Mercurial > repos > iuc > semibin_generate_sequence_features

annotate macros.xml @ 6:517069eeb0d5 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6
author iuc
date Tue, 28 Oct 2025 08:20:21 +0000
parents 8ba0c2edf3f3
children
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0
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
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diff changeset
1 <?xml version="1.0"?>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
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2 <macros>
5
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
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3 <token name="@TOOL_VERSION@">2.1.0</token>
6
517069eeb0d5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6
iuc
parents: 5
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4 <token name="@VERSION_SUFFIX@">1</token>
5
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
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5 <token name="@PROFILE@">21.01</token>
0
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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6 <xml name="biotools">
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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7 <xrefs>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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8 <xref type="bio.tools">semibin</xref>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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9 </xrefs>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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10 </xml>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
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11 <xml name="requirements">
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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12 <requirements>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
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13 <requirement type="package" version="@TOOL_VERSION@">semibin</requirement>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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14 <yield/>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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15 </requirements>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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16 </xml>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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17 <xml name="version">
2
ff4e487f4f7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 13abac83068b126399ec415141007a48c2efaa84
iuc
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18 <version_command>SemiBin2 -v</version_command>
0
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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19 </xml>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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20 <xml name="mode_fasta_bam">
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
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21 <conditional name="mode">
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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22 <expand macro="mode_select"/>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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23 <when value="single">
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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24 <expand macro="input-fasta-single"/>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
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25 <expand macro="input-bam-single"/>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
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26 </when>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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27 <when value="co">
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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28 <expand macro="input-fasta-single"/>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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29 <expand macro="input-bam-multi"/>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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30 </when>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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31 <when value="multi">
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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32 <expand macro="input-fasta-multi"/>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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33 <expand macro="input-bam-multi"/>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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34 </when>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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35 </conditional>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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36 </xml>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
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37 <xml name="mode_fasta">
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
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38 <conditional name="mode">
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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39 <expand macro="mode_select"/>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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40 <when value="single">
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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41 <expand macro="input-fasta-single"/>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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42 </when>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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43 <when value="co">
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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44 <expand macro="input-fasta-single"/>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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45 </when>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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46 <when value="multi">
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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47 <expand macro="input-fasta-multi"/>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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48 </when>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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49 </conditional>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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50 </xml>
5
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
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51 <xml name="mode_fasta_strobealign">
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
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52 <conditional name="mode">
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
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53 <expand macro="mode_select"/>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
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54 <when value="single">
