Mercurial > repos > iuc > recentrifuge
annotate recentrifuge.xml @ 3:b5407cc2bf51 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge commit 96f8a533278b4b6394aebd7a8f537513b0d29b1a
| author | iuc |
|---|---|
| date | Thu, 31 Aug 2023 04:46:52 +0000 |
| parents | fe733f05c2f8 |
| children |
| rev | line source |
|---|---|
|
0
09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
parents:
diff
changeset
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1 <?xml version="1.0" encoding="UTF-8"?> |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
parents:
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2 |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
parents:
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changeset
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3 <tool id="recentrifuge" name="Recentrifuge" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
parents:
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4 <description> |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
parents:
diff
changeset
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5 Robust comparative analysis and contamination removal for metagenomics |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
parents:
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changeset
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6 </description> |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
parents:
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7 <macros> |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
parents:
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8 <import>macro.xml</import> |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
parents:
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9 </macros> |
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1
fe733f05c2f8
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 9142693589056424fb64869b69dbc08b179f57ee
iuc
parents:
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10 <expand macro='edam'/> |
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0
09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
parents:
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11 <expand macro='xrefs'/> |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
parents:
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12 <expand macro="requirements" /> |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
parents:
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13 <expand macro="version_command" /> |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
parents:
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14 <command detect_errors="aggressive"><![CDATA[ |
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1
fe733f05c2f8
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 9142693589056424fb64869b69dbc08b179f57ee
iuc
parents:
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15 #import re |
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fe733f05c2f8
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 9142693589056424fb64869b69dbc08b179f57ee
iuc
parents:
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16 #*====================================== |
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fe733f05c2f8
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 9142693589056424fb64869b69dbc08b179f57ee
iuc
parents:
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17 Make a dir with all input files |
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fe733f05c2f8
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 9142693589056424fb64869b69dbc08b179f57ee
iuc
parents:
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18 ======================================*# |
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fe733f05c2f8
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 9142693589056424fb64869b69dbc08b179f57ee
iuc
parents:
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19 mkdir input_dir && |
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fe733f05c2f8
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 9142693589056424fb64869b69dbc08b179f57ee
iuc
parents:
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changeset
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20 #for $input in $input_file |
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fe733f05c2f8
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 9142693589056424fb64869b69dbc08b179f57ee
iuc
parents:
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21 #set input_identifier = re.sub('[^\s\w\-]', '_', str($input.element_identifier)) |
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fe733f05c2f8
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 9142693589056424fb64869b69dbc08b179f57ee
iuc
parents:
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22 #if $file_type.filetype == "centrifuge" |
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fe733f05c2f8
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 9142693589056424fb64869b69dbc08b179f57ee
iuc
parents:
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23 ln -s '$input' 'input_dir/${input_identifier}.out' && |
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fe733f05c2f8
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 9142693589056424fb64869b69dbc08b179f57ee
iuc
parents:
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24 #else if $file_type.filetype == "clark" |
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fe733f05c2f8
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 9142693589056424fb64869b69dbc08b179f57ee
iuc
parents:
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diff
changeset
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25 ln -s '$input' 'input_dir/${input_identifier}.csv' && |
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fe733f05c2f8
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 9142693589056424fb64869b69dbc08b179f57ee
iuc
parents:
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diff
changeset
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26 #else if $file_type.filetype == "kraken" |
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fe733f05c2f8
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 9142693589056424fb64869b69dbc08b179f57ee
iuc
parents:
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27 ln -s '$input' 'input_dir/${input_identifier}.krk' && |
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fe733f05c2f8
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 9142693589056424fb64869b69dbc08b179f57ee
iuc
parents:
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28 #else |
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fe733f05c2f8
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 9142693589056424fb64869b69dbc08b179f57ee
iuc
parents:
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29 ln -s '$input' 'input_dir/$input_identifier' && |
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fe733f05c2f8
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 9142693589056424fb64869b69dbc08b179f57ee
iuc
parents:
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30 #end if |
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fe733f05c2f8
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 9142693589056424fb64869b69dbc08b179f57ee
iuc
parents:
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31 #end for |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
parents:
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32 #*====================================== |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
parents:
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33 database input |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
parents:
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34 ======================================*# |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
parents:
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35 rcf |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
parents:
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36 -n $database.database_name.fields.path |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
parents:
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37 #*====================================== |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
parents:
