annotate cat_bins.xml @ 4:aaeb63501369 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit ec15da3a30507841856303de991cbe80c65128fd-dirty
author jjohnson
date Wed, 27 Nov 2019 10:27:23 -0500
parents 18ece3d5bcde
children 226949352e31
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1 <tool id="cat_bins" name="CAT bins" version="@VERSION@.0">
0
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2 <description>annotate with taxonomic classification</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="version_command" />
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8 <command detect_errors="exit_code"><![CDATA[
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9 #set $bin_dir = None
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10 #if len($mags) > 1:
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11 #set $bin_dir = 'inputs'
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12 mkdir -p $bin_dir &&
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13 #for mag in $mags:
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14 ln -s '$mag' $bin_dir/ &&
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15 #end for
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16 #end if
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17 CAT
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18 #if $bin_dir
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19 bins -s '.dat' -b $bin_dir
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20 #else
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21 bin -b '$mags'
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22 #end if
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23 @CAT_DB@
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24 @USE_INTERMEDIATES@
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25 @CUSTOM_SETTINGS@
4
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26 @DIAMOND_OPTIONS@
0
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27 && @TXT2TSV@ *.ORF2LCA.txt *.bin2classification.txt
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28 #if len($mags) > 1:
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29 #set pat = '$' + '{i/concatenated./}'
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30 && (for i in *.concatenated.*; do ln -s "\$i" "${pat}"; done)
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31 #end if
0
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32 @ADD_NAMES@
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33 @SUMMARISE@
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34 ]]></command>
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35 <inputs>
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36 <param name="mags" type="data" format="fasta" multiple="true" label="metagenome assembled genomes (MAGs/bins)"/>
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37 <expand macro="cat_db" />
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38 <expand macro="use_intermediates" />
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39 <expand macro="custom_settings" />
4
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40 <expand macro="diamond_options" />
0
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41 <expand macro="add_names" />
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42 <expand macro="summarise" />
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43 <expand macro="select_bat_outputs" />
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44 </inputs>
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45 <outputs>
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46 <expand macro="outputs" />
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47 </outputs>
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48 <tests>
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49 <test>
3
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50 <param name="mags" ftype="fasta" value="genome2.fna"/>
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51 <expand macro="test_catdb"/>
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52 <param name="select_outputs" value="bin2classification"/>
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53 <output name="bin2classification">
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54 <assert_contents>
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55 <has_text text="666" />
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56 </assert_contents>
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57 </output>
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58 </test>
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59 <test>
0
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60 <param name="mags" ftype="fasta" value="genome3.fna"/>
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61 <expand macro="test_catdb"/>
3
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62 <param name="select_outputs" value="bin2classification"/>
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63 <output name="bin2classification">
0
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64 <assert_contents>
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65 <has_text text="1639" />
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66 </assert_contents>
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67 </output>
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68 </test>
1
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69 <test>
0
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70 <param name="mags" ftype="fasta" value="genome2.fna,genome3.fna"/>
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71 <expand macro="test_catdb"/>
3
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72 <param name="select_outputs" value="bin2classification"/>
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73 <output name="bin2classification">
0
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74 <assert_contents>
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75 <has_text text="666" />
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76 <has_text text="1639" />
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77 </assert_contents>
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78 </output>
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79 </test>
3
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80 <test>
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81 <param name="mags" ftype="fasta" value="genome2.fna,genome3.fna"/>
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82 <expand macro="test_catdb"/>
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83 <param name="select_outputs" value="bin2classification"/>
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84 <param name="select_outputs" value="predicted_proteins_faa"/>
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85 <conditional name="names">
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86 <param name="add_names" value="both"/>
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87 </conditional>
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88 <param name="summarise" value="classification"/>
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89 <output name="predicted_proteins_faa">
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90 <assert_contents>
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91 <has_text text="contig_11394" />
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92 <has_text text="contig_4403" />
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93 </assert_contents>
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94 </output>
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95 <output name="orf2lca_names">
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96 <assert_contents>
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97 <has_text text="Listeria" />
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98 <has_text text="Vibrio" />
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99 </assert_contents>
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100 </output>
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101 <output name="classification_summary">
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102 <assert_contents>
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103 <has_text text="Listeria" />
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104 </assert_contents>
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105 </output>
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106 </test>
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107
0
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108 </tests>
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109 <help><![CDATA[
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110 **CAT bin or bins**
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111 Classify metagenomics assembled genomes.
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112
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113 @COMMON_HELP@
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114 ]]></help>
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115 <expand macro="citations" />
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116 </tool>