Mercurial > repos > iuc > cami_amber

annotate cami_amber.xml @ 7:2e7b727a0e05 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 15:07:49 +0000
parents e30bc6da7a36
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
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1 <tool id="cami_amber" name="CAMI AMBER" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
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2 <description>Evaluation package for MAGs</description>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
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3 <macros>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
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4 <import>macros.xml</import>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
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5 </macros>
7
2e7b727a0e05 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
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
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7 <expand macro="requirements" />
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
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8 <command detect_errors="exit_code">
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
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9 <![CDATA[
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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10
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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11 #set $path_to_html = $html.files_path
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
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12 #set $max = []
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
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13 #set $min = []
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
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14 #set $label = []
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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15
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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16 mkdir -p output inputs '$path_to_html' &&
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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17
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
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18 #if $tox.ncbi.is_select == 'yes':
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
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19 #if $tox.input.is_select == 'manually':
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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20 mkdir -p ncbi &&
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
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21 #for $file in $tox.ncbi_dir:
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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22 ln -s '$file' './ncbi/$file.element_identifier' &&
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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23 #end for
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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24 #end if
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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25 #end if
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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26
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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27 #for $i, $file in enumerate($input_files):
5
e30bc6da7a36 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
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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29 #if $file.labels:
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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30 $label.append($file.labels)
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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31 #end if
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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32 #end for
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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33
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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34 #if $genome.thresholds:
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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35 #for $i, $arg in enumerate($genome.thresholds):
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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36 #if $arg.min_completeness:
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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37 $min.append($arg.min_completeness)
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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38 #end if
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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39 #if $arg.max_contamination:
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
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40 $max.append($arg.max_contamination)
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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41 #end if
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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42 #end for
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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43 #end if
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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44
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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45 amber.py
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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46 -g '${gold_standard_file}'
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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47 #if $label:
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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48 #set $sep = ''
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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49 -l
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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50 '
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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51 #for $lab in $label:
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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52 $sep$lab
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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53 #set $sep = ','
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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54 #end for
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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55 '
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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56 #end if
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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57 -p ${filter}
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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58 #if $min_length:
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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59 -n $min_length
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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60 #end if
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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61 #if $desc:
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62 -d '${desc}'
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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63 #end if
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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64 #if $min:
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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65 #set $sep = ''
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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66 --min_completeness
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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67 '
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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68 #for $i in $min:
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69 $sep$i
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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70 #set $sep = ','
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71 #end for
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72 '
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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73 #end if
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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74 #if $max:
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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75 #set $sep = ''
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76 --max_contamination
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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77 '
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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78 #for $i in $max:
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79 $sep$i
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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80 #set$sep = ','
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81 #end for
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82 '
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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83 #end if
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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84 #if $genome.remove_genomes:
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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85 -r '$genome.remove_genomes'
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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86 #end if
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87 #if $genome.remove.is_select == 'yes':
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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88 -k '$genome.keyword'
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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89 #end if
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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90 #if $genome.genome_coverage:
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91 --genome_coverage '$genome.genome_coverage'
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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92 #end if
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93 #if $tox.ncbi.is_select == 'yes':
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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94 #if $tox.input.is_select == 'manually':
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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95 --ncbi_dir ncbi
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96 #else:
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97 --ncbi_dir '$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):
5
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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!">
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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!" />
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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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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!" />
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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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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" />
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iuc
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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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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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234 <repeat name="input_files">
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235 <param name="binning_files" value="naughty_carson_2" ftype="tabular"/>
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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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258 <section name="tox">
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259 <conditional name="ncbi">
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260 <param name="is_select" value="yes" />
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261 <conditional name="input" >
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262 <param name="is_select" value="manually" />
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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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269 <has_text text="test1" n="1" />
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270 <has_text text="test2" n="1" />
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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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275 <test expect_num_outputs="4">
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276 <param name="gold_standard_file" value="gsa_mapping.binning" ftype="tabular" />
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iuc
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277 <repeat name="input_files">
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278 <param name="binning_files" value="elated_franklin_0" ftype="tabular"/>
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279 </repeat>
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280 <repeat name="input_files">
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281 <param name="binning_files" value="goofy_hypatia_2" ftype="tabular"/>
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282 </repeat>
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283 <repeat name="input_files">
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284 <param name="binning_files" value="naughty_carson_2" ftype="tabular"/>
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285 </repeat>
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286 <param name="desc" value="TEST FOR GALAXY" />
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287 <section name="tox">
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288 <conditional name="ncbi">
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289 <param name="is_select" value="yes" />
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290 <conditional name="input" >
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291 <param name="is_select" value="data" />
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292 <param name="ncbi_dir" value="test-db-tox" />
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293 </conditional>
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294 </conditional>
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295 </section>
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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" />
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299 </assert_contents>
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300 </output>
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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" />
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303 <repeat name="input_files">
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304 <param name="binning_files" value="test_binning.tsv" ftype="tabular"/>
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305 </repeat>
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306 <repeat name="input_files">
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307 <param name="binning_files" value="test_binning2.tsv" ftype="tabular"/>
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308 </repeat>
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309 <section name="tox">
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310 <conditional name="ncbi">
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311 <param name="is_select" value="yes" />
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312 <conditional name="input" >
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313 <param name="is_select" value="data" />
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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">
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319 <assert_contents>
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320 <has_text text="genome_id" n="1" />
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321 <has_text text="sample_id" n="1" />
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322 </assert_contents>
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323 </output>
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324 <output name="metrics_genome">
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325 <assert_contents>
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326 <has_text text="precision_seq" n="1" />
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327 <has_text text="total_length" n="1" />
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328 </assert_contents>
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329 </output>
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330 </test>
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331 </tests>
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332 <help>
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333 <![CDATA[
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334 .. class:: infomark
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335
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336 **What is AMBER**
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337
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338 AMBER is an evaluation package for the comparative assessment of genome reconstructions and taxonomic assignments from metagenome benchmark datasets.