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
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55 <expand macro="input-fasta-single"/>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
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56 <expand macro="input-txt"/>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
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57 </when>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
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58 <when value="co">
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
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59 <expand macro="input-fasta-single"/>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
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60 <expand macro="input-txt"/>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
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61 </when>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
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62 <when value="multi">
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
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63 <expand macro="input-fasta-multi"/>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
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64 <expand macro="input-txt"/>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
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65 </when>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
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66 </conditional>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
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67 </xml>
0
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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68 <xml name="mode_select">
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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69 <param name="select" type="select" label="Binning mode">
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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70 <option value="single" selected="true">Single sample binning (each sample is assembled and binned independently)</option>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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71 <option value="co">Co-assembly binning (samples are co-assembled together and binned together)</option>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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72 <option value="multi">Multi-sample binning (multiple samples are assembled and binned individually, but information from multiple samples is used together)</option>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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73 </param>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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74 </xml>
5
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
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75 <xml name="bam_or_strobealign">
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
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76 <param name="align_select" type="select" label="Use bam or strobealign abundance files?" help="Strobealign abundance files can only be used when samples used in binning above or equal 5">
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
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77 <option value="bam">BAM</option>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
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78 <option value="txt">Strobealign-aemb file(s)</option>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
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79 </param>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
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80 </xml>
0
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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81 <xml name="input-fasta-single">
6
517069eeb0d5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6
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82 <param argument="--input-fasta" type="data" format="fasta,fasta.gz,fasta.bz2" label="Contig sequences"/>
0
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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83 </xml>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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84 <xml name="input-fasta-multi">
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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85 <conditional name="multi_fasta">
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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86 <param name="select" type="select" label="Contig files of the samples">
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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87 <option value="concatenated" selected="true">1 concatenated file (created using the dedicated tool) with all sample contigs </option>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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88 <option value="multi">1 contig file per sample</option>
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89 </param>
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90 <when value="concatenated">
6
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91 <param argument="--input-fasta" type="data" format="fasta,fasta.gz,fasta.bz2" label="Combined contig sequences"/>
0
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92 <expand macro="separator"/>
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93 </when>
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94 <when value="multi">
6
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95 <param argument="--input-fasta" type="data" multiple="true" format="fasta,fasta.gz,fasta.bz2" label="Contig sequences"/>
0
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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96 <expand macro="concat_min_len"/>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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97 </when>
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98 </conditional>
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99 </xml>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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100 <xml name="concat_min_len">
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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101 <param name="min_len" type="integer" min="0" value="0" label="Minimal length for contigs to be kept"/>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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102 </xml>
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103 <token name="@SINGLE_FASTA_FILES@"><![CDATA[
6
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104 ln -s '$input_fasta' 'contigs.$input_fasta.ext' &&
0
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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105 ]]></token>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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106 <token name="@FASTA_FILES@"><![CDATA[
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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107 #if $mode.select == 'single' or $mode.select == 'co'
6