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38 Recentrifuge input file |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
parents:
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39 ======================================*# |
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1
fe733f05c2f8
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 9142693589056424fb64869b69dbc08b179f57ee
iuc
parents:
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40 |
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0
09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
parents:
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41 #if $file_type.filetype == "centrifuge" |
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1
fe733f05c2f8
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 9142693589056424fb64869b69dbc08b179f57ee
iuc
parents:
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42 -f input_dir |
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fe733f05c2f8
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 9142693589056424fb64869b69dbc08b179f57ee
iuc
parents:
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43 #set $default_scoring = 'SHEL' |
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fe733f05c2f8
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 9142693589056424fb64869b69dbc08b179f57ee
iuc
parents:
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44 #else if $file_type.filetype == "kraken" |
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fe733f05c2f8
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 9142693589056424fb64869b69dbc08b179f57ee
iuc
parents:
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45 -k input_dir |
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fe733f05c2f8
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 9142693589056424fb64869b69dbc08b179f57ee
iuc
parents:
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46 #set $default_scoring = 'KRAKEN' |
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fe733f05c2f8
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 9142693589056424fb64869b69dbc08b179f57ee
iuc
parents:
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47 #else if $file_type.filetype == "clark" |
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fe733f05c2f8
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 9142693589056424fb64869b69dbc08b179f57ee
iuc
parents:
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48 -r input_dir |
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0
09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
parents:
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49 #set $default_scoring = 'SHEL' |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
parents:
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50 #else if $file_type.filetype == "lmat" |
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1
fe733f05c2f8
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 9142693589056424fb64869b69dbc08b179f57ee
iuc
parents:
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51 -l input_dir |
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0
09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
parents:
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52 #set $default_scoring = 'LMAT' |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
parents:
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53 #else if $file_type.filetype == "generic" |
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1
fe733f05c2f8
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 9142693589056424fb64869b69dbc08b179f57ee
iuc
parents:
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54 -g input_dir |
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0
09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
parents:
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55 --format '$file_type.format' |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
parents:
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56 #set $default_scoring = 'GENERIC' |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
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57 #end if |
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1
fe733f05c2f8
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 9142693589056424fb64869b69dbc08b179f57ee
iuc
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58 |
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0
09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
parents:
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59 #*====================================== |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
parents:
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60 Output options |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
parents:
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61 ======================================*# |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
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62 -e $output_option.extra |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
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63 -o output |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
parents:
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64 $output_option.nohtml |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
parents:
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65 #*====================================== |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
parents:
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66 Advanced options |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
parents:
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67 ======================================*# |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
parents:
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68 #if $advanced_option.controls |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
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69 --controls '$advanced_option.controls' |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
parents:
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70 #end if |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
parents:
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71 #if $advanced_option.scoring |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
parents:
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72 --scoring '$advanced_option.scoring' |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
parents:
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73 #else |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
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changeset
|
74 --scoring '$default_scoring' |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
parents:
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changeset
|
75 #end if |
|
09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
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76 #if $advanced_option.minscore_value |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
parents:
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77 --minscore '$advanced_option.minscore_value' |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
parents:
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changeset
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78 #end if |
|
09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
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79 #if $advanced_option.mintaxa |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
parents:
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changeset
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80 --mintaxa '$advanced_option.mintaxa' |
|
09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
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changeset
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81 #end if |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
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82 #if $advanced_option.exclude_taxa_name |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
parents:
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83 --exclude '$advanced_option.exclude_taxa_name' |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
parents:
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changeset
