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annotate cat_bins.xml @ 2:31853794ace2 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 2948f114101aeefa951f47df8ee3b25656d9680e
author iuc
date Thu, 09 Mar 2023 21:01:12 +0000
parents 18676df0cb3a
children 0e63d03c8790
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31853794ace2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 2948f114101aeefa951f47df8ee3b25656d9680e
iuc
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1 <tool id="cat_bins" name="CAT bins" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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[
2
31853794ace2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 2948f114101aeefa951f47df8ee3b25656d9680e
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9 #import re
0
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10 #set $bin_dir = None
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11 #if len($mags) > 1:
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12 #set $bin_dir = 'inputs'
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13 mkdir -p $bin_dir &&
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14 #for mag in $mags:
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31853794ace2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 2948f114101aeefa951f47df8ee3b25656d9680e
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15 #set input_identifier = re.sub('[^\s\w\-]', '_', str($mag.element_identifier))
31853794ace2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 2948f114101aeefa951f47df8ee3b25656d9680e
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16 ln -s '$mag' '${bin_dir}/${input_identifier}.FASTA' &&
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17 #end for
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18 #else
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19 #set $bin_file = re.sub('[^\s\w\-]', '_', str($mags[0].element_identifier))
31853794ace2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 2948f114101aeefa951f47df8ee3b25656d9680e
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20 ln -s $mags[0] '$bin_file' &&
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21 #end if
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22 CAT
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23 #if $bin_dir
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24 bins -s '.FASTA' -b '$bin_dir'
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25 #else
2
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26 bin -b '$bin_file'
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27 #end if
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28 @CAT_DB@
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29 @USE_INTERMEDIATES@
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30 @CUSTOM_SETTINGS@
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31 @DIAMOND_OPTIONS@
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32 && @TXT2TSV@ *.ORF2LCA.txt *.bin2classification.txt
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33 #if len($mags) > 1:
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34 #set pat = '$' + '{i/concatenated./}'
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35 && (for i in *.concatenated.*; do ln -s "\$i" "${pat}"; done)
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36 #end if
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37 @ADD_NAMES@
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38 @SUMMARISE@
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39 ]]></command>
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40 <inputs>
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41 <param name="mags" type="data" format="fasta" multiple="true" label="metagenome assembled genomes (MAGs/bins)"/>
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42 <expand macro="cat_db" />
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43 <expand macro="use_intermediates" />
1
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44 <expand macro="custom_settings_bins" />
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45 <expand macro="diamond_options" />
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46 <expand macro="add_names" />
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47 <expand macro="summarise" />
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48 <expand macro="select_bat_outputs" />
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49 </inputs>
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50 <outputs>
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51 <expand macro="outputs" />
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52 </outputs>
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53 <tests>
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54 <test>
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55 <param name="mags" ftype="fasta" value="genome2.fna"/>
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56 <expand macro="test_catdb"/>
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57 <param name="select_outputs" value="bin2classification"/>
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58 <output name="bin2classification">
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59 <assert_contents>
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60 <has_text text="666" />
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61 </assert_contents>
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62 </output>
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63 </test>
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64 <test>
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65 <param name="mags" ftype="fasta" value="genome3.fna"/>
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66 <expand macro="test_catdb"/>
0094893f5001 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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67 <param name="select_outputs" value="bin2classification"/>
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68 <output name="bin2classification">
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69 <assert_contents>
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70 <has_text text="1639" />
0094893f5001 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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71 </assert_contents>
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72 </output>
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73 </test>
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74 <test>
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75 <param name="mags" ftype="fasta" value="genome2.fna,genome3.fna"/>
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76 <expand macro="test_catdb"/>
0094893f5001 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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77 <param name="select_outputs" value="bin2classification"/>
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78 <output name="bin2classification">
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79 <assert_contents>
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80 <has_text text="666" />
0094893f5001 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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81 <has_text text="1639" />
0094893f5001 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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82 </assert_contents>
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83 </output>
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84 </test>
0094893f5001 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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85 <test>
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86 <param name="mags" ftype="fasta" value="genome2.fna,genome3.fna"/>
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87 <expand macro="test_catdb"/>
0094893f5001 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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88 <param name="select_outputs" value="bin2classification"/>
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31853794ace2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 2948f114101aeefa951f47df8ee3b25656d9680e
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89 <param name="select_outputs" value="predicted_proteins_faa"/>
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90 <param name="fraction" value="0.6"/>
0
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91 <conditional name="names">
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92 <param name="add_names" value="both"/>
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93 </conditional>
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94 <param name="summarise" value="classification"/>
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95 <output name="predicted_proteins_faa">
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96 <assert_contents>
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97 <has_text text="contig_11394" />
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98 <has_text text="contig_4403" />
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99 </assert_contents>
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100 </output>
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101 <output name="orf2lca_names">
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102 <assert_contents>
2
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103 <has_text text="Vibrionaceae" />
0
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104 <has_text text="Vibrio" />
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105 </assert_contents>
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106 </output>
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107 <output name="classification_summary">
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108 <assert_contents>
2
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109 <has_text text="Gammaproteobacteria" />
0
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110 </assert_contents>
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111 </output>
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112 </test>
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113
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114 </tests>
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115 <help><![CDATA[
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116 **CAT bin** or **CAT bins**
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117
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118 Classify metagenomics assembled genomes.
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119
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120 @COMMON_HELP@
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121
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122 **INPUTS**
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123
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124 One or more fasta files of metagenome assembled genomes.
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125
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126 @OUTPUTS_HELP@
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127
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128 **CAT bins**
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129
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130 Run Bin Annotation Tool (BAT) on a set of bins.
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131
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132 Required arguments:
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133 -b, --bin_folder Path to directory containing bins.
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134 -d, --database_folder Path to folder that contains database files.
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135 -t, --taxonomy_folder Path to folder that contains taxonomy files.
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136
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137
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138 @OPTIONS_HELP@
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139
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140 ]]></help>
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141 <expand macro="citations" />
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142 </tool>