Mercurial > repos > iuc > picrust2_shuffle_predictions

annotate macros.xml @ 0:881f2faa5fe7 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
author iuc
date Sat, 04 Mar 2023 20:28:14 +0000
parents
children 677f3c8db525
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
1 <?xml version="1.0"?>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
2 <macros>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
3 <token name="@TOOL_VERSION@">2.5.1</token>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
4 <token name="@VERSION_SUFFIX@">0</token>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
5 <token name="@PROFILE@">22.01</token>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
6 <xml name="bio_tool">
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
7 <xrefs>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
8 <xref type="bio.tools">picrust2</xref>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
9 </xrefs>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
10 </xml>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
11 <xml name="requirements">
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
12 <requirements>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
13 <requirement type="package" version="@TOOL_VERSION@">picrust2</requirement>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
14 <yield/>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
15 </requirements>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
16 </xml>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
17 <token name="@HELP_HEADER@">
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
18 What it does
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
19 ============
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
20
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
21 PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
22 Unobserved States) is a tool for predicting functional abundances based only on
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
23 marker gene sequences.
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
24
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
25 Read more about the tool: https://github.com/picrust/picrust2/wiki
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
26 </token>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
27 <xml name="citations">
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
28 <citations>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
29 <citation type="doi">10.1038/s41587-020-0548-6</citation>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
30 </citations>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
31 </xml>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
32
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
33
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
34
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
35 <token name="@VAR_ACCESS_FOO@"><![CDATA[
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
36 ## in picrust2_pipeline the parameters are within a section or a
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
37 ## conditional. in the separate sections they are not.
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
38 ## this function allows unified access
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
39 #def getVarCond($sec_cond, $var)
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
40 #if $varExists($var)
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
41 #return $getVar($var)
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
42 #else if $varExists($sec_cond + "." + $var)
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
43 #return $getVar($sec_cond + "." + $var)
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
44 #else
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
45 #return
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
46 #end if
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
47 #end def
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
48 ]]></token>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
49
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
50 <!-- macros for place_seqs -->
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
51
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
52 <token name="@PLACE_SEQS_PREPROCESSING@"><![CDATA[
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
53 ## determine project dir which is something like /lib/python3.8/site-packages/picrust2/default_files/
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
54 PROJECT_DIR=\$(python -c 'from picrust2 import default; print(default.project_dir)') &&
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
55 REF_DIR_BASE=\$PROJECT_DIR"/default_files/" &&
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
56 #if $getVarCond("place_seqs_section", "ref_dir.selector") == "custom"
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
57 mkdir -p custom/ &&
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
58 ln -s '$getVarCond("place_seqs_section", "ref_dir.custom_fna")' custom/custom.fna &&
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
59 ln -s '$getVarCond("place_seqs_section", "ref_dir.custom_hmm")' custom/custom.hmm &&
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
60 #if $getVarCond("place_seqs_section", "placement_tool") == "epa-ng"
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
61 ln -s '$getVarCond("place_seqs_section", "ref_dir.custom_model")' custom/custom.model &&
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
62 #else if $getVarCond("place_seqs_section", "placement_tool")
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
63 ln -s '$getVarCond("place_seqs_section", "ref_dir.custom_model")' custom/custom.raxml_info &&
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
64 #end if
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
65 ln -s '$getVarCond("place_seqs_section", "ref_dir.custom_tre")' custom/custom.tre &&
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
66 #end if
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
67 ]]></token>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
68 <token name="@PLACE_SEQS_PARAMS@"><![CDATA[
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
69 --study_fasta '$getVarCond("place_seqs_section", "study_fasta")'
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
70 --placement_tool '$getVarCond("place_seqs_section", "placement_tool")'
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
71 ## set refdir (default is prokaryotic), even if the default will
