Mercurial > repos > iuc > cami_amber

annotate cami_amber.xml @ 5:770bb9e271b2 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 430cd92e7151f4ff87796589e7f51e4007aca38f
author iuc
date Mon, 10 Feb 2025 15:06:22 +0000
parents e166d7bc8fb5
children
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c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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diff changeset
1 <tool id="cami_amber" name="CAMI AMBER" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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2 <description>Evaluation package for MAGs</description>
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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3 <macros>
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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4 <import>macros.xml</import>
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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5 </macros>
5
770bb9e271b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 430cd92e7151f4ff87796589e7f51e4007aca38f
iuc
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6 <expand macro="xrefs"/>
0
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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7 <expand macro="requirements" />
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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8 <command detect_errors="exit_code">
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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9 <![CDATA[
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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10
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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11 #set $path_to_html = $html.files_path
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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12 #set $max = []
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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13 #set $min = []
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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14 #set $label = []
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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15
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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16 mkdir -p output inputs '$path_to_html' &&
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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17
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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18 #if $tox.ncbi.is_select == 'yes':
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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19 #if $tox.input.is_select == 'manually':
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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20 mkdir -p ncbi &&
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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21 #for $file in $tox.ncbi_dir:
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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22 ln -s '$file' './ncbi/$file.element_identifier' &&
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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23 #end for
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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24 #end if
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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25 #end if
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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26
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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27 #for $i, $file in enumerate($input_files):
3
e166d7bc8fb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 04a067550f7d61ca8ff489e3de64efd0da3abcf1
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28 ln -s '$file.binning_files' './inputs/${i}.tsv' &&
0
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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29 #if $file.labels:
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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30 $label.append($file.labels)
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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31 #end if
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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32 #end for
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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34 #if $genome.thresholds:
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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35 #for $i, $arg in enumerate($genome.thresholds):
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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36 #if $arg.min_completeness:
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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37 $min.append($arg.min_completeness)
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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38 #end if
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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39 #if $arg.max_contamination:
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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40 $max.append($arg.max_contamination)
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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41 #end if
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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42 #end for
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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43 #end if
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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44
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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45 amber.py
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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46 -g '${gold_standard_file}'
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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47 #if $label:
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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48 #set $sep = ''
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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49 -l
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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50 '
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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51 #for $lab in $label:
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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52 $sep$lab
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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53 #set $sep = ','
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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54 #end for
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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55 '
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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56 #end if
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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57 -p ${filter}
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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58 #if $min_length:
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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59 -n $min_length
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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60 #end if
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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61 #if $desc:
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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62 -d '${desc}'
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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63 #end if
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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64 #if $min:
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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65 #set $sep = ''
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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66 --min_completeness
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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67 '
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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68 #for $i in $min:
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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69 $sep$i
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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70 #set $sep = ','
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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71 #end for
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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72 '
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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73 #end if
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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74 #if $max:
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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75 #set $sep = ''