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84 #end if |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
parents:
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85 #if $advanced_option.include_taxa_name |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
parents:
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changeset
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86 --include '$advanced_option.include_taxa_name' |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
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changeset
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87 #end if |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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88 $advanced_option.avoidcross |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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89 #*====================================== |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
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90 More advanced options |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
parents:
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91 ======================================*# |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
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92 #if $more_advanced_option.ctrlminscore |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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93 --ctrlminscore '$more_advanced_option.ctrlminscore' |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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94 #end if |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
parents:
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95 #if $more_advanced_option.ctrlmintaxa |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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96 --ctrlmintaxa '$more_advanced_option.ctrlmintaxa' |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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97 #end if |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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98 --summary $more_advanced_option.summary |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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99 $more_advanced_option.takeoutroot |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
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100 $more_advanced_option.nokollapse |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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101 $more_advanced_option.strain |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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102 $more_advanced_option.sequential |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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103 #*====================================== |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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104 Log file output |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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105 ======================================*# |
|
1
fe733f05c2f8
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 9142693589056424fb64869b69dbc08b179f57ee
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106 | tee "$logfile" |
|
0
09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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107 ]]> |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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108 </command> |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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109 <inputs> |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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110 <!-- INPUT FILES --> |
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1
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 9142693589056424fb64869b69dbc08b179f57ee
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111 <param name="input_file" type="data" format="tabular" multiple="true" optional="false" label="Select taxonomy file tabular formated"/> |
|
0
09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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112 <conditional name="file_type"> |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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113 <param name="filetype" type="select" display="radio" label="Type of input file (Centrifuge, CLARK, Generic, Kraken, LMAT)" help="(-f, -r, -g, -k, -l)"> |
|
09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
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114 <option value="centrifuge">Centrifuge</option> |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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115 <option value="clark">CLARK</option> |
|
09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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116 <option value="generic">Generic</option> |
|
09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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117 <option value="lmat" >LMAT</option> |
|
09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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|
118 <option value="kraken" >Kraken</option> |
|
09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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119 </param> |
|
09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
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120 <when value="centrifuge"/> |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
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121 <when value="lmat"/> |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
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122 <when value="clark"/> |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
parents:
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changeset
|
123 <when value="kraken"/> |
|
09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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124 <when value="generic"> |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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125 <param argument="--format" type="text" label="Format of the output files from a generic classifier" |
|
09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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126 help="string like 'TYP:csv,TID:1,LEN:3,SCO:6,UNC:0' |
|
09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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127 where valid file Types are csv/tsv/ssv, and the rest of fields indicate the number of column used (starting in 1) |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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|
128 for the TaxIDs assigned,the LENgth of the read, the SCOre given to the assignment"> |
|
09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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129 </param> |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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130 </when> |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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131 </conditional> |
|
09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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132 <!-- taxa databases --> |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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133 <section name="database" title="Database type" expanded="true"> |
|
09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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134 <param name="database_name" type="select" label="Cached database whith taxa ID"> |
|
09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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parents:
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135 <options from_data_table="ncbi_taxonomy"> |
|
09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
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|
136 <validator message="No NCBI database is available" type="no_options"/> |
|