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
72 ## be treated internally as `"\$REF_DIR_BASE"$ref_dir.selector`
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
73 ## picrust2 will complain about non-default reference files
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
74 ## specified with default pathway mapfile
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
75 #if $getVarCond("place_seqs_section", "ref_dir.selector") == "custom"
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
76 --ref_dir custom/
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
77 #else if $getVarCond("place_seqs_section", "ref_dir.selector") != "prokaryotic/pro_ref/"
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
78 --ref_dir "\$REF_DIR_BASE"$getVarCond("place_seqs_section", "ref_dir.selector")
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
79 #end if
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
80 --min_align $getVarCond("place_seqs_section", "min_align")
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
81 ]]></token>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
82 <xml name="place_seqs_params">
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
83 <param argument="--study_fasta" type="data" format="fasta" label="Study sequences" help="Sequences of the representative OTUs and/or ASVs. Sequences need to be on the positive strand and the headerline should be only one field, i.e. no additional whitespace-delimited fields"/>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
84 <param argument="--placement_tool" type="select" label="Placement tool" help="Used for placing sequences into reference tree">
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
85 <option value="epa-ng" selected="true">EPA-ng - Fast, parallel, highly accurate Maximum Likelihood Phylogenetic Placement, by the team behind RAxML(-ng)</option>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
86 <option value="sepp">SEPP - SATe-enabled Phylogenetic Placement</option>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
87 </param>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
88 <conditional name="ref_dir">
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
89 <param name="selector" type="select" label="Reference data" help="Used for sequence placement">
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
90 <option value="prokaryotic/pro_ref/" selected="true">Prokaryotic 16S rRNA gene</option>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
91 <!-- TODO https://github.com/picrust/picrust2/issues/276 -->
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
92 <option value="fungi/fungi_ITS/">Fungal ITS (only for epa-ng)</option>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
93 <option value="fungi/fungi_18S/">Fungal 18S (only for epa-ng)</option>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
94 <option value="custom">Custom reference sequence files</option>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
95 </param>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
96 <when value="prokaryotic/pro_ref/"/>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
97 <when value="fungi/fungi_ITS/"/>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
98 <when value="fungi/fungi_18S/"/>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
99 <when value="custom">
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
100 <param name="custom_fna" type="data" format="fasta" label="Multiple-sequence alignment of reference sequences"/>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
101 <param name="custom_hmm" type="data" format="hmm2,hmm3" label="Hidden-markov model of the multiple-sequence alignment" help="The HMM of the alignment can be created using hmmbuild"/>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
102 <param name="custom_tre" type="data" format="newick" label="Tree of the reference sequences"/>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
103 <param name="custom_model" type="data" format="txt" label="Modelfile" help="For epa-ng: output by RaXmL specifying the best parameters for the tree, for sepp see examples in PICRUSt2 repository"/>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
104 </when>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
105 </conditional>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
106 <param argument="--min_align" type="float" value="0.80" min="0.0" max="1.0" label="Minimum alignment length" help="Proportion of the total length of an input query sequence that must align with reference sequences. Sequences with lengths below this value will be excluded from the placement and all subsequent steps"/>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
107 </xml>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
108 <xml name="place_seqs_output" tokens="from_work_dir" token_label_suffix="">
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
109 <data name="out_tree" format="newick" from_work_dir="@FROM_WORK_DIR@/out.tre" label="${tool.name} on ${on_string}: Tree of reference and study 16S sequences @LABEL_SUFFIX@"/>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
110 <collection name="place_seqs_intermediate_output" type="list" label="${tool.name} on ${on_string}: Intermediate files @LABEL_SUFFIX@" >
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
111 <discover_datasets pattern="__name_and_ext__" directory="@FROM_WORK_DIR@/intermediate/place_seqs/"/>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
112 <yield/>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
113 </collection>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
114 </xml>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
115
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
116 <!-- parameters of hsp -->
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
117 <token name="@HSP_PARAMS@"><![CDATA[
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
118 ## hsp and picrust2_pipeline
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
119 #if $getVarCond("hsp_section", "trait_input.selector") == "default"
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
120 #if $varExists('trait_input.in_trait')
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
121 --in_trait '$trait_input.in_trait'
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
122 #else if $varExists('hsp_section.trait_input.in_traits')
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
123 --in_traits '$hsp_section.trait_input.in_traits'