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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76 --max_contamination
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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77 '
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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78 #for $i in $max:
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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79 $sep$i
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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80 #set$sep = ','
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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81 #end for
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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82 '
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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83 #end if
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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84 #if $genome.remove_genomes:
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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85 -r '$genome.remove_genomes'
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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86 #end if
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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87 #if $genome.remove.is_select == 'yes':
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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88 -k '$genome.keyword'
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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89 #end if
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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90 #if $genome.genome_coverage:
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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91 --genome_coverage '$genome.genome_coverage'
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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92 #end if
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93 #if $tox.ncbi.is_select == 'yes':
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94 #if $tox.input.is_select == 'manually':
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95 --ncbi_dir ncbi
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96 #else:
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97 --ncbi_dir '$tox.ncbi_dir.fields.path'
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98 #end if
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99 #end if
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100 -o output
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101 #for $i, $bin in enumerate($input_files):
3
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102 'inputs/${i}.tsv'
0
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103 #end for
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104
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105 &&
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106
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107 mv 'output/heatmap_bar.png' '$path_to_html'
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108
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109 ]]>
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110 </command>
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111 <inputs>
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112 <param argument="--gold_standard_file" format="tabular" type="data"
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113 label="Mapping of contigs or reads"
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114 help="Input the gold standard file here so amber know the correct IDs for each contig/read" />
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115 <repeat name="input_files" title="Binning files and names "
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116 help="Enter multiple binning files and names (names are optional). IMPORTANT: for each binning file you use in the program you need to state one label, this mean for example for 3 binning files you need 3 labels (3 slots) not more or less!">
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117 <param name="binning_files" format="tabular" type="data"
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118 label="Input bin files here" />
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119 <param argument="--labels" type="text" value="" optional="true"
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120 label="Name for bin" />
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121 </repeat>
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122 <param argument="--filter" type="integer" value="0" min="0"
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123 label="Filter out the n smallest genome bins"
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124 help="Optional filter for filter out the n smallest genome bins" />
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125 <param argument="--min_length" type="integer" value="" optional="true"
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126 label="Minimum length of sequences"
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127 help="Input how long the sequences has to be" />
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128 <param argument="--desc" type="text" value=""
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129 label="HTML description"
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130 help="Enter the HTML page description here" />
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131 <section name="genome" title="Genome binning-specific options" >
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132 <repeat name="thresholds" title="Min. completeness and max. contamination thresholds"
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133 help="Enter certain thresholds for min. completeness (Default %: 50,70,90) and certain thresholds for max. contamination (Default %: 5, 10), the program itself will transform it to %!" >
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134 <param argument="--min_completeness" type="integer" value="" min="0" max="100" optional="true"
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135 label="Min. completeness threshold" />
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136 <param argument="--max_contamination" type="integer" value="" min="0" max="100" optional="true"
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137 label="Max. contamination threshold" />
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138 </repeat>
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139 <param argument="--remove_genomes" type="data" format="tabular" optional="true"
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140 label="tsv file for genomes to remove"
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141 help="Input a tsv file with binid and type in each line. In the help section is an example. WARNING: IF THE LIST CONTAIN ALL GENOME THE PROGRAM WILL FAIL!" />
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142 <conditional name="remove">
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143 <param name="is_select" type="select" label="Remove one or all genomes which are in the list?"
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144 help="Select yes and enter a keyword to remove certain type of genomes which are in the list. When all genomes in the list should remove also select yes and do not enter a keyword!">
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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145 <option value="yes" selected="false">Yes</option>
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146 <option value="no" selected="true">No</option>
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147 </param>
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148 <when value="yes">
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149 <param argument="--keyword" type="text" value=""
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150 label="Keyword for removing certain genomes"
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151 help="Input a keyword which should be match with binid giving in the file for removing genomes. When no keyword is giving the program remove all genomes which are in the list!" />
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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152 </when>
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153 <when value="no" />
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154 </conditional>
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155 <param argument="--genome_coverage" type="data" format="tabular" optional="true"
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156 label="Genome coverages tsv file"
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157 help="Input a tsv file where the genome coverage is stated. Look at the help section to see how this file should look like!" />
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158 </section>
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159 <section name="tox" title="taxonomic binning-specific option">
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160 <conditional name="ncbi">
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161 <param name="is_select" type="select" label="Want to use the NCBI database?"
