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comparison place_seqs.xml @ 0:37c128deea66 draft

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planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
author iuc
date Sat, 04 Mar 2023 20:25:10 +0000
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-1:000000000000 0:37c128deea66
1 <tool id="picrust2_place_seqs" name="PICRUSt2 Sequence placement" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>into reference tree</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="bio_tool"/>
7 <expand macro="requirements"/>
8 <version_command>place_seqs.py -v</version_command>
9 <command detect_errors="exit_code"><![CDATA[
10 @VAR_ACCESS_FOO@
11 @PLACE_SEQS_PREPROCESSING@
12
13 #if $intermediate_check
14 mkdir intermediate &&
15 #end if
16
17 place_seqs.py
18 @PLACE_SEQS_PARAMS@
19 --out_tree '$out_tree'
20 --processes "\${GALAXY_SLOTS:-1}"
21 #if $intermediate_check
22 --intermediate 'intermediate/place_seqs'
23 #end if
24 ## not implemented --chunk_size hoping that the default is carefully chosen
25 ## otherwise one might need to compute a "good" value from the input size
26 ## and the number of available processors
27 ]]></command>
28 <inputs>
29 <expand macro="place_seqs_params"/>
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"/>
31 </inputs>
32 <outputs>
33 <expand macro="place_seqs_output" from_work_dir="./">
34 <filter>intermediate_check is True</filter>
35 </expand>
36 </outputs>
37 <tests>
38 <test expect_num_outputs="2">
39 <param name="study_fasta" ftype="fasta" value="study_seqs_test.fasta"/>
40 <param name="placement_tool" value="sepp"/>
41 <param name="intermediate_check" value="true"/>
42 <param name="min_align" value="0.80"/>
43 <output name="out_tree" ftype="newick">
44 <assert_contents>
45 <has_text text="643348582"/>
46 <has_n_lines n="1"/>
47 </assert_contents>
48 </output>
49 <output_collection name="place_seqs_intermediate_output" type="list" count="2">
50 <element name="query_align" ftype="stockholm">
51 <assert_contents>
52 <has_text text="STOCKHOLM 1.0"/>
53 <has_n_lines n="160106"/>
54 </assert_contents>
55 </element>
56 <element name="study_seqs_filtered" ftype="fasta">
57 <assert_contents>
58 <has_text text="02905cfb87861c837dde629596d9272b"/>
59 <has_n_lines n="10"/>
60 </assert_contents>
61 </element>
62 </output_collection>
63 <assert_command>
64 <!-- make sure that prokaryotic reference is implemented by not
65 setting the ref_dir parameter, i.e. use the programms default -->
66 <has_text text="prokaryotic/pro_ref/" negate="true"/>
67 <has_text text="--ref_dir" negate="true"/>
68 </assert_command>
69 </test>
70 <!-- input data does not really work with fungal reference - but sufficient for CLI test -->
71 <test expect_num_outputs="1" expect_exit_code="1" expect_failure="true">
72 <param name="study_fasta" ftype="fasta" value="study_seqs_test.fasta"/>
73 <param name="placement_tool" value="epa-ng"/>
74 <param name="min_align" value="0.10"/>
75 <conditional name="ref_dir">
76 <param name="selector" value="fungi/fungi_ITS/"/>
77 </conditional>
78 <assert_stderr>
79 <has_text text="all 5 input sequences aligned poorly to reference sequences"/>
80 </assert_stderr>
81 <assert_command>
82 <has_text text="fungi/fungi_ITS/"/>
83 <has_text text="--min_align 0.1"/>
84 </assert_command>
85 </test>
86 <test expect_num_outputs="1">
87 <param name="study_fasta" value="study_seqs_test2.fasta"/>
88 <param name="placement_tool" value="epa-ng"/>
89 <param name="min_align" value="0.80"/>
90 <param name="intermediate_check" value="false"/>
91 <conditional name="ref_dir">
92 <param name="selector" value="custom"/>
93 <param name="custom_fna" value="img_centroid_16S_aligned_head30.fna.gz"/>
94 <param name="custom_hmm" value="img_centroid_16S_aligned_head30.hmm"/>
95 <param name="custom_tre" value="img_centroid_16S_aligned_head30.tre"/>
96 <param name="custom_model" value="img_centroid_16S_aligned_head30.model"/>
97 </conditional>
98 <output name="out_tree" ftype="newick">
99 <assert_contents>
100 <has_text text="2511231175_test"/>
101 <has_n_lines n="1"/>
102 </assert_contents>
103 </output>
104 <assert_command>
105 <has_text text="custom/"/>
106 </assert_command>
107 </test>
108 </tests>
109 <help><![CDATA[
110 @HELP_HEADER@
111
112 Place Seqs (Sequence placement)
113 ===============================
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.
115
116 Note
117 ====
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.
119
120 Input
121 =====
122 The study sequences (i.e. FASTA of amplicon sequence variants or operational taxonomic units)
123
124 Output
125 ======
126 Output tree with placed study sequences.
127
128 ]]></help>
129 <citations>
130 <citation type="doi">10.1038/s41587-020-0548-6</citation>
131 </citations>
132 </tool>