Mercurial > repos > iuc > jellyfish

annotate jellyfish.xml @ 1:11658afb8c87 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 173be51ac6f23888ad4065877762b67e4cc9ed6e
author iuc
date Wed, 01 Nov 2023 09:32:45 +0000
parents b4038a4d48f5
children dcd30574a456
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
1 <tool id="jellyfish" name="jellyfish" version="@WRAPPER_VERSION@+@VERSION_SUFFIX@" profile="20.01">
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
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2 <macros>
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
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3 <token name="@WRAPPER_VERSION@">2.3.0</token>
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
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4 <token name="@VERSION_SUFFIX@">galaxy0</token>
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
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5 </macros>
1
11658afb8c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 173be51ac6f23888ad4065877762b67e4cc9ed6e
iuc
parents: 0
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6 <xrefs>
11658afb8c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 173be51ac6f23888ad4065877762b67e4cc9ed6e
iuc
parents: 0
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7 <xref type="bio.tools">Jellyfish</xref>
11658afb8c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 173be51ac6f23888ad4065877762b67e4cc9ed6e
iuc
parents: 0
diff changeset
8 </xrefs>
0
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
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9 <requirements>
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
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10 <requirement type="package" version="@WRAPPER_VERSION@">kmer-jellyfish</requirement>
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
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11 </requirements>
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
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12 <command detect_errors="exit_code"><![CDATA[
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
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13 jellyfish
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
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14 #if $commands.command == "count":
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
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15 count
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
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16 --mer-len $commands.mer_len
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
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17 --size $commands.size
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
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18 #if $commands.counter_len:
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
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19 --counter-len $commands.counter_len
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
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20 #end if
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
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21 $commands.canonical
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
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22 #if $commands.bloom.filters == "bc":
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
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23 --bc '$commands.bloom.bloom_file'
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
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24 #if $commands.bloom.bf_fp:
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
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25 --bf-fp $commands.bloom.bf_fp
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
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26 #end if
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
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27 #else if $commands.bloom.filters == "bf_size":
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
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28 --bf-size $commands.bloom.bf_size
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
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29 #if $commands.bloom.bf_fp:
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
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30 --bf-fp $commands.bloom.bf_fp
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
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31 #end if
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
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32 #end if
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
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33 #if $commands.if:
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
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34 --if '$commands.if'
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
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35 #end if
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
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36 #if $commands.reprobes:
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
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37 --reprobes $commands.reprobes
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
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38 #end if
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
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39 #if $commands.text == "text":
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
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40 --text
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
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41 #end if
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
42 #if $commands.lower_count:
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
43 --lower-count $commands.lower_count
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
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44 #end if
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
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diff changeset
45 #if $commands.upper_count:
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
46 --upper-count $commands.upper_count
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
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47 #end if
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
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48 '$commands.input'
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
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49 #else if $commands.command == "histo":
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
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50 histo
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
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51 #if $commands.low:
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
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52 --low $commands.low
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
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53 #end if
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
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54 #if $commands.high:
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
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55 --high $commands.high
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
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56 #end if
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
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57 #if $commands.increment:
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
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58 --increment $commands.increment
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