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162 help="Select yes if you want to use the NCBI database to evaluate taxonomic binning">
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163 <option value="yes" selected="false">Yes</option>
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164 <option value="no" selected="true">No</option>
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165 </param>
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166 <when value="yes">
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167 <conditional name="input">
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168 <param name="is_select" type="select" label="Select how you want to use NCBI database"
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169 help="Either select manually input or data manager. For more help read the help of the type of the input you selected." >
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170 <option value="manually">Manually</option>
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171 <option value="data">Data manager</option>
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diff changeset
172 </param>
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173 <when value="manually">
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174 <param argument="--ncbi_dir" format="tabular" type="data" multiple="true"
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175 label="Input .dmp files"
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176 help="To use the NCBI database we need to provide followed .dmp files: nodes.dmp, names.dmp and merged.dmp. You can get the via download of this file **ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz** and unzip it!" />
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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177 </when>
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178 <when value="data" >
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179 <param argument="--ncbi_dir" type="select"
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180 label="Assessing taxonomic binning"
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181 help="Include the NCBI taxonomy database. For this you can use the data manager data_manager_fetch_ncbi_taxonomy which can be install via galaxy. For more help look at the help section at the bottom!" >
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182 <options from_data_table="ncbi_taxonomy">
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183 <validator message="No NCBI database is available" type="no_options"/>
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184 </options>
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185 </param>
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186 </when>
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187 </conditional>
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188 </when>
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189 <when value="no"/>
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190 </conditional>
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191 </section>
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192 </inputs>
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193 <outputs>
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194 <data name="html" format="html" from_work_dir="output/index.html" label="${tool.name}: HTML" />
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195 <data name="result" format="tabular" from_work_dir="output/results.tsv" label="${tool.name}: Results" />
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196 <data name="metrics_genome" format="tabular" from_work_dir="output/genome_metrics_cami1.tsv" label="${tool.name}: Genome metrics" />
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197 <data name="metrics_bin" format="tabular" from_work_dir="output/bin_metrics.tsv" label="${tool.name}: Bin metrics" />
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198 </outputs>
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199 <tests>
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200 <test expect_num_outputs="4">
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201 <param name="gold_standard_file" value="gsa_mapping.binning" ftype="tabular" />
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202 <repeat name="input_files">
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203 <param name="binning_files" value="elated_franklin_0" ftype="tabular"/>
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204 </repeat>
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iuc
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205 <repeat name="input_files">
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206 <param name="binning_files" value="goofy_hypatia_2" ftype="tabular"/>
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207 </repeat>
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208 <repeat name="input_files">
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209 <param name="binning_files" value="naughty_carson_2" ftype="tabular"/>
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210 </repeat>
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211 <output name="metrics_bin">
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212 <assert_contents>
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213 <has_text text="genome_id" n="1" />
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214 <has_text text="sample_id" n="1" />
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215 </assert_contents>
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216 </output>
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217 <output name="metrics_genome">
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218 <assert_contents>
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219 <has_text text="precision_seq" n="1" />
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220 <has_text text="total_length" n="1" />
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221 </assert_contents>
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222 </output>
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223 </test>
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224 <test expect_num_outputs="4">
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225 <param name="gold_standard_file" value="gsa_mapping.binning" ftype="tabular" />
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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226 <repeat name="input_files">
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227 <param name="binning_files" value="elated_franklin_0" ftype="tabular"/>
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228 <param name="labels" value="test1" />
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229 </repeat>
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iuc
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230 <repeat name="input_files">
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231 <param name="binning_files" value="goofy_hypatia_2" ftype="tabular"/>
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232 <param name="labels" value="test2" />
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233 </repeat>
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iuc
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234 <repeat name="input_files">
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235 <param name="binning_files" value="naughty_carson_2" ftype="tabular"/>
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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236 <param name="labels" value="test3" />
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237 </repeat>
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238 <param name="filter" value="1" />
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239 <param name="min_length" value="200" />
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240 <section name="genome" >
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241 <repeat name="thresholds" >
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242 <param name="max_contamination" value="2" />
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243 <param name="min_completeness" value="50" />
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244 </repeat>
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245 <repeat name="thresholds" >
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246 <param name="min_completeness" value="70" />
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247 </repeat>
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iuc
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248 <repeat name="thresholds" >
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249 <param name="min_completeness" value="90" />
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250 </repeat>
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251 <param name="genome_coverage" value="cami2_mouse_gut_average_genome_coverage.tsv" ftype="tabular" />
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252 <param name="remove_genomes" value="unique_common.tsv" ftype="tabular" />
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253 <conditional name="remove" >
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254 <param name="is_select" value="yes" />
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255 <param name="keyword" value="circular element" />
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256 </conditional>
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257 </section>
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iuc
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258 <section name="tox">
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iuc
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259 <conditional name="ncbi">
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iuc
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260 <param name="is_select" value="yes" />
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iuc
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diff changeset
261 <conditional name="input" >
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262 <param name="is_select" value="manually" />
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iuc
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263 <param name="ncbi_dir" value="test-db/nodes.dmp,test-db/merged.dmp,test-db/names.dmp" ftype="tabular" />
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264 </conditional>
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265 </conditional>
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266 </section>
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267 <output name="result">
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268 <assert_contents>
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iuc
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269 <has_text text="test1" n="1" />
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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270 <has_text text="test2" n="1" />
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iuc
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271 <has_text text="test3" n="1" />
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272 </assert_contents>
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273 </output>
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274 </test>
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iuc
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275 <test expect_num_outputs="4">
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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276 <param name="gold_standard_file" value="gsa_mapping.binning" ftype="tabular" />