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
124 #else
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
125 #raise Exception("wrapper must define in_trait / in_traits")
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
126 #end if
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
127 #else if $getVarCond("hsp_section", "trait_input.selector") == "custom"
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
128 #if $varExists('trait_input.observed_trait_table')
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
129 --observed_trait_table '$trait_input.observed_trait_table'
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
130 #else if $varExists('hsp_section.trait_input.custom_trait_tables')
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
131 --custom_trait_tables '$hsp_section.trait_input.custom_trait_tables'
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
132 --marker_gene_table '$hsp_section.trait_input.marker_gene_table'
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
133 #else
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
134 #raise Exception("wrapper must define observed_trait_table / (custom_trait_tables + marker_gene_table)")
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
135 #end if
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
136 #end if
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
137
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
138
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
139 --hsp_method '$getVarCond("hsp_section", "hsp_method_options.hsp_method")'
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
140 #if $getVarCond("hsp_section", "hsp_method_options.hsp_method") == "mp"
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
141 --edge_exponent $getVarCond("hsp_section", "hsp_method_options.edge_exponent")
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
142 #else if $getVarCond("hsp_section", "") == "emp_prob"
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
143 ## special treatment of seed (option absent in picrust2_pipeline)
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
144 #if $varExists('hsp_method_options') and has_attrib($hsp_method_options, "seed")
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
145 --seed $hsp_method_options.seed
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
146 #end if
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
147 #end if
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
148 ## hsp and picrust2_pipeline use different CLI params to toggle NSTI computation
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
149 #if $varExists('calculate_NSTI')
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
150 $calculate_NSTI
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
151 #else if $varExists('hsp_section.skip_nsti')
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
152 $hsp_section.skip_nsti
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
153 #else
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
154 #raise Exception("wrapper must define calculate_NSTI / skip_nsti")
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
155 #end if
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
156 ]]></token>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
157 <!-- - one of nsti_[true,false]value must be given: CLI param
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
158 differs between hsp and picrust2_pipeline
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
159 - nsti_checked must be set accordingly to true or false
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
160
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
161 furthermore there three yields can be used (2 names & 1 unnamed)
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
162 - the unnamed is used to add the seed param for hsp (for \-\-hsp_method emp_prob)
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
163 - the named yield `add_default_traits` is used to add two default trait tables for hsp
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
164 - the named yield `custom_traits` is used for the different parameters
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
165 to specify custom trait tables in hsp (observed_trait_table) and
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
166 picrust2_pipeline (custom_trait_tables, marker_gene_table)
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
167 -->
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
168 <xml name="hsp_params" tokens="nsti_checked,in_trait_arg,in_trait_multiple,in_trait_label_suff" token_nsti_truevalue="" token_nsti_falsevalue="" token_in_traits_help="">
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
169 <conditional name="trait_input">
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
170 <param name="selector" type="select" label="Trait table@IN_TRAIT_LABEL_SUFF@" help="i.e. which gene families to predict">
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
171 <option value="default" selected="true">Default trait table@IN_TRAIT_LABEL_SUFF@</option>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
172 <option value="custom">Customized trait table@IN_TRAIT_LABEL_SUFF@</option>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
173 </param>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
174 <when value="default">
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
175 <param argument="@IN_TRAIT_ARG@" type="select" multiple="@IN_TRAIT_MULTIPLE@" optional="false" label="Pre-calculated trait table@IN_TRAIT_LABEL_SUFF@" help="@IN_TRAITS_HELP@">
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
176 <option value="COG">Clusters of Orthologous Genes database (COG)</option>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
177 <option value="EC" selected="true">Enzyme Commission number database (EC number)</option>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
178 <option value="KO" selected="true">KEGG Orthology database (KO)</option>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
179 <option value="PFAM">Pfam database</option>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
180 <option value="TIGRFAM">TIGRFAM database</option>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
181 <yield name="add_default_traits"/>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
182 </param>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
183 </when>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
184 <when value="custom">
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