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108 ln -s '$input_fasta' 'contigs.$input_fasta.ext' &&
0
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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109 #else
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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110 #if $mode.multi_fasta.select == 'concatenated'
6
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111 ln -s '$input_fasta' 'contigs.$input_fasta.ext' &&
0
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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112 #set $separator = $mode.multi_fasta.separator
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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113 #else
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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114 #for $e in $mode.multi_fasta.input_fasta
6
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115 #set $identifier = re.sub('[^\s\w\-]', '_', str($e.element_identifier))
517069eeb0d5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6
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116 ln -s '$e' '${identifier}.$e.ext' &&
0
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117 #end for
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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118 #set $separator = ':'
2
ff4e487f4f7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 13abac83068b126399ec415141007a48c2efaa84
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119 SemiBin2 concatenate_fasta
6
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120 --input-fasta
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121 #for $e in $mode.multi_fasta.input_fasta
517069eeb0d5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6
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122 #set $identifier = re.sub('[^\s\w\-]', '_', str($e.element_identifier))
517069eeb0d5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6
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123 '${identifier}.$e.ext'
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124 #end for
0
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125 --output 'output'
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126 --separator '$separator'
2
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127 --compression none
0
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128 -m $mode.multi_fasta.min_len
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129 &&
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130 ln -s 'output/concatenated.fa' 'contigs.fasta' &&
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131 #end if
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132 #end if
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133 ]]></token>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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134 <xml name="separator">
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135 <param argument="--separator" type="text" value=":" label="Separator in the contig file between sample name and contig name"/>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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136 </xml>
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137 <xml name="input-bam-single">
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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138 <param argument="--input-bam" type="data" format="bam" label="Read mapping to the contigs" help="Sorted BAM files"/>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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139 </xml>
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140 <xml name="input-bam-multi">
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141 <param argument="--input-bam" type="data" format="bam" multiple="true" label="Read mapping to the contigs" help="One file per sample, sorted BAM files"/>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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142 </xml>
5
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143 <!-- Strobealign files -->
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144 <xml name="input-txt">
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145 <param argument="--abundance" type="data" format="txt" label="Read mapping to the contigs" multiple="true" help="Strobealign abundance files"/>
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146 </xml>
0
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147 <token name="@BAM_FILES@"><![CDATA[
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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148 #if $mode.select == 'single'
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149 #set $identifier = re.sub('[^\s\w\-]', '_', str($mode.input_bam.element_identifier))
5
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150 ln -s '$mode.input_bam' '${identifier}.bam' &&
0
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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151 #else
5
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152 #for $e in $mode.input_bam
6
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153 #set $identifier = re.sub('[^\s\w\-]', '_', str($e.element_identifier))
0
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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154 ln -s '$e' '${identifier}.bam' &&
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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155 #end for
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156 #end if
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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157 ]]></token>
5
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
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diff changeset
158 <token name="@STROBEALIGN_FILES@"><![CDATA[
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
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159 #for $e in $mode.align_select.abundance
6
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160 #set $identifier = re.sub('[^\s\w\-]', '_', str($e.element_identifier))
5
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
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161 ln -s '$e' '${identifier}.txt' &&
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
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diff changeset
162 #end for
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diff changeset
163 ]]></token>
3
0608cf7dc528 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
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diff changeset
164 <xml name="ref_select_cannot">
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165 <param name="select" type="select" label="Reference database">
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166 <option value="cached">Cached database</option>
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diff changeset
167 <option value="taxonomy">Pre-computed taxonomy</option>
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168 </param>
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169 </xml>
0
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diff changeset
170 <xml name="ref_select">
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
171 <param name="select" type="select" label="Reference database">
