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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 13abac83068b126399ec415141007a48c2efaa84
author iuc
date Fri, 10 Nov 2023 20:49:03 +0000
parents 4d561bdc2c31
children
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1 <?xml version="1.0"?>
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2 <macros>
2
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3 <token name="@TOOL_VERSION@">2.0.2</token>
0
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4 <token name="@VERSION_SUFFIX@">0</token>
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5 <token name="@PROFILE@">21.01</token>
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6 <xml name="biotools">
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7 <xrefs>
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8 <xref type="bio.tools">semibin</xref>
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9 </xrefs>
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10 </xml>
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11 <xml name="requirements">
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12 <requirements>
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13 <requirement type="package" version="@TOOL_VERSION@">semibin</requirement>
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14 <yield/>
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15 </requirements>
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16 </xml>
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17 <xml name="version">
2
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18 <version_command>SemiBin2 -v</version_command>
0
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19 </xml>
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20 <xml name="mode_fasta_bam">
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21 <conditional name="mode">
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22 <expand macro="mode_select"/>
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23 <when value="single">
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24 <expand macro="input-fasta-single"/>
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25 <expand macro="input-bam-single"/>
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26 </when>
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27 <when value="co">
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28 <expand macro="input-fasta-single"/>
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29 <expand macro="input-bam-multi"/>
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30 </when>
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31 <when value="multi">
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32 <expand macro="input-fasta-multi"/>
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33 <expand macro="input-bam-multi"/>
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34 </when>
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35 </conditional>
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36 </xml>
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37 <xml name="mode_fasta">
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38 <conditional name="mode">
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39 <expand macro="mode_select"/>
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40 <when value="single">
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41 <expand macro="input-fasta-single"/>
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42 </when>
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43 <when value="co">
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44 <expand macro="input-fasta-single"/>
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45 </when>
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46 <when value="multi">
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47 <expand macro="input-fasta-multi"/>
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48 </when>
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49 </conditional>
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50 </xml>
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51 <xml name="mode_select">
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52 <param name="select" type="select" label="Binning mode">
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53 <option value="single" selected="true">Single sample binning (each sample is assembled and binned independently)</option>
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54 <option value="co">Co-assembly binning (samples are co-assembled together and binned together)</option>
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55 <option value="multi">Multi-sample binning (multiple samples are assembled and binned individually, but information from multiple samples is used together)</option>
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56 </param>
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57 </xml>
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58 <xml name="input-fasta-single">
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59 <param argument="--input-fasta" type="data" format="fasta,fasta.gz" label="Contig sequences"/>
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60 </xml>
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61 <xml name="input-fasta-multi">
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62 <conditional name="multi_fasta">
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63 <param name="select" type="select" label="Contig files of the samples">
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64 <option value="concatenated" selected="true">1 concatenated file (created using the dedicated tool) with all sample contigs </option>
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65 <option value="multi">1 contig file per sample</option>
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66 </param>
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67 <when value="concatenated">
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68 <param argument="--input-fasta" type="data" format="fasta,fasta.gz" label="Combined contig sequences"/>
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69 <expand macro="separator"/>
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70 </when>
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71 <when value="multi">
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72 <param argument="--input-fasta" type="data" multiple="true" format="fasta,fasta.gz" label="Contig sequences"/>
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73 <expand macro="concat_min_len"/>
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74 </when>
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75 </conditional>
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76 </xml>
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77 <xml name="concat_min_len">
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78 <param name="min_len" type="integer" min="0" value="0" label="Minimal length for contigs to be kept"/>
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79 </xml>
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80 <token name="@SINGLE_FASTA_FILES@"><![CDATA[
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81 #if $input_fasta.ext.endswith(".gz")
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82 gunzip -c '$input_fasta' > 'contigs.fasta' &&
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83 #else
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84 ln -s '$input_fasta' 'contigs.fasta' &&
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85 #end if
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
86 ]]></token>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
87 <token name="@FASTA_FILES@"><![CDATA[
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
88 #if $mode.select == 'single' or $mode.select == 'co'
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
89 #if $mode.input_fasta.ext.endswith(".gz")
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
90 gunzip -c '$mode.input_fasta' > 'contigs.fasta' &&
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
91 #else
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
92 ln -s '$mode.input_fasta' 'contigs.fasta' &&
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
93 #end if
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
94 #else
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
95 #if $mode.multi_fasta.select == 'concatenated'
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
96 #if $mode.multi_fasta.input_fasta.ext.endswith(".gz")
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
97 gunzip -c '$mode.multi_fasta.input_fasta' > 'contigs.fasta' &&
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
98 #else
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
99 ln -s '$mode.multi_fasta.input_fasta' 'contigs.fasta' &&
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
100 #end if
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
101 #set $separator = $mode.multi_fasta.separator
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
102 #else
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
103 #for $e in $mode.multi_fasta.input_fasta
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