185 <yield name="custom_traits"/>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
186 </when>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
187 </conditional>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
188 <conditional name="hsp_method_options">
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
189 <param argument="--hsp_method" type="select" label="Hidden-state prediction method">
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
190 <option value="mp" selected="true">Predict discrete traits by: Maximum parsimony (mp)</option>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
191 <option value="emp_prob">Predict discrete traits by: Empirical state probabilities across tips (emp_prob)</option>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
192 <option value="subtree_average">Predict continuous traits by: Subtree averaging (subtree_average)</option>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
193 <option value="pic">Predict continuous traits by: phylogentic independent contrast (pic)</option>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
194 <option value="scp">Reconstruct continuous traits by: squared-change parsimony (scp)</option>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
195 </param>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
196 <when value="mp">
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
197 <param argument="--edge_exponent" type="float" value="0.5" min="0.0" label="Transition cost weight" help="Specifies weighting transition costs by the inverse length of edge lengths. If 0, then edge lengths do not influence predictions"/>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
198 </when>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
199 <when value="emp_prob">
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
200 <yield/>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
201 </when>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
202 <when value="subtree_average"/>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
203 <when value="pic"/>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
204 <when value="scp"/>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
205 </conditional>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
206 <param argument="@NSTI_TRUEVALUE@@NSTI_FALSEVALUE@" type="boolean" truevalue="@NSTI_TRUEVALUE@" falsevalue="@NSTI_FALSEVALUE@" checked="@NSTI_CHECKED@" label="Calculate NSTI and add to output file" help="And add to output file"/>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
207 </xml>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
208
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
209 <!-- parameters of the metagenome_pipeline -->
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
210
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
211 <token name="@PREPARE_METAGENOME_PIPELINE_PARAMS@"><![CDATA[
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
212 #set $_input=$getVarCond("metagenome_pipeline_section", "input")
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
213 #if $_input.ext == "mothur.shared"
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
214 #set ext="msf"
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
215 #else if $_input.ext == "tabular"
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
216 #set ext="tsv"
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
217 #else if $_input.ext.startswith('biom')
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
218 #set ext="biom"
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
219 #else
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
220 >&2 "unknown extension $_input.ext"
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
221 exit 1;
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
222 #end if
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
223 ln -s '$input' 'input.$ext' &&
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
224 ]]></token>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
225 <token name="@METAGENOME_PIPELINE_PARAMS@"><![CDATA[
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
226 --input 'input.$ext'
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
227 #if $getVarCond("metagenome_pipeline_section", "input_options.selector") == "ASV"
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
228 --min_reads $getVarCond("metagenome_pipeline_section", "input_options.min_reads")
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
229 --min_samples $getVarCond("metagenome_pipeline_section", "input_options.min_samples")
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
230 #end if
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
231 $getVarCond("metagenome_pipeline_section", "stratified_output.selector")
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
232 #if $getVarCond("metagenome_pipeline_section", "stratified_output.selector") != ''
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
233 $getVarCond("metagenome_pipeline_section", "stratified_output.wide_table")
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
234 #end if
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
235 $getVarCond("metagenome_pipeline_section", "skip_norm")
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
236 --max_nsti $getVarCond("metagenome_pipeline_section", "max_nsti")
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
237 ]]></token>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
238 <xml name="metagenome_pipeline_params" tokens="stratified_arg">
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
239 <param argument="--input" type="data" format="tabular,biom1,biom2,mothur.shared" label="Sequence abundance table (OTUs or ASVs)" help="The sequence abundances should be in read counts and not relative abundances. The tool will normalize the input sequence abundance table by the predicted number of marker genes"/>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
240 <conditional name="input_options">
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
241 <param name="selector" type="select" label="Sequence abundance table type">
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
242 <option value="OTU" selected="true">Operational Taxonomic Units (OTU)</option>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
243 <option value="ASV">Amplicon Sequence Variants (ASV)</option>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
244 </param>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
245 <when value="OTU">
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