3
0608cf7dc528 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 2
diff changeset
172 <option value="ml" selected="true">Use SemiBin ML function</option>
0608cf7dc528 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 2
diff changeset
173 <option value="cached">Cached database</option>
0
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
174 <option value="taxonomy">Pre-computed taxonomy</option>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
175 </param>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
176 </xml>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
177 <xml name="cached_db">
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
178 <param name="cached_db" label="Cached databases" type="select">
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
179 <options from_data_table="gtdb">
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
180 <validator message="No GTDB database is available" type="no_options" />
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
181 </options>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
182 </param>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
183 </xml>
3
0608cf7dc528 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 2
diff changeset
184 <xml name="ref-single-cannot">
0608cf7dc528 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 2
diff changeset
185 <conditional name="ref">
0608cf7dc528 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 2
diff changeset
186 <expand macro="ref_select_cannot"/>
0608cf7dc528 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 2
diff changeset
187 <when value="cached">
0608cf7dc528 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 2
diff changeset
188 <expand macro="cached_db"/>
0608cf7dc528 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 2
diff changeset
189 </when>
0608cf7dc528 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 2
diff changeset
190 <when value="taxonomy">
0608cf7dc528 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 2
diff changeset
191 <param argument="--taxonomy-annotation-table" type="data" format="tabular" label="Pre-computed mmseqs2 format taxonomy TSV file"/>
0608cf7dc528 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 2
diff changeset
192 </when>
0608cf7dc528 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 2
diff changeset
193 </conditional>
0608cf7dc528 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 2
diff changeset
194 </xml>
0608cf7dc528 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 2
diff changeset
195 <xml name="ref-multi-cannot">
0608cf7dc528 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 2
diff changeset
196 <conditional name="ref">
0608cf7dc528 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 2
diff changeset
197 <expand macro="ref_select_cannot"/>
0608cf7dc528 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 2
diff changeset
198 <when value="cached">
0608cf7dc528 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 2
diff changeset
199 <expand macro="cached_db"/>
0608cf7dc528 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 2
diff changeset
200 </when>
0608cf7dc528 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 2
diff changeset
201 <when value="taxonomy">
0608cf7dc528 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 2
diff changeset
202 <param argument="--taxonomy-annotation-table" type="data" format="tabular" multiple="true" label="Pre-computed mmseqs2 format taxonomy TSV file" help="One per bin file"/>
0608cf7dc528 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 2
diff changeset
203 </when>
0608cf7dc528 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 2
diff changeset
204 </conditional>
0608cf7dc528 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 2
diff changeset
205 </xml>
0
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
206 <xml name="ref-single">
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
207 <conditional name="ref">
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
208 <expand macro="ref_select"/>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
209 <when value="cached">
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
210 <expand macro="cached_db"/>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
211 </when>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
212 <when value="taxonomy">
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
213 <param argument="--taxonomy-annotation-table" type="data" format="tabular" label="Pre-computed mmseqs2 format taxonomy TSV file"/>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
214 </when>
3
0608cf7dc528 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 2
diff changeset
215 <when value="ml"/>
0
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
216 </conditional>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
217 </xml>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
218 <xml name="ref-multi">
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
219 <conditional name="ref">
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
220 <expand macro="ref_select"/>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
221 <when value="cached">
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
222 <expand macro="cached_db"/>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
223 </when>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
224 <when value="taxonomy">
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
225 <param argument="--taxonomy-annotation-table" type="data" format="tabular" multiple="true" label="Pre-computed mmseqs2 format taxonomy TSV file" help="One per bin file"/>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
226 </when>
3
0608cf7dc528 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 2
diff changeset
227 <when value="ml"/>
0
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
228 </conditional>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
229 </xml>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
230 <xml name="ref_single">
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
231 <conditional name="ref">
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
232 <expand macro="ref_select"/>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
233 <when value="cached">
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
234 <expand macro="cached_db"/>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
235 </when>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
236 <when value="taxonomy">
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
237 <param argument="--taxonomy-annotation-table" type="data" format="tabular" label="Pre-computed mmseqs2 format taxonomy TSV file"/>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
238 </when>
3
0608cf7dc528 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 2
diff changeset
239 <when value="ml"/>
0
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
240 </conditional>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
241 </xml>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
242 <xml name="min_len">
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
243 <conditional name="min_len">
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
244 <param name="method" type="select" label="Method to set up the minimal length for contigs in binning">
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
245 <option value="automatic">Automatic</option>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