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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277 <repeat name="input_files">
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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278 <param name="binning_files" value="elated_franklin_0" ftype="tabular"/>
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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279 </repeat>
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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diff changeset
280 <repeat name="input_files">
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iuc
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281 <param name="binning_files" value="goofy_hypatia_2" ftype="tabular"/>
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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282 </repeat>
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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283 <repeat name="input_files">
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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284 <param name="binning_files" value="naughty_carson_2" ftype="tabular"/>
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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285 </repeat>
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iuc
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286 <param name="desc" value="TEST FOR GALAXY" />
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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287 <section name="tox">
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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288 <conditional name="ncbi">
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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289 <param name="is_select" value="yes" />
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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290 <conditional name="input" >
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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291 <param name="is_select" value="data" />
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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292 <param name="ncbi_dir" value="test-db-tox" />
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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293 </conditional>
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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294 </conditional>
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295 </section>
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iuc
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296 <output name="html">
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297 <assert_contents>
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298 <has_text text="TEST FOR GALAXY" n="1" />
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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299 </assert_contents>
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300 </output>
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iuc
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301 </test><test expect_num_outputs="4">
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302 <param name="gold_standard_file" value="test_gold.tsv" ftype="tabular" />
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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303 <repeat name="input_files">
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iuc
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304 <param name="binning_files" value="test_binning.tsv" ftype="tabular"/>
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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305 </repeat>
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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306 <repeat name="input_files">
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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307 <param name="binning_files" value="test_binning2.tsv" ftype="tabular"/>
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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308 </repeat>
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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309 <section name="tox">
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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310 <conditional name="ncbi">
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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311 <param name="is_select" value="yes" />
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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312 <conditional name="input" >
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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313 <param name="is_select" value="data" />
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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314 <param name="ncbi_dir" value="test-db-tox" />
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315 </conditional>
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316 </conditional>
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317 </section>
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318 <output name="metrics_bin">
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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319 <assert_contents>
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iuc
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320 <has_text text="genome_id" n="1" />
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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321 <has_text text="sample_id" n="1" />
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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322 </assert_contents>
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323 </output>
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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324 <output name="metrics_genome">
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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325 <assert_contents>
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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326 <has_text text="precision_seq" n="1" />
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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327 <has_text text="total_length" n="1" />
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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328 </assert_contents>
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329 </output>
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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330 </test>
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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331 </tests>
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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332 <help>
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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333 <![CDATA[
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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334 .. class:: infomark
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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335
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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336 **What is AMBER**
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337
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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338 AMBER is an evaluation package for the comparative assessment of genome reconstructions and taxonomic assignments from metagenome benchmark datasets.
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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339
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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340 .. class:: infomark
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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341
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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342 **What it does**
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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343
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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344 AMBER calculate multiple metrics per bin and multiple metrics per sample. Each of them are provided then in results rankings, and comparative visualizations for assessing multiple programs or parameter effects.
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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345
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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346 For more information please visit `AMBER in GitHub <https://github.com/CAMI-challenge/AMBER>`_.
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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347
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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348 **Input**
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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349
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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350 AMBER use only 2 required inputs:
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351
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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352 - The golden standard file (biobox format)
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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353
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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354 This file can be created via the add_length tool
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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355
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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356 .. class:: infomark
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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357
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
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358 Example(tab separated)
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359
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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diff changeset
360 ::
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
361
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
362 @Version:0.9.1
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
363 @SampleID:CAMI_low
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
364
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
365 @@SEQUENCEID BINID _LENGTH
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
366 RL|S1|C10817 Sample18_57 20518
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
367 RL|S1|C11497 Sample22_57 37672
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
368 RL|S1|C6571 evo_1286_AP.033 69914
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
369 RL|S1|C10560 evo_1286_AP.033 995657
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
370 RL|S1|C13546 evo_1286_AP.033 626775
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
371
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
372 Note: This file looks similar to the binning files but the only different which is also is important is the length column.