246 </when>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
247 <when value="ASV">
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
248 <param argument="--min_reads" type="integer" min="1" value="1" label="Minimum number of reads across all samples for each input ASV" help="ASVs below this cut-off will be counted as part of the RARE category in the stratified output"/>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
249 <param argument="--min_samples" type="integer" min="1" value="1" label="Minimum number of samples that an ASV needs to be identfied within" help="ASVs below this cut-off will be counted as part of the RARE category in the stratified output"/>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
250 </when>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
251 </conditional>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
252 <yield/>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
253 <param argument="--max_nsti" type="float" min="0" value="2.0" label="Maximum Nearest-sequenced taxon index (NSTI)" help="Sequences with larger values will be excluded"/>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
254 <conditional name="stratified_output">
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
255 <param argument="@STRATIFIED_ARG@" name="selector" type="select" label="Generate an output table stratified by sequences">
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
256 <option value="" selected="true">No</option>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
257 <option value="@STRATIFIED_ARG@">Yes [will increase run-time]</option>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
258 </param>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
259 <when value=""/>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
260 <when value="@STRATIFIED_ARG@">
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
261 <param argument="--wide_table" type="boolean" truevalue="--wide_table" falsevalue="" checked="false" label="Output wide-format stratified table of metagenome predictions" help="This is the deprecated method of generating stratified tables since it is extremely memory intensive"/>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
262 </when>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
263 </conditional>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
264 <param argument="--skip_norm" type="boolean" truevalue="--skip_norm" falsevalue="" checked="false" label="Skip normalizing sequence abundances by predicted marker gene copy numbers"/>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
265 </xml>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
266
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
267 <!-- pathway_pipeline macros-->
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
268 <token name="@PATHWAY_PIPELINE_PARAMS@"><![CDATA[
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
269 ## in pathway_pipeline its --map while in picrust2_pipeline its --pathway_map
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
270 #if $varExists('map') and $map
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
271 --map '$map'
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
272 #else if $varExists('predict_pathways.pathway_map') and $predict_pathways.pathway_map
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
273 --pathway_map '$predict_pathways.pathway_map'
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
274 #end if
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
275 $getVarCond("predict_pathways", "skip_minpath")
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
276 $getVarCond("predict_pathways", "no_gap_fill")
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
277 $getVarCond("predict_pathways", "regrouping.no_regroup")
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
278 #if $getVarCond("predict_pathways", "regrouping.no_regroup") == '' and $getVarCond("predict_pathways", "regrouping.regroup_map")
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
279 --regroup_map '$getVarCond("predict_pathways", "regroup_map")'
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
280 #end if
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
281 $getVarCond("predict_pathways", "strat_output.per_sequence_contrib")
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
282 #if $getVarCond("predict_pathways", "strat_output.per_sequence_contrib") != ""
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
283 --per_sequence_function '$getVarCond("predict_pathways", "strat_output.per_sequence_function")'
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
284 --per_sequence_abun '$getVarCond("predict_pathways", "strat_output.per_sequence_abun")'
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
285 $getVarCond("predict_pathways", "strat_output.wide_table")
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
286 #end if
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
287 $getVarCond("predict_pathways", "coverage")
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
288 ]]></token>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
289 <xml name="pathway_pipeline_params" tokens="mapargument">
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
290 <param argument="@MAPARGUMENT@" type="data" format="txt,tabular" optional="true" label="Customized table mapping of pathways to reactions" help="Default mapping file is Maps MetaCyc reactions to prokaryotic MetaCyc pathways"/>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
291 <param argument="--skip_minpath" type="boolean" truevalue="" falsevalue="--skip_minpath" checked="true" label="Run MinPath to identify which pathways are present as a first pass"/>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
292 <param argument="--no_gap_fill" type="boolean" truevalue="" falsevalue="--no_gap_fill" checked="true" label="Perform gap filling before predicting pathway abundances"/>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
293 <conditional name="regrouping">
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
294 <param argument="--no_regroup" type="select" label="Regroup input gene families to reactions">
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
295 <option value="">Yes</option>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
296 <option value="--no_regroup">No</option>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
297 </param>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
298 <when value="">
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