104 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($e.element_identifier))
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
105 #if $e.ext.endswith(".gz")
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
106 gunzip -c '$e' > '${identifier}.fasta' &&
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
107 #else
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
108 ln -s '$e' '${identifier}.fasta' &&
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
109 #end if
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
110 #end for
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
111 #set $separator = ':'
2
dbf5571a8140 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 13abac83068b126399ec415141007a48c2efaa84
iuc
parents: 1
diff changeset
112 SemiBin2 concatenate_fasta
0
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
113 --input-fasta *.fasta
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
114 --output 'output'
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
115 --separator '$separator'
2
dbf5571a8140 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 13abac83068b126399ec415141007a48c2efaa84
iuc
parents: 1
diff changeset
116 --compression none
0
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
117 -m $mode.multi_fasta.min_len
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
118 &&
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
119 ln -s 'output/concatenated.fa' 'contigs.fasta' &&
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
120 #end if
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
121 #end if
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
122 ]]></token>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
123 <xml name="separator">
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
124 <param argument="--separator" type="text" value=":" label="Separator in the contig file between sample name and contig name"/>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
125 </xml>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
126 <xml name="input-bam-single">
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
127 <param argument="--input-bam" type="data" format="bam" label="Read mapping to the contigs" help="Sorted BAM files"/>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
128 </xml>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
129 <xml name="input-bam-multi">
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
130 <param argument="--input-bam" type="data" format="bam" multiple="true" label="Read mapping to the contigs" help="One file per sample, sorted BAM files"/>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
131 </xml>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
132 <token name="@BAM_FILES@"><![CDATA[
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
133 #if $mode.select == 'single'
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
134 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($input_bam.element_identifier))
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
135 ln -s '$input_bam' '${identifier}.bam' &&
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
136 #else
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
137 #for $e in $input_bam
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
138 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($e.element_identifier))
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
139 ln -s '$e' '${identifier}.bam' &&
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
140 #end for
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
141 #end if
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
142 ]]></token>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
143 <xml name="ref_select">
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
144 <param name="select" type="select" label="Reference database">
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
145 <option value="cached" selected="true">Cached database</option>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
146 <option value="taxonomy">Pre-computed taxonomy</option>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
147 </param>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
148 </xml>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
149 <xml name="cached_db">
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
150 <param name="cached_db" label="Cached databases" type="select">
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
151 <options from_data_table="gtdb">
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
152 <validator message="No GTDB database is available" type="no_options" />
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
153 </options>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
154 </param>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
155 </xml>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
156 <xml name="ref-single">
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
157 <conditional name="ref">
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
158 <expand macro="ref_select"/>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
159 <when value="cached">
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
160 <expand macro="cached_db"/>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
161 </when>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
162 <when value="taxonomy">
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
163 <param argument="--taxonomy-annotation-table" type="data" format="tabular" label="Pre-computed mmseqs2 format taxonomy TSV file"/>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
164 </when>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
165 </conditional>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
166 </xml>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
167 <xml name="ref-multi">
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
168 <conditional name="ref">
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
169 <expand macro="ref_select"/>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
170 <when value="cached">
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
171 <expand macro="cached_db"/>
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172 </when>
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173 <when value="taxonomy">
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174 <param argument="--taxonomy-annotation-table" type="data" format="tabular" multiple="true" label="Pre-computed mmseqs2 format taxonomy TSV file" help="One per bin file"/>
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175 </when>
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176 </conditional>
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177 </xml>
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178 <xml name="ref_single">
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179 <conditional name="ref">
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parents:
diff changeset
180 <expand macro="ref_select"/>
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181 <when value="cached">
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parents:
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182 <expand macro="cached_db"/>
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183 </when>
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184 <when value="taxonomy">
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185 <param argument="--taxonomy-annotation-table" type="data" format="tabular" label="Pre-computed mmseqs2 format taxonomy TSV file"/>
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186 </when>
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187 </conditional>
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188 </xml>
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189 <xml name="min_len">
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190 <conditional name="min_len">
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191 <param name="method" type="select" label="Method to set up the minimal length for contigs in binning">
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192 <option value="automatic">Automatic</option>
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193 <option value="min-len">Manual</option>
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194 <option value="ratio">Computation based on ratio of the number of base pairs</option>
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195 </param>
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196 <when value="automatic"/>
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197 <when value="min-len">
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198 <param argument="--min-len" type="integer" min="0" value="0" label="Minimal length for contigs in binning"/>
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199 </when>
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parents:
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200 <when value="ratio">
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201 <param argument="--ratio" type="float" min="0" max="1" value="0.05" label="Ratio of the number of base pairs of contigs between 1000-2500 bp below which the minimal length will be set as 1000bp, otherwise 2500bp."/>
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202 </when>
