has been successfully used for mapping to an 85 gigabase soil metagenome with over |
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07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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351 200 million contigs. the indexing phase is very fast compared to other aligners. |
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07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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352 |
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07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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353 BBMap can output many different statistics files; an empirical read quality histogram, insert-size distribution, and genome |
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07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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354 coverage with or without generating a sam file. It is useful in quality control of libraries and sequencing runs or |
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07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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355 evaluating new sequencing platforms. |
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07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
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356 |
|
07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
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357 **Options** |
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07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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358 |
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07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
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359 *Bam sorting mode* - the generated bam files can be sorted according to three criteria: coordinates, names and input order. |
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07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
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360 |
|
07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
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361 * Sort by chromosomal coordinates - the file is sorted by coordinates (i.e., the reads from the beginning of the first |
|
07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
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362 chromosome are first in the file. |
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07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
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363 * Sort by read names - the file is sorted by the reference ID (i.e., the QNAME field). |
|
07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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364 * Not sorted (sorted as input) - the file is sorted in the order of the reads in the input file. |
|
07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
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365 |
|
07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
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366 </help> |
|
07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
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367 <expand macro="citations"/> |
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07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
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368 </tool> |
|
07a6e49c7d74
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
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369 |