246 <option value="min-len">Manual</option>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
247 <option value="ratio">Computation based on ratio of the number of base pairs</option>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
248 </param>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
249 <when value="automatic"/>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
250 <when value="min-len">
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
251 <param argument="--min-len" type="integer" min="0" value="0" label="Minimal length for contigs in binning"/>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
252 </when>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
253 <when value="ratio">
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
254 <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."/>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
255 </when>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
256 </conditional>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
257 </xml>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
258 <token name="@MIN_LEN@"><![CDATA[
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259 #if $min_len.method == 'min-len'
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260 --min-len $min_len.min_len
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261 #else if $min_len.method == 'ratio'
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262 --ratio $min_len.ratio
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263 #end if
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264 ]]></token>
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265 <xml name="random-seed">
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266 <param argument="--random-seed" type="integer" min="0" value="0" label="Random seed to reproduce result"/>
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267 </xml>
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268 <xml name="ml-threshold">
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269 <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."/>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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270 </xml>
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271 <xml name="epoches">
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272 <param argument="--epoches" type="integer" min="0" value="20" label="Number of epoches used in the training process"/>
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273 </xml>
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274 <xml name="batch-size">
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275 <param argument="--batch-size" type="integer" min="0" value="2048" label="Batch size used in the training process"/>
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276 </xml>
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277 <xml name="orf-finder">
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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278 <param argument="--orf-finder" type="select" label="ORF finder used to estimate the number of bins">
2
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279 <option value="fast-naive" selected="true">Fast-Naive</option>
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280 <option value="prodigal">Prodigal</option>
0
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281 </param>
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282 </xml>
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283 <xml name="max-node">
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284 <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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285 </xml>
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286 <xml name="max-edges">
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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287 <param argument="--max-edges" type="integer" min="0" value="200" label="Maximum number of edges that can be connected to one contig"/>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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288 </xml>
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289 <xml name="environment">
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290 <param argument="--environment" type="select" optional="true" label="Environment for the built-in model">
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291 <option value="" selected="true">None</option>
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292 <option value="human_gut">Human gut</option>
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293 <option value="dog_gut">Dog gut</option>
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294 <option value="ocean">Ocean</option>
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295 <option value="soil">Soil</option>
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296 <option value="cat_gut">Cat gut</option>
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297 <option value="human_oral">Human oral</option>
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298 <option value="mouse_gut">Mouse gut</option>
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299 <option value="pig_gut">Pig gut</option>
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300 <option value="built_environment">Built environment</option>
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301 <option value="wastewater">Wastewater</option>
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302 <option value="global">Global</option>
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303 </param>
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304 </xml>
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305 <xml name="minfasta-kbs">
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306 <param argument="--minfasta-kbs" type="integer" min="0" value="200" label="Miminimum bin size in Kbps"/>
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307 </xml>
2
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308 <xml name="write_pre_reclustering_bins">
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309 <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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310 </xml>
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311 <xml name="data">
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312 <param argument="--data" type="data" format="csv" label="Train data"/>
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313 </xml>
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314 <xml name="data_output_single">
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315 <data name="single_data" format="csv" from_work_dir="output/data.csv" label="${tool.name} on ${on_string}: Training data">
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316 <filter>input_type_select['mode']['select']=="single" or input_type_select['mode']['select']=="co"</filter>
0
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317 </data>
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318 <data name="single_data_split" format="csv" from_work_dir="output/data_split.csv" label="${tool.name} on ${on_string}: Split training data">
5
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319 <filter>input_type_select['mode']['select']=="single" or input_type_select['mode']['select']=="co"</filter>
0
