Mercurial > repos > iuc > qiime_pick_otus
comparison pick_otus.xml @ 5:127947ced93f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
author | iuc |
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date | Sat, 05 Aug 2017 07:34:24 -0400 |
parents | f77fff416ea7 |
children | 241c55a65e1f |
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4:8d91fd23b326 | 5:127947ced93f |
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1 <tool id="qiime_pick_otus" name="Pick OTUs" version="@WRAPPER_VERSION@.0"> | 1 <tool id="qiime_pick_otus" name="Perform OTU picking" version="@WRAPPER_VERSION@.0"> |
2 <description></description> | 2 <description> (pick_otus)</description> |
3 <macros> | 3 <macros> |
4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
5 </macros> | 5 </macros> |
6 <expand macro="requirements"> | 6 <expand macro="requirements"> |
7 <requirement type="package" version="2.1b">sortmerna</requirement> | 7 <requirement type="package" version="2.1b">sortmerna</requirement> |
9 <!--<requirement type="package" version="2.2.22">blast-legacy</requirement>--> | 9 <!--<requirement type="package" version="2.2.22">blast-legacy</requirement>--> |
10 <requirement type="package" version="4.6.6">cd-hit</requirement> | 10 <requirement type="package" version="4.6.6">cd-hit</requirement> |
11 </expand> | 11 </expand> |
12 <version_command>pick_otus.py --version</version_command> | 12 <version_command>pick_otus.py --version</version_command> |
13 <command detect_errors="aggressive"><![CDATA[ | 13 <command detect_errors="aggressive"><![CDATA[ |
14 pick_otus.py | 14 pick_otus.py |
15 --input_seqs_filepath '$input_seqs_filepath' | 15 --input_seqs_filepath '$input_seqs_filepath' |
16 --output_dir pick_otus | 16 --output_dir pick_otus |
17 --otu_picking_method '$method.otu_picking_method' | 17 --otu_picking_method '$method.otu_picking_method' |
18 | 18 |
19 #if $method.otu_picking_method == "sortmerna" | 19 #if $method.otu_picking_method == "sortmerna" |
20 #if $method.references.source_selector == 'history' | 20 #if $method.references.source_selector == 'history' |
21 --refseqs_fp '$method.references.refseqs_fp' | 21 --refseqs_fp '$method.references.refseqs_fp' |
22 #else if $method.references.source_selector == 'cached' | 22 #else if $method.references.source_selector == 'cached' |
23 --refseqs_fp '$method.references.refseqs_fp.fields.path' | 23 --refseqs_fp '$method.references.refseqs_fp.fields.path' |
24 #end if | |
25 --sortmerna_e_value '$method.sortmerna_e_value' | |
26 --sortmerna_coverage '$method.sortmerna_coverage' | |
27 #if $method.sortmerna_tabular.test == 'yes' | |
28 --sortmerna_tabular | |
29 --sortmerna_best_N_alignments '$method.sortmerna_tabular.sortmerna_best_N_alignments' | |
30 #end if | |
31 --sortmerna_max_pos '$method.sortmerna_max_pos' | |
32 --similarity '$method.similarity' | |
33 $method.suppress_prefilter_exact_match | |
34 --threads \${GALAXY_SLOTS:-2} | |
35 #else if $method.otu_picking_method == "mothur" | |
36 --clustering_algorithm '$method.clustering_algorithm' | |
37 #else if $method.otu_picking_method == "trie" | |
38 $method.trie_reverse_seqs | |
39 #else if $method.otu_picking_method == "uclust_ref" | |
40 #if $method.references.source_selector == 'history' | |
41 --refseqs_fp '$method.references.refseqs_fp' | |
42 #else if $method.references.source_selector == 'cached' | |
43 --refseqs_fp '$method.references.refseqs_fp.fields.path' | |
44 #end if | |
45 --similarity '$method.similarity' | |
46 $method.enable_rev_strand_match | |
47 $method.suppress_presort_by_abundance_uclust | |
48 $method.suppress_new_clusters | |
49 --max_accepts '$method.max_accepts' | |
50 --max_rejects '$method.max_rejects' | |
51 --stepwords '$method.stepwords' | |
52 --word_length '$method.word_length' | |
53 #else if $method.otu_picking_method == "blast" | |
54 #if $method.references.source_selector == 'history' | |
55 --refseqs_fp '$method.references.refseqs_fp' | |
56 #else if $method.references.source_selector == 'cached' | |
57 --refseqs_fp '$method.references.refseqs_fp.fields.path' | |
58 #end if | |
59 --max_e_value_blast '$method.max_e_value_blast' | |
60 --min_aligned_percent '$method.min_aligned_percent' | |
61 --similarity '$method.similarity' | |
62 #else if $method.otu_picking_method == "sumaclust" | |
63 --similarity '$method.similarity' | |
64 '$method.sumaclust_exact' | |
65 --denovo_otu_id_prefix '$method.denovo_otu_id_prefix' | |
66 $method.suppress_prefilter_exact_match | |