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59 #end if
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
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60 $commands.full
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
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61 '$commands.input'
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
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62 -o jellyfish_histo.txt
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
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63 #else if $commands.command == "dump":
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
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64 dump
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
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65 #if $commands.lower_count:
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
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66 --lower-count $commands.lower_count
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
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67 #end if
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
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68 #if $commands.upper_count:
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
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69 --upper-count $commands.upper_count
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
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70 #end if
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
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71 #if $commands.format.format_select == "column":
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
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72 --column
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
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73 $commands.format.tab
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
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74 '$commands.input'
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
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75 #if $commands.format.tab == "--tab":
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
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76 -o jellyfish_dump.tsv
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
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77 #else:
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
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78 -o jellyfish_dump.txt
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
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79 #end if
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
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80 #else:
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
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81 '$commands.input'
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
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82 -o jellyfish_dump.fasta
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
83 #end if
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
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84 ## #else if $commands.command == "bc":
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
85 ## #else if $commands.command == "info":
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
86 ## #else if $commands.command == "stats":
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
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87 ## #else if $commands.command == "merge":
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
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88 ## #else if $commands.command == "query":
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
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89 #end if
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90 ]]></command>
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91 <inputs>
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92 <conditional name="commands">
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93 <param name="command" type="select" label="Jellyfish command: ">
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94 <option value="count"/>
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95 <option value="histo"/>
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96 <option value="dump"/>
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97 <!-- <option value="bc"/>
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98 <option value="info"/>
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99 <option value="stats"/>
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100 <option value="merge"/>
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101 <option value="query"/> -->
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102 </param>
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103 <when value="count">
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104 <param name="input" type="data" format="fasta,fastq,fastqsanger" label="Input data file"/>
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105 <param argument="--mer-len" type="integer" value="20" min="1" label="Length of mer" />
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106 <param argument="--size" type="integer" value="32" min="1" label="Initial hash size" />
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107 <param argument="--counter-len" type="integer" min="1" optional="true" label="Counter Length in bits" />
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108 <param argument="--canonical" type="boolean" truevalue="--canonical" falsevalue="" label="Count both strand and canonical representation" />
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109 <conditional name="bloom">
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110 <param name="filters" type="select" label="Use bloom filters">
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111 <option value="default">Default</option>
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112 <option value="bc">Bloom counter to filter out singleton mers</option>
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113 <option value="bf_size">Use bloom filter to count high-frequency mers</option>
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114 </param>
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115 <when value="default"/>
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116 <when value="bc">
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117 <param name="bloom_file" type="data" format="tabular,tsv" label="Bloom counter file"/>
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118 <param argument="--bf-fp" type="float" label="False positive rate of bloom filter" optional="true"/>
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119 </when>
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120 <when value="bf_size">
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121 <param name="bf_size" argument="--bf-size" type="integer" label="Use bloom filter to count high-frequency mers" min="1" optional="true"/>
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122 <param argument="--bf-fp" type="float" label="False positive rate of bloom filter" optional="true"/>
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123 </when>
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124 </conditional>
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125 <param argument="--if" type="data" format="txt" label="Count only k-mers in this file" optional="true"/>
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126 <param argument="--reprobes" type="integer" label="Maximum number of repropbes" min="1" optional="true"/>
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127 <param argument="--text" type="boolean" label="Dump in text format" truevalue="text" falsevalue="jf"/>