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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320 </data>
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321 </xml>
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322 <xml name="data_output_multi">
0
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323 <collection name="multi_data" type="list" label="${tool.name} on ${on_string}: Training data per sample">
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324 <filter>input_type_select['mode']['select']=="multi"</filter>
0
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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325 <discover_datasets pattern="(?P&lt;designation&gt;.*)\/data.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/>
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326 </collection>
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327 <collection name="multi_data_split" type="list" label="${tool.name} on ${on_string}: Split training data per sample">
5
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328 <filter>input_type_select['mode']['select']=="multi"</filter>
0
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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329 <discover_datasets pattern="(?P&lt;designation&gt;.*)\/data_split.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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330 </collection>
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331 </xml>
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332 <xml name="generate_sequence_features_extra_outputs">
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333 <data name="single_cov" format="csv" from_work_dir="output/*_data_cov.csv" label="${tool.name} on ${on_string}: Coverage">
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334 <filter>input_type_select['mode']['select']=="single" and extra_output and "coverage" in extra_output</filter>
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335 <filter>input_type_select['input_type']=="bam"</filter>
0
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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336 </data>
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337 <data name="single_split_cov" format="csv" from_work_dir="output/*_data_split_cov.csv" label="${tool.name} on ${on_string}: Coverage (split data)">
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diff changeset
338 <filter>input_type_select['mode']['select']=="single" and extra_output and "coverage" in extra_output</filter>
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339 <filter>input_type_select['input_type']=="bam"</filter>
0
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
340 </data>
1
0ae1a2636de5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
341 <collection name="co_cov" type="list" label="${tool.name} on ${on_string}: Coverage (co_cov)">
5
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
342 <filter>input_type_select['mode']['select']=="co" and extra_output and "coverage" in extra_output</filter>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
343 <filter>input_type_select['input_type']=="bam"</filter>
0
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
344 <discover_datasets pattern=".*\.bam_(?P&lt;designation&gt;.*)_data_cov\.csv" format="csv" directory="output/" />
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
345 </collection>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
346 <collection name="co_split_cov" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample">
5
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
347 <filter>input_type_select['mode']['select']=="co" and extra_output and "coverage" in extra_output</filter>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
348 <filter>input_type_select['input_type']=="bam"</filter>
0
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
349 <discover_datasets pattern=".*\.bam_(?P&lt;designation&gt;.*)_data_split_cov\.csv" format="csv" directory="output/" />
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
350 </collection>
5
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
351 <data name="cov_txt" label="${tool.name} on ${on_string}: Coverage (split data) per sample (aemb)" from_work_dir="output/cov_split.csv" format="csv">
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
352 <filter>input_type_select['mode']['select']=="single" or input_type_select['mode']['select']=="co" and extra_output and "coverage" in extra_output</filter>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
353 <filter>input_type_select['input_type']=="txt"</filter>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
354 </data>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
355 <data name="co_cov_txt" label="${tool.name} on ${on_string}: Coverage (aemb)" format="csv" from_work_dir="output/cov.csv">
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
356 <filter>input_type_select['mode']['select']=="single" or input_type_select['mode']['select']=="co" and extra_output and "coverage" in extra_output</filter>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
357 <filter>input_type_select['input_type']=="txt"</filter>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
358 </data>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
359 <collection name="multi_split_cov_txt" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample (multi_split_cov) (aemb)">
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
360 <filter>input_type_select['mode']['select']=="multi" and extra_output and "coverage" in extra_output</filter>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
361 <filter>input_type_select['input_type']=="txt"</filter>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
362 <discover_datasets pattern="(?P&lt;designation&gt;.*)\/data_split_cov.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
363 </collection>
1
0ae1a2636de5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
364 <collection name="multi_cov" type="list" label="${tool.name} on ${on_string}: Coverage (multi_cov)">
5
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
365 <filter>input_type_select['mode']['select']=="multi" and extra_output and "coverage" in extra_output</filter>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
366 <filter>input_type_select['input_type']=="bam"</filter>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
367 <discover_datasets pattern=".*\.bam_(?P&lt;designation&gt;.*)_data_cov.csv" format="csv" directory="output/samples/" recurse="true"/>
0
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
368 </collection>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
369 <collection name="multi_cov_sample" type="list" label="${tool.name} on ${on_string}: Coverage per sample">
5
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
370 <filter>input_type_select['mode']['select']=="multi" and extra_output and "coverage" in extra_output</filter>
0
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
371 <discover_datasets pattern="(?P&lt;designation&gt;.*)\/data_cov.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
372 </collection>
1
0ae1a2636de5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
373 <collection name="multi_split_cov" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample (multi_split_cov)">
5
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
