Mercurial > repos > devteam > bowtie2
annotate bowtie2_macros.xml @ 31:0d4acadabb04 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit f25b49ba5f2f3e5542e75224948818c32dea920a
| author | iuc |
|---|---|
| date | Mon, 26 Feb 2024 08:50:20 +0000 |
| parents | 03e9b2fbc005 |
| children | d5ceb9f3c25b |
| rev | line source |
|---|---|
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
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1 <macros> |
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31
0d4acadabb04
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit f25b49ba5f2f3e5542e75224948818c32dea920a
iuc
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2 <token name="@TOOL_VERSION@">2.5.3</token> |
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30
03e9b2fbc005
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 3ae56dd669038a65c3f60ba64c67cbefb254ab5e
iuc
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3 <token name="@VERSION_SUFFIX@">0</token> |
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15
43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
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4 <!-- Import this at the top of your command block and then |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
diff
changeset
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5 define rg_auto_name. --> |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
diff
changeset
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6 <token name="@define_read_group_helpers@"> |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
diff
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7 #def identifier_or_name($input1) |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
diff
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8 #if hasattr($input1, 'element_identifier') |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
diff
changeset
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9 #return $input1.element_identifier |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
diff
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10 #else |
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17
66f992977578
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
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11 #return $input1.name.rstrip('.gz').rstrip('.fastq').rstrip('.fq').rstrip('.bz2') |
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15
43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
diff
changeset
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12 #end if |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
diff
changeset
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13 #end def |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
diff
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14 |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
diff
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15 #def clean(name) |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
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16 #import re |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
diff
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17 #set $name_clean = re.sub('[^\w\-_\.]', '_', $name) |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
diff
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18 #return $name_clean |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
diff
changeset
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19 #end def |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
diff
changeset
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20 |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
diff
changeset
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21 #def read_group_name_default($input1, $input2=None) |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
diff
changeset
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22 #if $input2 is None |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
diff
changeset
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23 #return $clean($identifier_or_name($input1)) |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
diff
changeset
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24 #else |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
diff
changeset
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25 #import itertools |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
diff
changeset
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26 #set $input_name1 = $clean($identifier_or_name($input1)) |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
diff
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27 #set $input_name2 = $clean($identifier_or_name($input2)) |
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27
a6d65b0c67af
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit d142d9cd5a8db8a87184c4b7622ea8de8355894f"
iuc
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28 #set $common_prefix = ''.join([c[0] for c in itertools.takewhile(lambda x: all(x[0] == y for y in x), zip(*[$input_name1, $input_name2]))]) |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
diff
changeset
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29 #if len($common_prefix) > 3 |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
diff
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30 #return $common_prefix |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
diff
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31 #else |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
diff
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32 #return $input_name1 |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
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33 #end if |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
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34 #end if |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
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35 #end def |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
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36 |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
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37 #def format_read_group(prefix, value, quote='', arg='') |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
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38 #if $value |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
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39 #return $arg + $quote + $prefix + $value + $quote |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
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40 #else |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
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41 #return '' |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
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42 #end if |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
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43 #end def |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
diff
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44 |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
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45 #def rg_param(name) |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
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46 #if $varExists("rg") |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
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47 #return $rg.get($name, None) |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
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48 #else |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
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49 #return $getVar($name, None) |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
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50 #end if |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
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51 #end def |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
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52 |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