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203 </conditional>
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204 </xml>
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205 <token name="@MIN_LEN@"><![CDATA[
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206 #if $min_len.method == 'min-len'
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207 --min-len $min_len.min_len
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208 #else if $min_len.method == 'ratio'
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209 --ratio $min_len.ratio
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210 #end if
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211 ]]></token>
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212 <xml name="random-seed">
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213 <param argument="--random-seed" type="integer" min="0" value="0" label="Random seed to reproduce result"/>
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214 </xml>
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215 <xml name="ml-threshold">
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216 <param argument="--ml-threshold" type="integer" min="0" value="" optional="true" label="Length threshold for generating must-link constraints" help="If no value is given, the threshold is calculated from the contig, and the default minimum value is 4,000 bp."/>
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217 </xml>
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218 <xml name="epoches">
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219 <param argument="--epoches" type="integer" min="0" value="20" label="Number of epoches used in the training process"/>
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220 </xml>
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221 <xml name="batch-size">
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222 <param argument="--batch-size" type="integer" min="0" value="2048" label="Batch size used in the training process"/>
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223 </xml>
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224 <xml name="orf-finder">
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225 <param argument="--orf-finder" type="select" label="ORF finder used to estimate the number of bins">
2
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226 <option value="fast-naive" selected="true">Fast-Naive</option>
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227 <option value="prodigal">Prodigal</option>
0
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228 <option value="fraggenescan">Fraggenescan</option>
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229 </param>
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230 </xml>
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231 <xml name="max-node">
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232 <param argument="--max-node" type="float" min="0" max="1" value="1" label="Fraction of contigs that considered to be binned"/>
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233 </xml>
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234 <xml name="max-edges">
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235 <param argument="--max-edges" type="integer" min="0" value="200" label="Maximum number of edges that can be connected to one contig"/>
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236 </xml>
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237 <xml name="environment">
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238 <param argument="--environment" type="select" optional="true" label="Environment for the built-in model">
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239 <option value="" selected="true">None</option>
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240 <option value="human_gut">Human gut</option>
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241 <option value="dog_gut">Dog gut</option>
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242 <option value="ocean">Ocean</option>
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243 <option value="soil">Soil</option>
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244 <option value="cat_gut">Cat gut</option>
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245 <option value="human_oral">Human oral</option>
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246 <option value="mouse_gut">Mouse gut</option>
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247 <option value="pig_gut">Pig gut</option>
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248 <option value="built_environment">Built environment</option>
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249 <option value="wastewater">Wastewater</option>
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250 <option value="global">Global</option>
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251 </param>
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252 </xml>
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253 <xml name="minfasta-kbs">
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254 <param argument="--minfasta-kbs" type="integer" min="0" value="200" label="Miminimum bin size in Kbps"/>
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255 </xml>
2
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256 <xml name="write_pre_reclustering_bins">
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257 <param argument="--write-pre-reclustering-bins" type="boolean" truevalue="--write-pre-reclustering-bins" falsevalue="" checked="false" label="Return also the pre reclustered bins?"/>
0
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258 </xml>
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259 <xml name="data">
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260 <param argument="--data" type="data" format="csv" label="Train data"/>
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261 </xml>
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262 <xml name="data_output_single">
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263 <data name="single_data" format="csv" from_work_dir="output/data.csv" label="${tool.name} on ${on_string}: Training data">
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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264 <filter>mode["select"]=="single" or mode["select"]=="co"</filter>
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265 </data>
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266 <data name="single_data_split" format="csv" from_work_dir="output/data_split.csv" label="${tool.name} on ${on_string}: Split training data">
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267 <filter>mode["select"]=="single" or mode["select"]=="co"</filter>
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268 </data>
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269 </xml>
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270 <xml name="data_output_multi">
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271 <collection name="multi_data" type="list" label="${tool.name} on ${on_string}: Training data per sample">
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272 <filter>mode["select"]=="multi"</filter>
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273 <discover_datasets pattern="(?P&lt;designation&gt;.*)\/data.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/>
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274 </collection>
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275 <collection name="multi_data_split" type="list" label="${tool.name} on ${on_string}: Split training data per sample">
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276 <filter>mode["select"]=="multi"</filter>
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277 <discover_datasets pattern="(?P&lt;designation&gt;.*)\/data_split.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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278 </collection>
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279 </xml>
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280 <xml name="generate_sequence_features_extra_outputs">
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281 <data name="single_cov" format="csv" from_work_dir="output/*_data_cov.csv" label="${tool.name} on ${on_string}: Coverage">
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282 <filter>mode["select"]=="single" and extra_output and "coverage" in extra_output</filter>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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283 </data>
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284 <data name="single_split_cov" format="csv" from_work_dir="output/*_data_split_cov.csv" label="${tool.name} on ${on_string}: Coverage (split data)">
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285 <filter>mode["select"]=="single" and extra_output and "coverage" in extra_output</filter>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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286 </data>
1
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287 <collection name="co_cov" type="list" label="${tool.name} on ${on_string}: Coverage (co_cov)">
0