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
373
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
374 - Multiple binning files (biobox format)
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
375
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
376 Files can be created via the convert_to_biobox tool
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
377
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
378 .. class:: infomark
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
379
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
380 Example(tab separated):
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
381
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
382 ::
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
383
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
384 #CAMI Format for Binning
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
385 @Version:0.9.0
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
386 @SampleID:CAMI_low
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
387 @@SEQUENCEID BINID
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
388 RL|S1|C10 Bin_034
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
389 RL|S1|C100 Bin_023
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
390 RL|S1|C1000 Bin_034
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
391 RL|S1|C10000 Bin_019
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
392 RL|S1|C10002 Bin_035
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
393 RL|S1|C10004 Bin_035
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
394 RL|S1|C10008 Bin_034
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
395 RL|S1|C10011 Bin_035
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
396 RL|S1|C10012 Bin_013
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
397 RL|S1|C10014 Bin_035
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
398
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
399 There are also additional inputs which can be used:
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
400
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
401 - A genome list which should be removed(tabular format)
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
402
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
403 .. class:: infomark
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
404
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
405 Example(tab separated):
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
406
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
407 ::
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
408
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
409 evo_1035930.029 common strain
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
410 1035930 common strain
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
411 evo_1035930.032 common strain
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
412 evo_1035930.011 common strain
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
413 evo_1286_AP.033 common strain
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
414 1286_AP common strain
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
415 evo_1286_AP.026 common strain
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
416 evo_1286_AP.037 common strain
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
417 evo_1286_AP.008 common strain
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
418 1052944 common strain
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
419 1053058 common strain
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
420 1052947 common strain
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
421 evo_1049056.013 common strain
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
422 evo_1049056.031 common strain
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
423 evo_1049056.011 common strain
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
424 1049056 common strain
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
425 evo_1049056.039 common strain
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
426
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
427 Note: The first column contain the BINID and the second contain any kind of string. IMPORTANT: The argument where to state a keyword has to match to the anything in the second column to filter these kind of genomes out. If there is no keyword stated it can happen if the remove list contain all genomes which should be used then AMBER will fail since there are no genomes left to use!
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
428
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
429 - Genome coverage file (tabular format)
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
430
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
431 .. class:: infomark
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
432
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
433 Example(tab separated):
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
434
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
435 ::
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
436
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
437 @SampleID:gsa_pooled
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
438 @@GENOMEID COVERAGE
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
439 4378740.0 82.85111527272727
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
440 4378740.1 27.159305090909097
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
441 denovo10559.0 2.1596957142857143
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
442 179927.0 1.6946866666666667
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
443 denovo8373.1 2.07144
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
444 136604.0 9.150489565217391
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
445 denovo8373.0 1.1413460000000002
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
446 269378.0 8.051563333333332
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
447 190114.0 18.253119629629627
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
448 228140.0 3.078681818181818
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
449 135956.0 121.52672015625001
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
450 259846.0 12.298210588235296
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
451 162576.0 9.57867191489362
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
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452 184966.0 14.461031521739134
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454 There is also an option to include the NCBI database in AMBER. This can be used when including the link which is stated in the data manager: **data_manager_fetch_ncbi_taxonomy**. This data manager download the current version of the database and store all files for you. If there are questions about data manager maybe have a look at this `Tutorial <https://usegalaxy.eu/training-material/topics/admin/tutorials/reference-genomes/tutorial.html>`_.
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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455
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456 **Output**
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457
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458 AMBER will output 3 tsv files where each metrics value is stated. The important output is the HTML file where all data are included and also can be visualized with certain plots!
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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460 **Additional information**
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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461
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462 The package **Bokeh** will create warnings which can be ignored since the only tell you that certain functions in the code are swapped with the new functions. AMBER was tested with the stated version of **Bokeh** and with the newest version of it and both generate the same output!
c2162f17ceb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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463 ]]>
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464 </help>
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465 <expand macro="citations" />
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466 </tool>