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53 #set $use_rg = True |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
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54 </token> |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
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55 <!-- preconditions use_rg and rg_auto_name have been |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
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56 defined. |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
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57 --> |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
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58 <token name="@set_read_group_vars@"> |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
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59 #if $use_rg |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
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60 #if $rg_param('read_group_id_conditional') is None |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
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61 #set $rg_id = $rg_auto_name |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
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62 #elif $rg_param('read_group_id_conditional').do_auto_name |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
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63 #set $rg_id = $rg_auto_name |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
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64 #else |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
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65 #set $rg_id = str($rg_param('read_group_id_conditional').ID) |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
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66 #end if |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
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67 |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
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68 #if $rg_param('read_group_sm_conditional') is None |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
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69 #set $rg_sm = '' |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
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70 #elif $rg_param('read_group_sm_conditional').do_auto_name |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
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71 #set $rg_sm = $rg_auto_name |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
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72 #else |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
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73 #set $rg_sm = str($rg_param('read_group_sm_conditional').SM) |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
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74 #end if |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
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75 |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
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76 #if $rg_param('PL') |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
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77 #set $rg_pl = str($rg_param('PL')) |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents:
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78 #else |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
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79 #set $rg_pl = '' |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
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80 #end if |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
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81 |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
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82 #if $rg_param('read_group_lb_conditional') is None |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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83 #set $rg_lb = '' |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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84 #elif $rg_param('read_group_lb_conditional').do_auto_name |
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85 #set $rg_lb = $rg_auto_name |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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86 #else |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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87 #set $rg_lb = str($rg_param('read_group_lb_conditional').LB) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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88 #end if |
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89 |
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90 #if $rg_param('CN') |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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91 #set $rg_cn = str($rg_param('CN')) |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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92 #else |
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93 #set $rg_cn = '' |
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43d12513224b
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94 #end if |
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95 |
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96 #if $rg_param("DS") |
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97 #set $rg_ds = str($rg_param("DS")) |
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43d12513224b
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98 #else |
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99 #set $rg_ds = '' |
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100 #end if |
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101 |
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102 #if $rg_param("DT") |
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103 #set $rg_dt = str($rg_param("DT")) |
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43d12513224b
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104 #else |
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105 #set $rg_dt = '' |
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43d12513224b
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106 #end if |
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107 |
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108 #if $rg_param("FO") |
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109 #set $rg_fo = str($rg_param("FO")) |
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43d12513224b
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110 #else |
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111 #set $rg_fo = '' |
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112 #end if |
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113 |
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114 #if $rg_param("KS") |
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115 #set $rg_ks = str($rg_param("KS")) |
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116 #else |
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117 #set $rg_ks = '' |
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118 #end if |
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119 |
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120 #if $rg_param("PG") |
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121 #set $rg_pg = str($rg_param("PG")) |
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43d12513224b
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122 #else |
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123 #set $rg_pg = '' |
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43d12513224b
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124 #end if |
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125 |
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126 #if $rg_param("PI") != None |
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127 #set $rg_pi = str($rg_param("PI")) |
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128 #else |
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129 #set $rg_pi = '' |