09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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|
137 </options> |
|
09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
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138 </param> |
|
09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
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139 </section> |
|
09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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140 <!-- output name --> |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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|
141 <section name="output_option" title="Output options"> |
|
09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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142 <param argument="--extra" type="select" label="Type of extra output to be generated (default on CSV)" help="Default : CSV"> |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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143 <option value="CSV" selected="true" >CSV</option> |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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144 <option value="DYNOMICS">DYNOMICS</option> |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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145 <option value="FULL">FULL</option> |
|
09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
iuc
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146 <option value="TSV" >TSV</option> |
|
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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147 </param> |
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148 <param argument="--nohtml" type="boolean" truevalue="--nohtml" falsevalue="" label="Suppress saving the HTML output file" help="remove html output"/> |
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149 <param name="no_logfile" type="boolean" truevalue="True" falsevalue="False" label="Remove the log file"/> |
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150 </section> |
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151 <!-- ADVANCED OPTIONS --> |
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152 <section name="advanced_option" title="Coarse tuning of algorithm parameters"> |
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153 <param name="controls" type="integer" optional="true" value="0" label="Number of first samples will be treated as negative controls" help="Add control samples (default is 0)"/> |
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154 <param name="scoring" type="select" optional="true" label="Type of scoring to be applied" help="Scoring algorithm, depending of the input files, see the help section of the tools"> |
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155 <option value="SHEL">SHEL</option> |
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156 <option value="LENGTH">LENGTH</option> |
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157 <option value="LOGLENGTH">LOGLENGTH</option> |
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158 <option value="NORMA">NORMA</option> |
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159 <option value="LMAT">LMAT (only for LMAT input)</option> |
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160 <option value="CLARK_C">CLARK_C (only for Clark input)</option> |
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161 <option value="CLARK_G">CLARK_G (only for Clark input)</option> |
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162 <option value="KRAKEN">KRAKEN (only for kraken input)</option> |
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163 <option value="GENERIC">GENERIC (only for generic input)</option> |
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164 </param> |
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165 <param name="minscore_value" type="integer" optional="true" min="0" value="0" label="Minimum score/confidence of the classification of a |
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166 read to pass the quality filter" help="All pass by default (--minscore)"/> |
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167 <param name="mintaxa" type="integer" optional="true" min="0" value="0" label="Minimum taxa to avoid collapsing one level into the |
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168 parent" help="If not specified a value will be automatically |
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169 assigned (--mintaxa)"/> |
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170 <param name="exclude_taxa_name" argument="--exclude" type="text" optional="true" label="NCBI taxid code to exclude a taxon and all underneath" help="Default: no exclude"> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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171 <sanitizer invalid_char=""> |
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172 <valid initial="string.letters,string.digits"> |
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173 <add value="," /> |
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174 </valid> |
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175 </sanitizer> |
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176 <validator type="regex">[A-Za-z0-9,]+</validator> |
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177 </param> |
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178 <param name="include_taxa_name" argument="--include" type="text" optional="true" label="NCBI taxid code to include a taxon and all underneath" help="Default: all included"> |
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179 <sanitizer invalid_char=""> |
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180 <valid initial="string.letters,string.digits"> |
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181 <add value="," /> |
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182 </valid> |
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183 </sanitizer> |
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184 <validator type="regex">[A-Za-z0-9,]+</validator> |
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185 </param> |
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186 <param argument="--avoidcross" type="boolean" truevalue="--avoidcross" falsevalue="" label="Avoid cross analysis" help="Default: no"/> |
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187 </section> |
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188 <!-- Detailed more fine parameters --> |
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189 <section name="more_advanced_option" title=" Fine tuning of algorithm parameters"> |
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190 <param argument="--ctrlminscore" type="integer" optional="true" value="0" label="Minimum score in control samples to pass the filter" help="Minimum score/confidence of the classification of a read in control samples to pass the quality filter; it defaults to minscore"/> |
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191 <param argument="--ctrlmintaxa" type="integer" optional="true" value="0" label="Minimum taxa to avoid collapsing one level into the parent" help="If not specified a value will be automatically assigned"/> |
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192 <param argument="--summary" type="select" label="Add a summary of the analysis (default is Add)" help="Select to 'add' summary samples to other samples, or to 'only' show summary samples or to 'avoid' summaries at all"> |
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193 <option value="ADD" selected="true">Add</option> |
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194 <option value="ONLY">Only</option> |
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195 <option value="AVOID">Avoid</option> |
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196 </param> |
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197 <param argument="--takeoutroot" type="boolean" truevalue="--takeoutroot" falsevalue="" label="Remove counts directly assigned to the root level"/> |
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198 <param argument="--nokollapse" type="boolean" truevalue="--nokollapse" falsevalue="" label="Show the cellular organisms taxon" /> |