374 <filter>input_type_select['mode']['select']=="multi" and extra_output and "coverage" in extra_output</filter>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
375 <filter>input_type_select['input_type']=="bam"</filter>
0
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
376 <discover_datasets pattern=".*\.bam_(?P&lt;designation&gt;.*)_data_split_cov.csv" format="csv" directory="output/samples/" />
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
377 </collection>
1
0ae1a2636de5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
378 <collection name="multi_split_cov_sample" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample (multi_split_cov_sample)">
5
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
379 <filter>input_type_select['mode']['select']=="multi" and extra_output and "coverage" in extra_output</filter>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
380 <filter>input_type_select['input_type']=="bam"</filter>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
381 <discover_datasets pattern="(?P&lt;designation&gt;.*)\/data_split_cov.csv" format="csv" directory="output/samples/" match_relative_path="true" recurse="true"/>
0
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
382 </collection>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
383 <collection name="multi_contigs" type="list" label="${tool.name} on ${on_string}: Contigs">
5
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
384 <filter>input_type_select['mode']['select']=="multi" and extra_output and "contigs" in extra_output</filter>
0
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
385 <discover_datasets pattern="(?P&lt;designation&gt;.*).fa" format="fasta" directory="output/samples/" />
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
386 </collection>
5
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
387 </xml>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
388 <xml name="generate_sequence_features_extra_outputs_main">
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
389 <!-- Single -->
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
390 <data name="single_cov" format="csv" from_work_dir="output/*_data_cov.csv" label="${tool.name} on ${on_string}: Coverage">
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
391 <filter>mode['select']=="single" and extra_output and "coverage" in extra_output</filter>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
392 </data>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
393 <data name="single_split_cov" format="csv" from_work_dir="output/*_data_split_cov.csv" label="${tool.name} on ${on_string}: Coverage (split data)">
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
394 <filter>mode['select']=="single" and extra_output and "coverage" in extra_output</filter>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
395 </data>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
396 <!-- Bam co aligned -->
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
397 <collection name="co_cov_bam" type="list" label="${tool.name} on ${on_string}: Coverage (co_cov)">
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
398 <filter>mode['select']=="co" and extra_output and "coverage" in extra_output</filter>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
399 <filter>mode['align_select']</filter>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
400 <filter>mode['align_select']['align_select']=="bam"</filter>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
401 <discover_datasets pattern=".*\.bam_(?P&lt;designation&gt;.*)_data_cov\.csv" format="csv" directory="output/" />
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
402 </collection>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
403 <collection name="co_split_cov_bam" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample">
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
404 <filter>mode['select']=="co" and extra_output and "coverage" in extra_output</filter>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
405 <filter>mode['align_select']</filter>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
406 <filter>mode['align_select']['align_select']=="bam"</filter>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
407 <discover_datasets pattern=".*\.bam_(?P&lt;designation&gt;.*)_data_split_cov\.csv" format="csv" directory="output/" />
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
408 </collection>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
409
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
410 <!-- Bam Multi aligned -->
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
411 <collection name="multi_cov_bam" type="list" label="${tool.name} on ${on_string}: Coverage (multi_cov)">
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
412 <filter>mode['select']=="multi" and extra_output and "coverage" in extra_output</filter>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
413 <filter>mode['align_select']</filter>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
414 <filter>mode['align_select']['align_select']=="bam"</filter>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
415 <discover_datasets pattern=".*\.bam_(?P&lt;designation&gt;.*)_data_cov.csv" format="csv" directory="output/samples/" />
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
416 </collection>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
417 <collection name="multi_cov_sample_bam" type="list" label="${tool.name} on ${on_string}: Coverage per sample">
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
418 <filter>mode['select']=="multi" and extra_output and "coverage" in extra_output</filter>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
419 <filter>mode['align_select']</filter>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
420 <filter>mode['align_select']['align_select']=="bam"</filter>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
421 <discover_datasets pattern="(?P&lt;designation&gt;.*)\/data_cov.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
422 </collection>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
423 <collection name="multi_split_cov_bam" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample (multi_split_cov)">
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
424 <filter>mode['select']=="multi" and extra_output and "coverage" in extra_output</filter>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
425 <filter>mode['align_select']</filter>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
426 <filter>mode['align_select']['align_select']=="bam"</filter>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
427 <discover_datasets pattern=".*\.bam_(?P&lt;designation&gt;.*)_data_split_cov.csv" format="csv" directory="output/samples/" />
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
428 </collection>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
429 <collection name="multi_split_cov_sample_bam" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample (multi_split_cov_sample)">
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
430 <filter>mode['select']=="multi" and extra_output and "coverage" in extra_output</filter>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
431 <filter>mode['align_select']</filter>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
432 <filter>mode['align_select']['align_select']=="bam"</filter>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
433 <discover_datasets pattern=".*\.bam_(?P&lt;designation&gt;.*)_data_split_cov.csv" format="csv" directory="output/samples/" />