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130 #end if |
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131 |
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132 #if $rg_param("PU") |
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133 #set $rg_pu = str($rg_param("PU")) |
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43d12513224b
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134 #else |
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135 #set $rg_pu = '' |
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136 #end if |
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137 #end if |
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138 </token> |
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139 <token name="@set_use_rg_var@"> |
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140 #set $use_rg = str($rg.rg_selector) != "do_not_set" |
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141 </token> |
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142 <xml name="read_group_auto_name_conditional"> |
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143 <param name="do_auto_name" type="boolean" label="Auto-assign" help="Use dataset name or collection information to automatically assign this value" checked="false" /> |
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144 <when value="true"> |
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145 </when> |
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146 <when value="false"> |
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147 <yield /> |
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148 </when> |
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149 </xml> |
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150 <xml name="read_group_id_param"> |
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151 <param name="ID" type="text" value="" label="Read group identifier (ID)" help="This value must be unique among multiple samples in your experiment" optional="false"> |
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152 <validator type="empty_field" /> |
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153 </param> |
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154 </xml> |
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155 <xml name="read_group_id_conditional"> |
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156 <conditional name="read_group_id_conditional"> |
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157 <expand macro="read_group_auto_name_conditional"> |
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158 <expand macro="read_group_id_param" /> |
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159 </expand> |
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160 </conditional> |
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161 </xml> |
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162 <xml name="read_group_sm_param"> |
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163 <param name="SM" type="text" value="" label="Read group sample name (SM)" help="This value should be descriptive. Use pool name where a pool is being sequenced" /> |
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164 </xml> |
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165 <xml name="read_group_sm_conditional"> |
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166 <conditional name="read_group_sm_conditional"> |
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167 <expand macro="read_group_auto_name_conditional"> |
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168 <expand macro="read_group_sm_param" /> |
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169 </expand> |
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170 </conditional> |
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171 </xml> |
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172 <!-- Above SM param is optional (for SAM/BAM spec, this is required |
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173 as per Picard. |
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174 --> |
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175 <xml name="read_group_sm_param_required"> |
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176 <param name="SM" type="text" value="" label="Read group sample name (SM)" optional="false" help="This value should be descriptive. Use pool name where a pool is being sequenced"> |
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177 <validator type="empty_field" /> |
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178 </param> |
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179 </xml> |
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180 <xml name="read_group_sm_required_conditional"> |
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181 <conditional name="read_group_sm_conditional"> |
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182 <expand macro="read_group_auto_name_conditional"> |
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183 <expand macro="read_group_sm_param" /> |
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184 </expand> |
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185 </conditional> |
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186 </xml> |
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187 <xml name="read_group_pl_param"> |
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188 <param name="PL" type="select" label="Platform/technology used to produce the reads (PL)"> |
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189 <option value="CAPILLARY">CAPILLARY</option> |
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190 <option value="LS454">LS454</option> |
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191 <option selected="True" value="ILLUMINA">ILLUMINA</option> |
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192 <option value="SOLID">SOLID</option> |
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193 <option value="HELICOS">HELICOS</option> |
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194 <option value="IONTORRENT">IONTORRENT</option> |
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195 <option value="PACBIO">PACBIO</option> |
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196 </param> |
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197 </xml> |
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198 <xml name="read_group_lb_param"> |
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199 <param name="LB" type="text" label="Library name (LB)" optional="true" /> |
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200 </xml> |
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201 <xml name="read_group_lb_conditional"> |
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202 <conditional name="read_group_lb_conditional"> |
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203 <expand macro="read_group_auto_name_conditional"> |
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204 <expand macro="read_group_lb_param" /> |
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205 </expand> |
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206 </conditional> |
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207 </xml> |
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208 <xml name="read_group_lb_required_param"> |
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209 <param name="LB" type="text" label="Library name (LB)" optional="false"> |
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210 <validator type="empty_field" /> |
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211 </param> |
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212 </xml> |
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213 <xml name="read_group_lb_required_conditional"> |
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214 <conditional name="read_group_lb_conditional"> |
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215 <expand macro="read_group_auto_name_conditional"> |
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216 <expand macro="read_group_lb_required_param" /> |
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217 </expand> |