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199 <param argument="--strain" type="boolean" truevalue="--strain" falsevalue="" label="Strain level instead of species as the resolution limit for the robust contamination removal algorithm; use with caution, this is an experimental feature"/> |
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200 <param argument="--sequential" type="boolean" truevalue="--sequential" falsevalue="" label="Deactivate parallel processing"/> |
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201 </section> |
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202 </inputs> |
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203 <!-- OUTPUT FILE, TYPE DEPENDING ON extra PARAMETER --> |
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204 <outputs> |
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205 <data name="html_report" format="html" from_work_dir="output.rcf.html" label="${tool.name} on ${on_string}: html report"> |
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206 <filter> output_option['nohtml'] == False</filter> |
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207 </data> |
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1
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208 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log file"> |
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209 <filter> output_option['no_logfile'] == False </filter> |
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210 </data> |
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0
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211 <data name="data_csv" format="tabular" from_work_dir="output.rcf.data.csv" label="${tool.name} on ${on_string}: data.csv"> |
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212 <filter> output_option['extra'] == 'CSV' </filter> |
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213 </data> |
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214 <data name="stat_csv" format="tabular" from_work_dir="output.rcf.stat.csv" label="${tool.name} on ${on_string}: stat.csv"> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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215 <filter> output_option['extra'] == 'CSV' </filter> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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216 </data> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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217 <data name="data_tsv" format="tabular" from_work_dir="output.rcf.data.tsv" label="${tool.name} on ${on_string}: data tsv"> |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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218 <filter> output_option['extra'] == 'TSV' </filter> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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219 </data> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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220 <data name="stat_tsv" format="tabular" from_work_dir="output.rcf.stat.tsv" label="${tool.name} on ${on_string}: stat tsv"> |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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221 <filter> output_option['extra'] == 'TSV' </filter> |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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222 </data> |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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223 <data name="xls_report" format="xlsx" from_work_dir="output.rcf.xlsx" label="${tool.name} on ${on_string}: xlsx report"> |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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224 <filter> output_option['extra'] == 'FULL' or output_option['extra'] == 'DYNOMICS'</filter> |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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225 </data> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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226 </outputs> |
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227 <tests> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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228 <test expect_num_outputs="4"> <!-- kraken input and CSV output TEST_1--> |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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229 <section name="database"> |
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09b7b0b2e2c2
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230 <param name="database_name" value="test-db-2022"/> |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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231 </section> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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232 <param name="input_file" value="kraken_test/kraken.out"/> |
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09b7b0b2e2c2
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233 <conditional name="file_type"> |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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234 <param name="filetype" value="kraken"/> |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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235 </conditional> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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236 <section name="output_option"> |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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237 <param name="output_type" value="default_type"/> |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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238 </section> |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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239 <section name="more_advanced_option"> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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240 <param name="summary" value="AVOID"/> |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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241 </section> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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242 <output name="data_csv" file="kraken_test/test1_csv.rcf.data.csv" lines_diff="2"/> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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243 <output name="stat_csv" file="kraken_test/test1_csv.rcf.stat.csv" lines_diff="2"/> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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244 <output name="html_report" file="kraken_test/test1_csv.rcf.html" lines_diff="2"/> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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245 <output name="logfile" file="kraken_test/test1_csv.log" lines_diff="12"/> |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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246 </test> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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247 <test expect_num_outputs="3"> <!-- centrifuge input and full options with imported database TEST_2 --> |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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248 <section name="database"> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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249 <param name="database_name" value="test-db-2022"/> |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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250 </section> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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251 <param name="input_file" value="centrifuge_test/centrifuge.out"/> |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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252 <conditional name="file_type"> |
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09b7b0b2e2c2
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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253 <param name="filetype" value="centrifuge"/> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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254 </conditional> |