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
434 </collection>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
435 <collection name="multi_contigs" type="list" label="${tool.name} on ${on_string}: Contigs">
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
436 <filter>mode['select']=="multi" and extra_output and "contigs" in extra_output</filter>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
437 <discover_datasets pattern="(?P&lt;designation&gt;.*).fa" format="fasta" directory="output/samples/" />
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
438 </collection>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
439 <!-- Txt co aligned -->
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
440 <data name="co_split_cov_txt" label="${tool.name} on ${on_string}: Coverage (split data) per sample (aemb)" from_work_dir="output/cov_split.csv" format="csv">
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
441 <filter>mode['select']=="co" and extra_output and "coverage" in extra_output</filter>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
442 <filter>mode['align_select']</filter>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
443 <filter>mode['align_select']['align_select']=="txt"</filter>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
444 </data>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
445 <data name="co_cov_txt" label="${tool.name} on ${on_string}: Coverage (aemb)" format="csv" from_work_dir="output/cov.csv">
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
446 <filter>mode['select']=="co" and extra_output and "coverage" in extra_output</filter>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
447 <filter>mode['align_select']</filter>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
448 <filter>mode['align_select']['align_select']=="txt"</filter>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
449 </data>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
450 <!-- Txt multi aligned -->
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
451 <collection name="multi_cov_txt" type="list" label="${tool.name} on ${on_string}: Coverage per sample (aemb)">
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
452 <filter>mode['select']=="multi" and extra_output and "coverage" in extra_output</filter>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
453 <filter>mode['align_select']</filter>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
454 <filter>mode['align_select']['align_select'] =="txt"</filter>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
455 <discover_datasets pattern="(?P&lt;designation&gt;.*)\/data_cov.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
456 </collection>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
457 <collection name="multi_split_cov_txt" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample (multi_split_cov) (aemb)">
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
458 <filter>mode['select']=="multi" and extra_output and "coverage" in extra_output</filter>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
459 <filter>mode['align_select']</filter>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
460 <filter>mode['align_select']['align_select']=="txt"</filter>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
461 <discover_datasets pattern="(?P&lt;designation&gt;.*)\/data_split_cov.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
462 </collection>
0
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
463 </xml>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
464 <xml name="train_output">
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
465 <data name="model" format="h5" from_work_dir="output/model.h5" label="${tool.name} on ${on_string}: Semi-supervised deep learning model" />
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
466 </xml>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
467 <xml name="cannot_link_output">
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
468 <data name="cannot" format="txt" from_work_dir="output/cannot/cannot.txt" label="${tool.name} on ${on_string}: Cannot-link constraints" />
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
469 </xml>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
470 <token name="@HELP_HEADER@"><![CDATA[
5
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
471
0
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
472 What it does
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
473 ============
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
474
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
475 SemiBin is a Semi-supervised siamese neural network for metagenomic binning
5
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
476 ]]></token>
0
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
477 <token name="@HELP_INPUT_FASTA@"><![CDATA[
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
478 - Contigs in fasta for 1 or several samples from single or co-assembly
5
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
479 ]]></token>
0
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
480 <token name="@HELP_INPUT_BAM@"><![CDATA[
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
481 - BAM with reads mapping to the contigs
5
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
482 ]]></token>
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
483 <token name="@HELP_INPUT_STROBEALIGN@"><![CDATA[
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
484 - TXT alignment files that are the output of strobealign-aemb
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
485 ]]></token>
0
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
486 <token name="@HELP_CANNOT@"><![CDATA[
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
487 - Cannot-link constraints
5
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
488 ]]></token>
0
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
489 <token name="@HELP_DATA@"><![CDATA[
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
490 - Training data and split training data for the model
5
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
491 ]]></token>
0
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
492 <token name="@HELP_MODEL@"><![CDATA[
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
493 - Semi-supervised deep learning model
5
8ba0c2edf3f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
iuc
parents: 4
diff changeset
494 ]]></token>
0
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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496 - Reconstructed bins after reclustering
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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497 - Reconstructed bins before reclustering
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07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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499 <xml name="citations">
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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500 <citations>
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501 <citation type="doi">10.1038/s41467-022-29843-y</citation>
07bf5268724f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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502 </citations>
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503 </xml>
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504 </macros>