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218 </conditional> |
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219 </xml> |
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220 <xml name="read_group_cn_param"> |
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221 <param name="CN" type="text" label="Sequencing center that produced the read (CN)" /> |
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222 </xml> |
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223 <xml name="read_group_ds_param"> |
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224 <param name="DS" type="text" label="Description (DS)" /> |
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225 </xml> |
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226 <xml name="read_group_dt_param"> |
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227 <param name="DT" type="text" label="Date that run was produced (DT)" help="ISO8601 format date or date/time, like YYYY-MM-DD" /> |
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228 </xml> |
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229 <xml name="read_group_fo_param"> |
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230 <param name="FO" type="text" optional="true" label="Flow order (FO)" help="The array of nucleotide bases that correspond to the nucleotides used for each flow of each read. Multi-base flows are encoded in IUPAC format, and non-nucleotide flows by various other characters. Format: /\*|[ACMGRSVTWYHKDBN]+/"> |
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231 <validator type="regex" message="Invalid flow order">\*|[ACMGRSVTWYHKDBN]+$</validator> |
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232 </param> |
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233 </xml> |
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234 <xml name="read_group_ks_param"> |
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235 <param name="KS" type="text" label="The array of nucleotide bases that correspond to the key sequence of each read (KS)" /> |
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236 </xml> |
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237 <xml name="read_group_pg_param"> |
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238 <param name="PG" type="text" label="Programs used for processing the read group (PG)" /> |
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239 </xml> |
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240 <xml name="read_group_pi_param"> |
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241 <param name="PI" type="integer" optional="true" label="Predicted median insert size (PI)" /> |
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242 </xml> |
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243 <xml name="read_group_pu_param"> |
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244 <param name="PU" type="text" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" optional="True" /> |
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245 </xml> |
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246 <xml name="read_group_pu_required_param"> |
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247 <param name="PU" type="text" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" optional="False" /> |
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248 </xml> |
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249 <!-- Only ID is required - all groups available --> |
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250 <xml name="read_group_inputs_spec"> |
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251 <expand macro="read_group_id_conditional" /> |
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252 <expand macro="read_group_sm_conditional" /> |
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253 <expand macro="read_group_pl_param" /> |
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254 <expand macro="read_group_lb_conditional" /> |
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255 <expand macro="read_group_cn_param" /> |
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256 <expand macro="read_group_ds_param" /> |
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257 <expand macro="read_group_dt_param" /> |
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258 <expand macro="read_group_fo_param" /> |
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259 <expand macro="read_group_ks_param" /> |
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260 <expand macro="read_group_pg_param" /> |
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261 <expand macro="read_group_pi_param" /> |
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262 <expand macro="read_group_pu_param" /> |
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263 </xml> |
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264 <!-- ID, SM, LB, PU, PL all required - not ks, pg, or fo params. --> |
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265 <xml name="read_group_inputs_picard"> |
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266 <expand macro="read_group_id_conditional" /> |
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267 <expand macro="read_group_sm_required_conditional" /> |
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268 <expand macro="read_group_lb_required_conditional" /> |
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269 <expand macro="read_group_pl_param" /> |
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270 <expand macro="read_group_pu_required_param" /> |
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271 <expand macro="read_group_cn_param" /> |
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272 <expand macro="read_group_ds_param" /> |
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273 <expand macro="read_group_pi_param" /> |
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274 <expand macro="read_group_dt_param" /> |
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275 </xml> |
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276 <xml name="read_group_conditional"> |
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277 <conditional name="rg"> |
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278 <param name="rg_selector" type="select" label="Set read groups information?" help="Specifying read group information can greatly simplify your downstream analyses by allowing combining multiple datasets."> |
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279 <option value="set">Set read groups (SAM/BAM specification)</option> |
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280 <option value="set_picard">Set read groups (Picard style)</option> |
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281 <option value="set_id_auto">Automatically assign ID using name of history item(s)</option> |
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282 <option value="do_not_set" selected="True">Do not set</option> |
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283 </param> |
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284 <when value="set_picard"> |
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285 <expand macro="read_group_inputs_picard" /> |
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286 </when> |
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287 <when value="set"> |
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288 <expand macro="read_group_inputs_spec" /> |
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289 </when> |
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290 <when value="set_id_auto"> |
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291 </when> |
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292 <when value="do_not_set"> |
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293 </when> |
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294 </conditional> |
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295 </xml> |
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296 <xml name="paired_end_options"> |
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297 <conditional name="paired_options"> |
