Mercurial > repos > iuc > picrust2_place_seqs

annotate place_seqs.xml @ 1:a1dac088b84c draft default tip

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planemo upload for repository https://github.com/picrust/picrust2 commit f8c32a316582ff102c9b7edf3817000691ef9eea
author iuc
date Tue, 13 Aug 2024 12:10:32 +0000
parents 37c128deea66
children
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37c128deea66 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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1 <tool id="picrust2_place_seqs" name="PICRUSt2 Sequence placement" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>into reference tree</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="bio_tool"/>
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7 <expand macro="requirements"/>
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8 <version_command>place_seqs.py -v</version_command>
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9 <command detect_errors="exit_code"><![CDATA[
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10 @VAR_ACCESS_FOO@
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11 @PLACE_SEQS_PREPROCESSING@
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12
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13 #if $intermediate_check
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14 mkdir intermediate &&
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15 #end if
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16
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17 place_seqs.py
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18 @PLACE_SEQS_PARAMS@
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19 --out_tree '$out_tree'
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20 --processes "\${GALAXY_SLOTS:-1}"
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21 #if $intermediate_check
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22 --intermediate 'intermediate/place_seqs'
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23 #end if
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24 ## not implemented --chunk_size hoping that the default is carefully chosen
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25 ## otherwise one might need to compute a "good" value from the input size
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26 ## and the number of available processors
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27 ]]></command>
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28 <inputs>
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29 <expand macro="place_seqs_params"/>
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30 <param argument="--intermediate_check" type="boolean" truevalue="intermediate_check" falsevalue="" checked="false" label="Keep intermediate files" help="Intermediate output files will be deleted by default"/>
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31 </inputs>
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32 <outputs>
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33 <expand macro="place_seqs_output" from_work_dir="./">
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34 <filter>intermediate_check is True</filter>
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35 </expand>
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36 </outputs>
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37 <tests>
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38 <test expect_num_outputs="2">
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39 <param name="study_fasta" ftype="fasta" value="study_seqs_test.fasta"/>
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40 <param name="placement_tool" value="sepp"/>
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41 <param name="intermediate_check" value="true"/>
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42 <param name="min_align" value="0.80"/>
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43 <output name="out_tree" ftype="newick">
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44 <assert_contents>
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45 <has_text text="643348582"/>
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46 <has_n_lines n="1"/>
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47 </assert_contents>
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48 </output>
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49 <output_collection name="place_seqs_intermediate_output" type="list" count="2">
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50 <element name="query_align" ftype="stockholm">
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51 <assert_contents>
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52 <has_text text="STOCKHOLM 1.0"/>
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53 <has_n_lines n="160106"/>
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54 </assert_contents>
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55 </element>
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56 <element name="study_seqs_filtered" ftype="fasta">
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57 <assert_contents>
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58 <has_text text="02905cfb87861c837dde629596d9272b"/>
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59 <has_n_lines n="10"/>
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60 </assert_contents>
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61 </element>
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62 </output_collection>
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63 <assert_command>
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64 <!-- make sure that prokaryotic reference is implemented by not
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65 setting the ref_dir parameter, i.e. use the programms default -->
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66 <has_text text="prokaryotic/pro_ref/" negate="true"/>
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67 <has_text text="--ref_dir" negate="true"/>
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68 </assert_command>
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69 </test>
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70 <!-- input data does not really work with fungal reference - but sufficient for CLI test -->
1
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71 <test expect_exit_code="1" expect_failure="true">
0
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72 <param name="study_fasta" ftype="fasta" value="study_seqs_test.fasta"/>
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73 <param name="placement_tool" value="epa-ng"/>
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74 <param name="min_align" value="0.10"/>
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75 <conditional name="ref_dir">
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76 <param name="selector" value="fungi/fungi_ITS/"/>
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77 </conditional>
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78 <assert_stderr>
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79 <has_text text="all 5 input sequences aligned poorly to reference sequences"/>
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80 </assert_stderr>
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81 <assert_command>
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82 <has_text text="fungi/fungi_ITS/"/>
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83 <has_text text="--min_align 0.1"/>
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84 </assert_command>
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85 </test>
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86 <test expect_num_outputs="1">
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87 <param name="study_fasta" value="study_seqs_test2.fasta"/>
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88 <param name="placement_tool" value="epa-ng"/>
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89 <param name="min_align" value="0.80"/>
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90 <param name="intermediate_check" value="false"/>
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91 <conditional name="ref_dir">
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92 <param name="selector" value="custom"/>
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93 <param name="custom_fna" value="img_centroid_16S_aligned_head30.fna.gz"/>
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94 <param name="custom_hmm" value="img_centroid_16S_aligned_head30.hmm"/>
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95 <param name="custom_tre" value="img_centroid_16S_aligned_head30.tre"/>
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96 <param name="custom_model" value="img_centroid_16S_aligned_head30.model"/>
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97 </conditional>
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98 <output name="out_tree" ftype="newick">
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99 <assert_contents>
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100 <has_text text="2511231175_test"/>
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101 <has_n_lines n="1"/>
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102 </assert_contents>
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103 </output>
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104 <assert_command>
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105 <has_text text="custom/"/>
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106 </assert_command>
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107 </test>
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108 </tests>
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109 <help><![CDATA[
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110 @HELP_HEADER@
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111
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112 Place Seqs (Sequence placement)
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113 ===============================
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114 PICRUSt2 wraps HMMER to place study sequences into a reference multiple-sequence alignment and then places these sequences into the reference phylogeny with EPA-NG or SEPP. The "study sequences" referred to will be the representative OTUs and/or ASVs under the typical workflow. The tool GAPPA is used to convert the resulting .jplace object into newick format.
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115
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116 Note
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117 ====
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118 This is typically done to prepare for subsequent hidden-state prediction with PICRUSt2. Requires unaligned FASTA of study sequences. Users can specify a non-default reference files if needed.
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119
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120 Input
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121 =====
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122 The study sequences (i.e. FASTA of amplicon sequence variants or operational taxonomic units)
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123
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124 Output
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125 ======
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126 Output tree with placed study sequences.
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127
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128 ]]></help>
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129 <citations>
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130 <citation type="doi">10.1038/s41587-020-0548-6</citation>
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131 </citations>
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132 </tool>