Mercurial > repos > iuc > bbtools_bbduk

annotate macros.xml @ 3:008b8c6f6b26 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
author iuc
date Mon, 06 Feb 2023 18:04:39 +0000
parents 0247076a9567
children
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1 <macros>
3
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2 <token name="@TOOL_VERSION@">39.01</token>
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3 <token name="@VERSION_SUFFIX@">0</token>
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4 <token name="@PROFILE@">22.01</token>
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5 <xml name="edam_ontology">
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6 <edam_topics>
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7 <edam_topic>topic_0622</edam_topic> <!-- Genomics -->
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8 <edam_topic>topic_0091</edam_topic> <!-- Bioinformatics -->
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9 </edam_topics>
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10 <edam_operations>
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11 <edam_operation>operation_0496</edam_operation> <!-- Global alignment -->
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12 <edam_operation>operation_0491</edam_operation> <!-- Pairwise sequence alignment -->
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13 </edam_operations>
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14 </xml>
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15 <xml name="requirements">
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16 <requirements>
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17 <requirement type="package" version="@TOOL_VERSION@">bbmap</requirement>
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18 <requirement type="package" version="1.16.1">samtools</requirement> <!-- automatic solving installs 1.6 in some cases, instead -->
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19 </requirements>
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20 </xml>
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21 <macro name="dbKeyActionsBBMap">
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22 <expand macro="dbKeyActions">
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23 <option type="from_data_table" name="fasta_indexes" column="1" offset="0">
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24 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
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25 <filter type="param_value" ref="ref_source_cond.reference" column="1"/>
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26 </option>
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27 </expand>
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28 </macro>
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29 <macro name="dbKeyActions">
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30 <actions>
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31 <conditional name="ref_source_cond.ref_source">
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32 <when value="cached">
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33 <action type="metadata" name="dbkey">
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34 <yield/>
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35 </action>
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36 </when>
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37 <when value="history">
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38 <action type="metadata" name="dbkey">
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39 <option type="from_param" name="ref_source_cond.reference" param_attribute="dbkey"/>
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40 </action>
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41 </when>
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42 </conditional>
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43 </actions>
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44 </macro>
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45 <macro name="input_type_cond">
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46 <conditional name="input_type_cond">
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47 <param name="input_type" type="select" label="Choose the category of the files to be analyzed">
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48 <option value="single" selected="true">Single dataset</option>
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49 <option value="pair">Dataset pair</option>
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50 <option value="paired">List of dataset pairs</option>
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51 </param>
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52 <when value="single">
1
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53 <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Fastq file"/>
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54 </when>
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55 <when value="pair">
1
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56 <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Forward reads fastq file"/>
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57 <param name="read2" type="data" format="fastqsanger.gz,fastqsanger" label="Reverse reads fastq file"/>
0
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58 </when>
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59 <when value="paired">
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60 <param name="reads_collection" type="data_collection" format="fastqsanger,fastqsanger.gz" collection_type="paired" label="Collection of fastqsanger paired read files"/>
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61 </when>
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62 </conditional>
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63 </macro>
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64 <macro name="reference_source_cond">
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65 <conditional name="ref_source_cond">
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66 <param name="ref_source" type="select" label="Select reference genome source; a cached reference or one from the history">
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67 <option value="cached" selected="True">Use a cached reference</option>
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68 <option value="history">Use a reference from the history</option>
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69 </param>
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70 <when value="cached">
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71 <param name="reference" type="select" label="Using reference genome">
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72 <options from_data_table="fasta_indexes">
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73 <filter type="sort_by" column="2"/>
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74 <validator type="no_options" message="A built-in reference genome is not available"/>
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75 </options>
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76 </param>
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77 </when>
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78 <when value="history">
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79 <param name="reference" type="data" format="fasta" label="Using reference genome"/>
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80 </when>
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81 </conditional>
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82 </macro>
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83 <macro name="ktrim_cond">
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84 <conditional name="ktrim_cond">
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85 <param name="ktrim_select" type="select" label="Trim reads to remove bases matching reference kmers?">
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86 <option value="no" selected="true">No</option>
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87 <option value="yes">Yes</option>
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88 </param>
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89 <when value="no"/>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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90 <when value="yes">
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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91 <param argument="ktrim" type="select" label="Select trimming position">
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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92 <option value="r">Trim to the right</option>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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93 <option value="l">Trim to the left</option>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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94 </param>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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95 <param argument="minlength" type="integer" value="10" label="Minimum read length" help="Trimmed reads shorter than this will be discarded, pairs will be discarded if both are shorter."/>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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96 </when>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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97 </conditional>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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98 </macro>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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99 <xml name="citations">
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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100 <citations>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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101 <citation type="doi">
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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102 https://doi.org/10.1371/journal.pone.0185056
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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103 </citation>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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104 </citations>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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105 </xml>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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106 </macros>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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107