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298 <param name="paired_options_selector" type="select" label="Do you want to set paired-end options?" help="See "Alignment Options" section of Help below for information"> |
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299 <option value="no" selected="True">No</option> |
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300 <option value="yes">Yes</option> |
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301 </param> |
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302 <when value="yes"> |
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303 <param argument="-I" type="integer" value="0" min="0" label="Set the minimum fragment length for valid paired-end alignments" |
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304 help="E.g. if `-I 60` is specified and a paired-end alignment consists of two 20-bp alignments in the appropriate orientation with a 20-bp gap between them, that alignment is considered valid (as long as `-X` is also satisfied). A 19-bp gap would not be valid in that case. If trimming options `-3` or `-5` are also used, the `-I` constraint is applied with respect to the untrimmed mates. The larger the difference between `-I` and `-X`, the slower Bowtie 2 will run. This is because larger differences bewteen `-I` and `-X` require that Bowtie 2 scan a larger window to determine if a concordant alignment exists. For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very efficient. Default=0"/> |
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305 <param argument="-X" type="integer" value="500" min="0" label="Set the maximum fragment length for valid paired-end alignments" |
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306 help="E.g. if `-X 100` is specified and a paired-end alignment consists of two 20-bp alignments in the proper orientation with a 60-bp gap between them, that alignment is considered valid (as long as `-I` is also satisfied). A 61-bp gap would not be valid in that case. If trimming options `-3` or `-5` are also used, the `-X` constraint is applied with respect to the untrimmed mates, not the trimmed mates; Default=500"/> |
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307 <param name="fr_rf_ff" type="select" display="radio" label="Select the upstream/downstream mate orientations for a valid paired-end alignment against the forward reference strand" |
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308 help="--fr, --rf, or --ff; E.g., if `--fr` is specified and there is a candidate paired-end alignment where mate 1 appears upstream of the reverse complement of mate 2 and the fragment length constraints (`-I` and `-X`) are met, that alignment is valid. Also, if mate 2 appears upstream of the reverse complement of mate 1 and all other constraints are met, that too is valid. `--rf` likewise requires that an upstream mate1 be reverse-complemented and a downstream mate2 be forward-oriented. `--ff` requires both an upstream mate 1 and a downstream mate 2 to be forward-oriented; Default=--fr (appropriate for Illumina's Paired-end Sequencing Assay)"> |
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309 <option value="--fr" selected="True">--fr</option> |
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310 <option value="--rf">--rf</option> |
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311 <option value="--ff">--ff</option> |
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312 </param> |
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31
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313 <param argument="--no-mixed" type="boolean" truevalue="--no-mixed" falsevalue="" checked="False" label="Disable no-mixed behavior" help="--no-mixed; By default, when `bowtie2` cannot find a concordant or discordant alignment for a pair, it then tries to find alignments for the individual mates; default=False"/> |
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314 <param argument="--no-discordant" type="boolean" truevalue="--no-discordant" falsevalue="" checked="False" label="Disable no-discordant behavior" help="--no-discordant; By default, `bowtie2` looks for discordant alignments if it cannot find any concordant alignments. A discordant alignment is an alignment where both mates align uniquely, but that does not satisfy the paired-end constraints (`--fr`/`--rf`/`--ff`, `-I`, `-X`); default=False"/> |
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315 <param argument="--dovetail" type="boolean" truevalue="--dovetail" falsevalue="" checked="False" label="Allow mate dovetailing" help="--dovetail; If the mates `dovetail`, that is if one mate alignment extends past the beginning of the other such that the wrong mate begins upstream, consider that to be concordant. Default=False"/> |
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316 <param argument="--no-contain" type="boolean" truevalue="--no-contain" falsevalue="" checked="False" label="Disallow one mate alignment to contain another" help="--no-contain; If one mate alignment contains the other, consider that to be non-concordant. Default=False"/> |
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317 <param argument="--no-overlap" type="boolean" truevalue="--no-overlap" falsevalue="" checked="False" label="Disallow mate alignments to overlap" help="--no-overlap; If one mate alignment overlaps the other at all, consider that to be non-concordant. Default=False"/> |
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318 </when> |
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319 <when value="no"> |
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320 <!-- do nothing --> |
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321 </when> |
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322 </conditional> |
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323 </xml> |
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324 <xml name="align_unalign"> |
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325 <param name="unaligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads (in fastq format) to separate file(s)" help="--un/--un-conc (possibly with -gz or -bz2); This triggers --un parameter for single reads and --un-conc for paired reads" /> |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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326 <param name="aligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write aligned reads (in fastq format) to separate file(s)" help="--al/--al-conc (possibly with -gz or -bz2); This triggers --al parameter for single reads and --al-conc for paired reads" /> |
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43d12513224b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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327 </xml> |
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328 <xml name="dbKeyActions"> |
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329 <conditional name="reference_genome.source"> |
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330 <when value="indexed"> |
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331 <action type="metadata" name="dbkey"> |
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332 <option type="from_data_table" name="bowtie2_indexes" column="1"> |
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333 <filter type="param_value" ref="reference_genome.index" column="0"/> |
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334 </option> |
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335 </action> |
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336 </when> |
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337 <when value="history"> |
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338 <action type="metadata" name="dbkey"> |
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339 <option type="from_param" name="reference_genome.own_file" param_attribute="dbkey" /> |
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340 </action> |
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341 </when> |
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342 </conditional> |
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343 </xml> |
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344 </macros> |