299 <param argument="--regroup_map" type="data" format="tabular" optional="true" label="Mapfile of ids to regroup gene families to before running MinPath" help="Keep empty to use the default mapping file (ec_level4_to_metacyc_rxn.tsv contained in PICRUSt2)"/>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
300 </when>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
301 <when value="--no_regroup"/>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
302 </conditional>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
303 <conditional name="strat_output">
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
304 <param argument="--per_sequence_contrib" type="select" label="Calculate pathway abundances for each individual predicted genome" help="The output will be the predicted pathway abundance contributed by each individual sequence. This is in contrast to the default stratified output, which is the contribution to the community-wide pathway abundances. Note this will greatly increase the runtime. Experimental pathway coverage stratified by contributing sequence will also be output when --coverage is set">
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
305 <option value="--per_sequence_contrib">Yes</option>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
306 <option value="" selected="true">No</option>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
307 </param>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
308 <when value="--per_sequence_contrib">
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
309 <param argument="--per_sequence_abun" type="data" format="tabular" label="Table of sequence abundances across samples normalized by marker copy number" help="Typically the normalized sequence abundance table output at the metagenome pipeline step. This input is required when the per sequence contrib option is set"/>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
310 <param argument="--per_sequence_function" type="data" format="tabular" label="Table of function abundances per sequence, which was outputted at the hidden-state prediction step" help="This input is required when the per sequence contrib option is set. Note that this file should be the same input table as used for the metagenome pipeline step"/>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
311 <!-- TODO maybe deprecate .. because complicated anyway as its used in metagenome_pipeline as well and help says deprecated as well -->
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
312 <param argument="--wide_table" type="boolean" truevalue="--wide_table" falsevalue="" checked="false" label="Output wide-format stratified table (DEPRECATED)" help="Instead of the metagenome contribution table. This is the deprecated method of generating
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
313 stratified tables since it is extremely memory intensive"/>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
314 </when>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
315 <when value=""/>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
316 </conditional>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
317 <param argument="--coverage" type="boolean" truevalue="--coverage" falsevalue="" checked="false" label="Calculate pathway coverages as well as abundances" help="Experimental and only useful for advanced users"/>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
318 </xml>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
319 <xml name="pathways_output" tokens="from_work_dir" token_label_suffix="">
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
320 <data name="pathways_output" format="tabular" from_work_dir="@FROM_WORK_DIR@/pathways_out/path_abun_unstrat.tabular" label="${tool.name} on ${on_string}: Pathway abundances">
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
321 <yield/>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
322 </data>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
323 <collection name="pathways_intermediate_output" type="list" label="${tool.name} on ${on_string}: Intermediate files @LABEL_SUFFIX@" >
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
324 <discover_datasets pattern="__name_and_ext__" directory="@FROM_WORK_DIR@/intermediate/pathways/" format="tabular"/>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
325 <yield name="intermediate_filter"/>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
326 </collection>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
327 <data format="tabular" name="path_cov_unstrat" from_work_dir="@FROM_WORK_DIR@/pathways_out/path_cov_unstrat.tabular" label="${tool.name} on ${on_string}: Pathway coverage @LABEL_SUFFIX@" >
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
328 <yield/>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
329 <yield name="coverage_filter"/>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
330 </data>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
331 <data format="tabular" name="path_abun_unstrat_per_seq" from_work_dir="@FROM_WORK_DIR@/pathways_out/path_abun_unstrat_per_seq.tabular" label="${tool.name} on ${on_string}: Pathway abundance unstratified per sequence @LABEL_SUFFIX@" >
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
332 <yield/>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
333 <yield name="per_sequence_filter"/>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
334 </data>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
335 <data format="tabular" name="path_abun_predictions" from_work_dir="@FROM_WORK_DIR@/pathways_out/path_abun_predictions.tabular" label="${tool.name} on ${on_string}: Pathway abundance predictions @LABEL_SUFFIX@" >
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
336 <yield/>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
337 <yield name="per_sequence_filter"/>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
338 </data>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
339 <data format="tabular" name="path_abun_contrib" from_work_dir="@FROM_WORK_DIR@/pathways_out/path_abun_contrib.tabular" label="${tool.name} on ${on_string}: Pathway abundance contributed @LABEL_SUFFIX@" >
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
340 <yield/>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
341 <yield name="per_sequence_filter"/>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
342 </data>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
343 </xml>
881f2faa5fe7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
344 </macros>