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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288 <filter>mode["select"]=="co" and extra_output and "coverage" in extra_output</filter>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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289 <discover_datasets pattern=".*\.bam_(?P&lt;designation&gt;.*)_data_cov\.csv" format="csv" directory="output/" />
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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290 </collection>
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291 <collection name="co_split_cov" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample">
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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292 <filter>mode["select"]=="co" and extra_output and "coverage" in extra_output</filter>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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293 <discover_datasets pattern=".*\.bam_(?P&lt;designation&gt;.*)_data_split_cov\.csv" format="csv" directory="output/" />
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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294 </collection>
1
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295 <collection name="multi_cov" type="list" label="${tool.name} on ${on_string}: Coverage (multi_cov)">
0
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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296 <filter>mode["select"]=="multi" and extra_output and "coverage" in extra_output</filter>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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297 <discover_datasets pattern=".*\.bam_(?P&lt;designation&gt;.*)_data_cov.csv" format="csv" directory="output/samples/" />
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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298 </collection>
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299 <collection name="multi_cov_sample" type="list" label="${tool.name} on ${on_string}: Coverage per sample">
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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300 <filter>mode["select"]=="multi" and extra_output and "coverage" in extra_output</filter>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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301 <discover_datasets pattern="(?P&lt;designation&gt;.*)\/data_cov.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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302 </collection>
1
4d561bdc2c31 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
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parents: 0
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303 <collection name="multi_split_cov" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample (multi_split_cov)">
0
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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304 <filter>mode["select"]=="multi" and extra_output and "coverage" in extra_output</filter>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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305 <discover_datasets pattern=".*\.bam_(?P&lt;designation&gt;.*)_data_split_cov.csv" format="csv" directory="output/samples/" />
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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306 </collection>
1
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parents: 0
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307 <collection name="multi_split_cov_sample" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample (multi_split_cov_sample)">
0
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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308 <filter>mode["select"]=="multi" and extra_output and "coverage" in extra_output</filter>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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309 <discover_datasets pattern="(?P&lt;designation&gt;.*)\/data_split_cov.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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310 </collection>
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311 <collection name="multi_contigs" type="list" label="${tool.name} on ${on_string}: Contigs">
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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312 <filter>mode["select"]=="multi" and extra_output and "contigs" in extra_output</filter>
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313 <discover_datasets pattern="(?P&lt;designation&gt;.*).fa" format="fasta" directory="output/samples/" />
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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314 </collection>
2
dbf5571a8140 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 13abac83068b126399ec415141007a48c2efaa84
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315
0
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316 </xml>
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317 <xml name="train_output">
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318 <data name="model" format="h5" from_work_dir="output/model.h5" label="${tool.name} on ${on_string}: Semi-supervised deep learning model" />
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319 </xml>
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320 <xml name="cannot_link_output">
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321 <data name="cannot" format="txt" from_work_dir="output/cannot/cannot.txt" label="${tool.name} on ${on_string}: Cannot-link constraints" />
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322 </xml>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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323 <token name="@HELP_HEADER@"><![CDATA[
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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324 What it does
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325 ============
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326
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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327 SemiBin is a Semi-supervised siamese neural network for metagenomic binning
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328
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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329 ]]></token>
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330 <token name="@HELP_INPUT_FASTA@"><![CDATA[
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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331 - Contigs in fasta for 1 or several samples from single or co-assembly
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332 ]]></token>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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333 <token name="@HELP_INPUT_BAM@"><![CDATA[
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334 - BAM with reads mapping to the contigs
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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335 ]]></token>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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336 <token name="@HELP_CANNOT@"><![CDATA[
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337 - Cannot-link constraints
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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338 ]]></token>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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339 <token name="@HELP_DATA@"><![CDATA[
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340 - Training data and split training data for the model
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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341 ]]></token>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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342 <token name="@HELP_MODEL@"><![CDATA[
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343 - Semi-supervised deep learning model
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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344 ]]></token>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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345 <token name="@HELP_BINS@"><![CDATA[
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346 - Reconstructed bins after reclustering
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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347 - Reconstructed bins before reclustering
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348 ]]></token>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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349 <xml name="citations">
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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350 <citations>
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351 <citation type="doi">10.1038/s41467-022-29843-y</citation>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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352 </citations>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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353 </xml>
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4d561bdc2c31 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
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354 </macros>