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128 <param argument="--lower-count" type="integer" label="Lower count" min="1" optional="true" help="Don't output k-mer with count less than this value"/>
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129 <param argument="--upper-count" type="integer" label="upper count" min="1" optional="true" help="Don't output k-mer with count greater than this value"/>
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130 </when>
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131 <when value="histo">
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132 <param name="input" type="data" format="jellyfish" label="Input data file"/>
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133 <param argument="--low" type="integer" min="1" label="Lower count value of histogram" optional="true"/>
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134 <param argument="--high" type="integer" min="1" label="Upper count value of histogram" optional="true"/>
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135 <param argument="--increment" type="integer" min="1" label="Increment value for buckets" optional="true"/>
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136 <param argument="--full" type="boolean" label="Full histogram. Don't skip count 0" truevalue="--full" falsevalue=""/>
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137 </when>
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138 <when value="dump">
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139 <param name="input" type="data" format="jellyfish" label="Input data file"/>
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140 <conditional name="format">
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141 <param name="format_select" type="select" label="Output format">
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142 <option value="fasta"/>
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143 <option value="column"/>
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144 </param>
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145 <when value="fasta"/>
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146 <when value="column">
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147 <param argument="--tab" type="boolean" label="Use tab separator" truevalue="--tab" falsevalue=""/>
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148 </when>
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149 </conditional>
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150 <param argument="--lower-count" type="integer" min="0" optional="true" label="Don't output k-mer with count less than lower-count" />
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151 <param argument="--upper-count" type="integer" min="1" optional="true" label="Don't output k-mer with count greater than upper-count" />
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152 </when>
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153 <!-- <when value="bc">
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154 </when>
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155 <when value="info">
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156
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
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157 </when>
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158 <when value="stats">
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159
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
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160 </when>
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161 <when value="merge">
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162
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
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163 </when>
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164 <when value="query">
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165
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
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166 </when> -->
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167 </conditional>
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168 </inputs>
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169 <outputs>
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170 <data name="jellyfish_db" format="jellyfish" from_work_dir="mer_counts.jf" label="${tool.name} on ${on_string}: jellyfish db">
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171 <filter>commands["command"] == "count" and not commands["text"]</filter>
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172 </data>
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173 <data name="jellyfish_db_txt" format="txt" from_work_dir="mer_counts.jf" label="${tool.name} on ${on_string}: jellyfish db text">
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diff changeset
174 <filter>commands["command"] == "count" and commands["text"]</filter>
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
175 </data>
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
176 <data name="jellyfish_histo" format="txt" from_work_dir="jellyfish_histo.txt" label="${tool.name} on ${on_string}: histogram">
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
177 <filter>commands["command"] == "histo"</filter>
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
178 </data>
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
179 <data name="jellyfish_fasta" format="fasta" from_work_dir="jellyfish_dump.fasta" label="${tool.name} on ${on_string}: fasta dump">
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
180 <filter>commands["command"] == "dump" and commands["format"]["format_select"] == "fasta"</filter>
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
181 </data>
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
182 <data name="jellyfish_txt" format="txt" from_work_dir="jellyfish_dump.txt" label="${tool.name} on ${on_string}: txt dump">
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
183 <filter>commands["command"] == "dump" and commands["format"]["format_select"] == "column" and not commands["format"]["tab"]</filter>
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
184 </data>
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
185 <data name="jellyfish_tsv" format="tsv" from_work_dir="jellyfish_dump.tsv" label="${tool.name} on ${on_string}: tabular dump">
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
186 <filter>commands["command"] == "dump" and commands["format"]["format_select"] == "column" and commands["format"]["tab"]</filter>
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
187 </data>
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
188 </outputs>
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
189 <tests>
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
190 <test expect_num_outputs="1">
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
191 <conditional name="commands">
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
192 <param name="commands" value="count"/>
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
193 <param name="input" value="test.fastq"/>
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
194 <param name="mer_len" value="22"/>
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
195 <param name="size" value="16"/>
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
196 <param name="canonical" value="--canonical"/>
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
197 </conditional>
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
198 <output name="jellyfish_db" file="out.jf" compare="sim_size" delta="1000"/>
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
199 </test>
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
200 <test expect_num_outputs="1">
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
201 <conditional name="commands">
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
202 <param name="commands" value="count"/>
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
