annotate generate_cannot_links.xml @ 3:68d2cd0be567 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
author iuc
date Tue, 25 Mar 2025 15:53:41 +0000
parents a6f004bc73bf
children
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1 <tool id="semibin_generate_cannot_links" name="SemiBin: Contig annotations" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>
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3
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4 </description>
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5 <macros>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="biotools"/>
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9 <expand macro="requirements"/>
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10 <expand macro="version"/>
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11 <command detect_errors="exit_code"><![CDATA[
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12 #import re
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13 @FASTA_FILES@
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14 SemiBin2
0
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15 generate_cannot_links
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16 --input-fasta 'contigs.fasta'
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17 --output 'output'
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18 --cannot-name 'cannot'
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19 #if $mode.ref.select == "cached"
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20 --reference-db-data-dir '$mode.ref.cached_db.fields.path'
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21 #end if
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22 #if $mode.ref.select == "taxonomy"
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23 --taxonomy-annotation-table '$mode.ref.taxonomy_annotation_table'
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24 #end if
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25 @MIN_LEN@
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26 #if $ml_threshold:
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27 --ml-threshold $ml_threshold
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28 #end if
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29 --cannot-name 'cannot'
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30 --threads \${GALAXY_SLOTS:-1}
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31 --processes \${GALAXY_SLOTS:-1}
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32 ]]></command>
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33 <inputs>
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34 <conditional name="mode">
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35 <expand macro="mode_select"/>
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36 <when value="single">
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37 <expand macro="input-fasta-single"/>
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38 <expand macro="ref-single-cannot"/>
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39 </when>
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40 <when value="co">
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41 <expand macro="input-fasta-single"/>
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42 <expand macro="ref-single-cannot"/>
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43 </when>
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44 <when value="multi">
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45 <expand macro="input-fasta-multi"/>
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46 <expand macro="ref-multi-cannot"/>
0
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47 </when>
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48 </conditional>
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49 <expand macro="min_len"/>
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50 <expand macro="ml-threshold"/>
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51 </inputs>
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52 <outputs>
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53 <expand macro="cannot_link_output"/>
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54 </outputs>
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55 <tests>
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56 <test expect_num_outputs="1">
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57 <conditional name="mode">
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58 <param name="select" value="single"/>
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59 <param name="input_fasta" ftype="fasta" value="input_single.fasta"/>
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60 <conditional name="ref">
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61 <param name="select" value="taxonomy"/>
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62 <param name="taxonomy_annotation_table" value="taxonomy.tsv"/>
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63 </conditional>
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64 </conditional>
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65 <conditional name="min_len">
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66 <param name="method" value="min-len"/>
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67 <param name="min_len" value="0" />
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68 </conditional>
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69 <output name="cannot" ftype="txt">
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70 <assert_contents>
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71 <has_text text="g1k_0,g4k_0"/>
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72 <has_text text="g2k_3,g4k_5"/>
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73 <has_text text="g4k_6,g4k_5"/>
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74 </assert_contents>
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75 </output>
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76 </test>
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77 <test expect_num_outputs="1">
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78 <conditional name="mode">
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79 <param name="select" value="single"/>
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80 <param name="input_fasta" ftype="fasta" value="input_single.fasta"/>
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81 <conditional name="ref">
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82 <param name="select" value="taxonomy"/>
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83 <param name="taxonomy_annotation_table" value="taxonomy.tsv"/>
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84 </conditional>
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85 </conditional>
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86 <conditional name="min_len">
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87 <param name="method" value="min-len"/>
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88 <param name="min_len" value="0" />
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89 </conditional>
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90 <output name="cannot" ftype="txt">
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91 <assert_contents>
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92 <has_text text="g1k_0,g4k_0"/>
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93 <has_text text="g2k_3,g4k_5"/>
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94 <has_text text="g4k_6,g4k_5"/>
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95 </assert_contents>
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96 </output>
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97 </test>
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98 <test expect_num_outputs="1">
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99 <conditional name="mode">
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100 <param name="select" value="single"/>
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101 <param name="input_fasta" ftype="fasta" value="input_single.fasta"/>
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102 <conditional name="ref">
3
68d2cd0be567 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
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103 <param name="select" value="cached"/>
0
078414a1226b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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104 <param name="cached_db" value="test-db"/>
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105 </conditional>
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106 </conditional>
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107 <conditional name="min_len">
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108 <param name="method" value="min-len"/>
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109 <param name="min_len" value="0" />
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110 </conditional>
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111 <output name="cannot" ftype="txt">
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112 <assert_contents>
3
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113 <has_n_lines n='300' delta="10"/>
0
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114 </assert_contents>
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115 </output>
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116 </test>
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117 </tests>
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118 <help><![CDATA[
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119 @HELP_HEADER@
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120
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121 This tool runs the contig annotations using mmseqs with GTDB and generate cannot-link file used in the semi-supervised deep learning model training.
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122
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123 Inputs
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124 ======
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125
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126 @HELP_INPUT_FASTA@
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127
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128 Outputs
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129 =======
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130
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131 @HELP_CANNOT@
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132
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133 ]]></help>
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134 <expand macro="citations"/>
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135 </tool>