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255 <section name="output_option"> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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256 <param name="extra" value="CSV"/> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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257 <param name="nohtml" value="true"/> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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258 </section> |
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259 <section name="advanced_option"> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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260 <param name="controls" value="0"/> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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261 <param name="scoring" value="NORMA"/> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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262 <param name="minscore_value" value="1"/> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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263 <param name="avoidcross" value="true"/> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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264 </section> |
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265 <section name="more_advanced_option"> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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266 <param name="ctrlminscore" value="1"/> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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267 <param name="summary" value="AVOID"/> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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268 </section> |
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269 <output name="stat_csv" file="centrifuge_test/test2_csv.rcf.stat.csv" lines_diff="2"/> |
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270 <output name="data_csv" file="centrifuge_test/test2_csv.rcf.data.csv" lines_diff="2"/> |
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271 <output name="logfile" file="centrifuge_test/test2_csv.log" lines_diff="12"/> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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272 </test> |
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273 <test expect_num_outputs="3"> <!-- kraken input cached DB several option added TEST_3 --> |
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274 <section name="database"> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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275 <param name="database_name" value="test-db-2022"/> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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276 </section> |
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277 <param name="input_file" value="kraken_test/kraken.out"/> |
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278 <conditional name="file_type"> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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279 <param name="filetype" value="kraken"/> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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280 </conditional> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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281 <section name="output_option" > |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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282 <param name="extra" value="TSV"/> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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283 <param name="nohtml" value="true"/> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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284 </section> |
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285 <section name="advanced_option"> |
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286 <param name="scoring" value="LOGLENGTH"/> |
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287 </section> |
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288 <section name="more_advanced_option"> |
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289 <param name="summary" value="ONLY"/> |
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290 <param name="strain" value="true"/> |
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291 </section> |
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292 <output name="data_tsv" file="kraken_test/test3_rcf.data.tsv" lines_diff="2"/> |
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293 <output name="stat_tsv" file="kraken_test/test3_rcf.stat.tsv" lines_diff="2"/> |
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294 <output name="logfile" file="kraken_test/test3_tsv.log" lines_diff="12"/> |
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295 </test> |
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296 <test expect_num_outputs="3"> <!-- Test sumarized output TEST_4 --> |
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297 <section name="database"> |
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298 <param name="database_name" value="test-db-2022"/> |
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299 </section> |
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300 <param name="input_file" value="centrifuge_test/centrifuge.out,centrifuge_test/centrifuge_1.out,centrifuge_test/centrifuge_2.out"/> |
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301 <conditional name="file_type"> |
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302 <param name="filetype" value="centrifuge"/> |
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303 </conditional> |
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304 <section name="output_option" > |
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305 <param name="extra" value="TSV"/> |
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306 <param name="no_logfile" value="True"/> |
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307 </section> |
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308 <section name="advanced_option"> |
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309 <param name="scoring" value="LENGTH"/> |
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310 </section> |
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311 <section name="more_advanced_option"> |
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312 <param name="summary" value="ADD"/> |
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313 <param name="strain" value="true"/> |
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314 </section> |
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315 <output name="data_tsv" file="centrifuge_test/test4_rcf.data.tsv" lines_diff="2"/> |
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316 <output name="stat_tsv" file="centrifuge_test/test4_rcf.stat.tsv" lines_diff="2"/> |
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317 <output name="html_report" file="centrifuge_test/test4_tsv.html" lines_diff="12"/> |
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318 </test> |
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319 </tests> |
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320 <help><![CDATA[ |
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321 **What it does** |
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322 |
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323 With Recentrifuge, researchers can interactively explore what organisms are in their samples and at which level of confidence, enabling robust comparative analysis of multiple samples in any metagenomic study. |
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324 |
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325 * Removes diverse contaminants, including crossovers, using a novel robust contamination removal algorithm. |
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326 * Provides a confidence level for every result, since the calculated score propagates to all the downstream analysis and comparisons. |
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327 * Unveils the generalities and specificities in the metagenomic samples, thanks to a new comparative analysis engine. |
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328 |