203 <param name="input" value="test.fastq"/>
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
204 <param name="mer_len" value="22"/>
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
205 <param name="size" value="16"/>
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
206 <param name="canonical" value="--canonical"/>
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
207 <conditional name="bloom">
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
208 <param name="filters" value="bf_size"/>
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
209 <param name="bf_size" value="2"/>
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
210 <param name="bf_fp" value="0.01"/>
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
211 </conditional>
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
212 <param name="text" value="text"/>
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
213 <param name="lower" value="1"/>
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
214 <param name="upper" value="20"/>
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
215 </conditional>
1
11658afb8c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 173be51ac6f23888ad4065877762b67e4cc9ed6e
iuc
parents: 0
diff changeset
216 <output name="jellyfish_db_txt">
11658afb8c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 173be51ac6f23888ad4065877762b67e4cc9ed6e
iuc
parents: 0
diff changeset
217 <assert_contents>
11658afb8c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 173be51ac6f23888ad4065877762b67e4cc9ed6e
iuc
parents: 0
diff changeset
218 <has_line line="GTGATCGAGAGCCACAGCGTTA 1"/>
11658afb8c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 173be51ac6f23888ad4065877762b67e4cc9ed6e
iuc
parents: 0
diff changeset
219 <has_line line="GCCTAGTCGGGATCGTCACCTA 1"/>
11658afb8c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 173be51ac6f23888ad4065877762b67e4cc9ed6e
iuc
parents: 0
diff changeset
220 </assert_contents>
11658afb8c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 173be51ac6f23888ad4065877762b67e4cc9ed6e
iuc
parents: 0
diff changeset
221 </output>
0
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
222 </test>
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
223 <test expect_num_outputs="1">
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
224 <conditional name="commands">
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
225 <param name="command" value="histo"/>
1
11658afb8c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 173be51ac6f23888ad4065877762b67e4cc9ed6e
iuc
parents: 0
diff changeset
226 <param name="input" value="out.jf" ftype="jellyfish"/>
0
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
227 <param name="low" value="1"/>
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
228 <param name="high" value="10000"/>
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
229 <param name="full" value="--full"/>
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
230 <param name="increment" value="100"/>
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
231 </conditional>
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
232 <output name="jellyfish_histo" ftype="txt" file="histo.txt"/>
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
233 </test>
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
234 <test expect_num_outputs="1">
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
235 <conditional name="commands">
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
236 <param name="command" value="dump"/>
1
11658afb8c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 173be51ac6f23888ad4065877762b67e4cc9ed6e
iuc
parents: 0
diff changeset
237 <param name="input" value="out.jf" ftype="jellyfish"/>
0
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
238 <param name="lower_count" value="3"/>
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
239 </conditional>
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
240 <output name="jellyfish_fasta" ftype="fasta" file="dump.fasta"/>
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
241 </test>
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
242 <test expect_num_outputs="1">
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
243 <conditional name="commands">
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
244 <param name="command" value="dump"/>
1
11658afb8c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 173be51ac6f23888ad4065877762b67e4cc9ed6e
iuc
parents: 0
diff changeset
245 <param name="input" value="out.jf" ftype="jellyfish"/>
0
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
246 <conditional name="format">
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
247 <param name="format_select" value="column"/>
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
248 <param name="tab" value="--tab"/>
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
249 </conditional>
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
250 <param name="upper_count" value="100"/>
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
251 </conditional>
1
11658afb8c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 173be51ac6f23888ad4065877762b67e4cc9ed6e
iuc
parents: 0
diff changeset
252 <output name="jellyfish_tsv" ftype="tsv">
11658afb8c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 173be51ac6f23888ad4065877762b67e4cc9ed6e
iuc
parents: 0
diff changeset
253 <assert_contents>
11658afb8c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 173be51ac6f23888ad4065877762b67e4cc9ed6e
iuc
parents: 0
diff changeset
254 <has_line line="GTGATCGAGAGCCACAGCGTTA&#9;1"/>
11658afb8c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 173be51ac6f23888ad4065877762b67e4cc9ed6e
iuc
parents: 0
diff changeset
255 <has_line line="GCCTAGTCGGGATCGTCACCTA&#9;1"/>
11658afb8c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 173be51ac6f23888ad4065877762b67e4cc9ed6e
iuc
parents: 0
diff changeset
256 </assert_contents>
11658afb8c87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 173be51ac6f23888ad4065877762b67e4cc9ed6e
iuc
parents: 0
diff changeset
257 </output>
0
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
258 </test>
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
259 </tests>
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
parents:
diff changeset
260 <help><![CDATA[
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
iuc
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261 Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. Jellyfish can count k-mers using an order of magnitude less memory and an order of magnitude faster than other k-mer counting packages by using an efficient encoding of a hash table and by exploiting the "compare-and-swap" CPU instruction to increase parallelism.
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
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262
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
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263 JELLYFISH is a command-line program that reads FASTA and multi-FASTA files containing DNA sequences. It outputs its k-mer counts in a binary format, which can be translated into a human-readable text format using the "jellyfish dump" command, or queried for specific k-mers with "jellyfish query". See the documentation for details.
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
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264 ]]></help>
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
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265 <citations>
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
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266 <citation type="doi">10.1093/bioinformatics/btr011</citation>
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
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267 </citations>
b4038a4d48f5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 28e5c48aea5bca6ed90af701616d9fed79b74235"
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268 </tool>