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339
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340 .. class:: infomark
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341
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342 **What it does**
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343
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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.
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345
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346 For more information please visit `AMBER in GitHub <https://github.com/CAMI-challenge/AMBER>`_.
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347
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348 **Input**
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349
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350 AMBER use only 2 required inputs:
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351
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352 - The golden standard file (biobox format)
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353
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354 This file can be created via the add_length tool
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355
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356 .. class:: infomark
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357
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358 Example(tab separated)
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359
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360 ::
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361
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362 @Version:0.9.1
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363 @SampleID:CAMI_low
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364
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365 @@SEQUENCEID BINID _LENGTH
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366 RL|S1|C10817 Sample18_57 20518
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367 RL|S1|C11497 Sample22_57 37672
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368 RL|S1|C6571 evo_1286_AP.033 69914
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369 RL|S1|C10560 evo_1286_AP.033 995657
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370 RL|S1|C13546 evo_1286_AP.033 626775
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371
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372 Note: This file looks similar to the binning files but the only different which is also is important is the length column.
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373
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374 - Multiple binning files (biobox format)
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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375
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376 Files can be created via the convert_to_biobox tool
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377
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378 .. class:: infomark
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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379
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380 Example(tab separated):
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381
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382 ::
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383
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384 #CAMI Format for Binning
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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385 @Version:0.9.0
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386 @SampleID:CAMI_low
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387 @@SEQUENCEID BINID
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388 RL|S1|C10 Bin_034
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389 RL|S1|C100 Bin_023
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390 RL|S1|C1000 Bin_034
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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391 RL|S1|C10000 Bin_019
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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392 RL|S1|C10002 Bin_035
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
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393 RL|S1|C10004 Bin_035
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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394 RL|S1|C10008 Bin_034
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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395 RL|S1|C10011 Bin_035
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
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396 RL|S1|C10012 Bin_013
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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397 RL|S1|C10014 Bin_035
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398
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399 There are also additional inputs which can be used:
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400
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401 - A genome list which should be removed(tabular format)
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402
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403 .. class:: infomark
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404
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405 Example(tab separated):
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406
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407 ::
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408
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iuc
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409 evo_1035930.029 common strain
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
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410 1035930 common strain
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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411 evo_1035930.032 common strain
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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412 evo_1035930.011 common strain
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413 evo_1286_AP.033 common strain
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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414 1286_AP common strain
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
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415 evo_1286_AP.026 common strain
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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416 evo_1286_AP.037 common strain
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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417 evo_1286_AP.008 common strain
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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418 1052944 common strain
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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419 1053058 common strain
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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420 1052947 common strain
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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421 evo_1049056.013 common strain
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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422 evo_1049056.031 common strain
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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423 evo_1049056.011 common strain
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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424 1049056 common strain
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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425 evo_1049056.039 common strain
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426
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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!
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428
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429 - Genome coverage file (tabular format)
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430
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431 .. class:: infomark
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432
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433 Example(tab separated):
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434
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435 ::
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436
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437 @SampleID:gsa_pooled
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438 @@GENOMEID COVERAGE
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439 4378740.0 82.85111527272727
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440 4378740.1 27.159305090909097
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441 denovo10559.0 2.1596957142857143
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442 179927.0 1.6946866666666667
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443 denovo8373.1 2.07144
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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444 136604.0 9.150489565217391
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445 denovo8373.0 1.1413460000000002
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446 269378.0 8.051563333333332
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447 190114.0 18.253119629629627
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448 228140.0 3.078681818181818
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449 135956.0 121.52672015625001
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450 259846.0 12.298210588235296
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451 162576.0 9.57867191489362
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452 184966.0 14.461031521739134
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453
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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>`_.
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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!
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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459
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460 **Additional information**
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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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!
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
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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>