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329 |
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330 Recentrifuge is especially useful when a more reliable detection of minority organisms is needed (e.g. in the case of low microbial biomass metagenomic studies) |
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331 in clinical, environmental, or forensic analysis. Beyond the standard confidence levels, Recentrifuge implements others devoted to variable length reads, |
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332 very convenient for complex datasets generated by nanopore sequencers. |
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333 |
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334 **Input option** |
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335 Recentrifuge can deal with some different taxonomic output files. |
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336 Input files can come from centrifuge, kraken, clark of lmat software. |
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337 A generic fonction to accept other files is available but need to add information of the file content. |
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338 If generic is choose, the option format need a string like : 'TYP:csv,TID:1,LEN:3,SCO:6,UNC:0'. |
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339 Where TYP are csv/tsv/ssv, and the rest of fields indicate the number of column used (starting in 1) |
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340 for the TaxIDs assigned,the LENgth of the read, the SCOre given to the assignment" |
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341 |
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342 |
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343 **Database for recentrifuge** |
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344 Recentrifuge first need the taxonomic database from NCBI (nodes.dmp and names.dmp). |
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345 We also provide the option to directly load necessary files from history as a dataset list. |
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346 1. cached for already installed taxonomic databases |
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347 2. history to load from your history |
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348 |
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349 |
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350 **Output options** |
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351 1. Depending of the option provided, the file output format can be csv, tsv or xlsx and be combine in one or more files (extra). |
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352 3. By default a html file is generated to visualize data, could be remove using the nohtml option |
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353 |
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354 |
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355 **Advanced options** |
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356 1. Recentrifuge can integrate sample in the data which are negative control to normalize the data |
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357 2. Scoring is an option to choose the score method for the read classified by taxonomic tools : |
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358 SHEL (Single Hit Equivalent Length): This is a score value in pair bases roughly equivalent to a single hit to the database. |
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359 KRAKEN: This scoring scheme is only available for this classifier. It divides the k-mer hit count of the top assignment by the total k-mers in the read and multiplies the result by 100 to give a percentage of coverage (the fraction of the read k-mers covered by k-mers belonging to the read final assignment). This is the default scoring scheme for Kraken samples, and it supports the mixing of samples with different read length. |
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360 LENGTH: The score of a read will be its length (or the combined length of mate pairs). |
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361 LOGLENGTH: Logarithm (base 10) of the length score. |
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362 NORMA: This score is the normalized score SHEL / LENGTH in percentage, so it takes into account both the assignment quality and the length of the read. Very useful when both the score assignments and lengths are variable among the reads. |
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363 LMAT: This scoring scheme is only available for this classifier. |
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364 CLARK_C: This scoring scheme is not available for other classifiers. It takes the confidence score as the score for a read, conf=h1/(h1+h2), or 1-conf=h2/(h1+h2) in case the majority of a read is not classified (1st assignment unclassified). See CLARK's README file for details on how h1 and h2 are calculated. If you use this scoring, you will probably want to filter to a minimum of 0.5 (-y 0.5) or beyond, as under 0.5 the assignments have very low confidence. |
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365 CLARK_G: This scheme scores every read with its CLARK gamma score, so it is only available for this classifier. |
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366 3. You can choose a filter for read quality using the minscore option (--minscore) |
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367 4. You can include or exclude specific taxa using the NCBI taxid code |
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368 |
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369 |
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370 **More advanced options** |
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371 1. You can choose a filter for read quality specifically on the control samples |
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372 2. You cans specify the minimum taxa value to avoid collapsing one level into parent |
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373 3. A summary option is available produce a summary file |
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374 Some other options are available and explicite in the more advanced panel of the tool |
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375 |
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376 |
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377 rcf - Release 1.8.1 - Mar 2022 |
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378 |
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379 Copyright (C) 2017–2022, Jose Manuel Martí Martínez |
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380 |
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381 This program is free software: you can redistribute it and/or modify |
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382 it under the terms of the GNU Affero General Public License as |
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383 published by the Free Software Foundation, either version 3 of the |
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384 License, or (at your option) any later version. |
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385 |
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386 This program is distributed in the hope that it will be useful, |
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387 but WITHOUT ANY WARRANTY; without even the implied warranty of |
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388 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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389 GNU Affero General Public License for more details. |
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390 |
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391 You should have received a copy of the GNU Affero General Public License |
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392 along with this program. If not, see <https://www.gnu.org/licenses/>. |
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393 ]]></help> |
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394 <expand macro="citations"/> |
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395 </tool> |