67 --threads \${GALAXY_SLOTS:-2} | |
68 #else if $method.otu_picking_method == "swarm" | |
69 --denovo_otu_id_prefix '$method.denovo_otu_id_prefix' | |
70 --swarm_resolution '$method.swarm_resolution' | |
71 --threads \${GALAXY_SLOTS:-2} | |
72 #else if $method.otu_picking_method == "prefix_suffix" | |
73 --prefix_length '$method.prefix_length' | |
74 --suffix_length '$method.suffix_length' | |
75 #else if $method.otu_picking_method == "cdhit" | |
76 --similarity '$method.similarity' | |
77 #else if $method.otu_picking_method == "uclust" | |
78 --similarity '$method.similarity' | |
79 --denovo_otu_id_prefix '$method.denovo_otu_id_prefix' | |
80 $method.enable_rev_strand_match | |
81 $method.suppress_presort_by_abundance_uclust | |
82 $method.optimal_uclust | |
83 $method.exact_uclust | |
84 $method.user_sort | |
85 --max_accepts '$method.max_accepts' | |
86 --max_rejects '$method.max_rejects' | |
87 --stepwords '$method.stepwords' | |
88 --word_length '$method.word_length' | |
89 $method.suppress_uclust_stable_sort | |
90 $method.suppress_prefilter_exact_match | |
91 #end if | |
92 | |
93 #if str($prefix_prefilter_length) != '' | |
94 --prefix_prefilter_length '$prefix_prefilter_length' | |
95 #end if | |
96 $trie_prefilter | |
97 --non_chimeras_retention '$non_chimeras_retention' | |
98 | |
99 #if $method.otu_picking_method == "sortmerna" | |
100 && | |
101 rm pick_otus/sortmerna_otus.log | |
102 #end if | 24 #end if |
25 --sortmerna_e_value '$method.sortmerna_e_value' | |
26 --sortmerna_coverage '$method.sortmerna_coverage' | |
27 #if $method.sortmerna_tabular.test == 'yes' | |
28 --sortmerna_tabular | |
29 --sortmerna_best_N_alignments '$method.sortmerna_tabular.sortmerna_best_N_alignments' | |
30 #end if | |
31 --sortmerna_max_pos '$method.sortmerna_max_pos' | |
32 --similarity '$method.similarity' | |
33 $method.suppress_prefilter_exact_match | |
34 --threads \${GALAXY_SLOTS:-2} | |
35 #else if $method.otu_picking_method == "mothur" | |
36 --clustering_algorithm '$method.clustering_algorithm' | |
37 #else if $method.otu_picking_method == "trie" | |
38 $method.trie_reverse_seqs | |
39 #else if $method.otu_picking_method == "uclust_ref" | |
40 #if $method.references.source_selector == 'history' | |
41 --refseqs_fp '$method.references.refseqs_fp' | |
42 #else if $method.references.source_selector == 'cached' | |
43 --refseqs_fp '$method.references.refseqs_fp.fields.path' | |
44 #end if | |
45 --similarity '$method.similarity' | |
46 $method.enable_rev_strand_match | |
47 $method.suppress_presort_by_abundance_uclust | |
48 $method.suppress_new_clusters | |
49 --max_accepts '$method.max_accepts' | |
50 --max_rejects '$method.max_rejects' | |
51 --stepwords '$method.stepwords' | |
52 --word_length '$method.word_length' | |
53 #else if $method.otu_picking_method == "blast" | |
54 #if $method.references.source_selector == 'history' | |
55 --refseqs_fp '$method.references.refseqs_fp' | |
56 #else if $method.references.source_selector == 'cached' | |
57 --refseqs_fp '$method.references.refseqs_fp.fields.path' | |
58 #end if | |
59 --max_e_value_blast '$method.max_e_value_blast' | |
60 --min_aligned_percent '$method.min_aligned_percent' | |
61 --similarity '$method.similarity' | |
62 #else if $method.otu_picking_method == "sumaclust" | |
63 --similarity '$method.similarity' | |
64 '$method.sumaclust_exact' | |
65 --denovo_otu_id_prefix '$method.denovo_otu_id_prefix' | |
66 $method.suppress_prefilter_exact_match | |
67 --threads \${GALAXY_SLOTS:-2} | |
68 #else if $method.otu_picking_method == "swarm" | |
69 --denovo_otu_id_prefix '$method.denovo_otu_id_prefix' | |
70 --swarm_resolution '$method.swarm_resolution' | |
71 --threads \${GALAXY_SLOTS:-2} | |
72 #else if $method.otu_picking_method == "prefix_suffix" | |
73 --prefix_length '$method.prefix_length' | |
74 --suffix_length '$method.suffix_length' | |
75 #else if $method.otu_picking_method == "cdhit" | |
76 --similarity '$method.similarity' | |
77 #else if $method.otu_picking_method == "uclust" | |
78 --similarity '$method.similarity' | |
79 --denovo_otu_id_prefix '$method.denovo_otu_id_prefix' | |
80 $method.enable_rev_strand_match | |
81 $method.suppress_presort_by_abundance_uclust | |
82 $method.optimal_uclust | |
83 $method.exact_uclust | |
84 $method.user_sort | |
85 --max_accepts '$method.max_accepts' | |
86 --max_rejects '$method.max_rejects' | |
87 --stepwords '$method.stepwords' | |
88 --word_length '$method.word_length' | |
89 $method.suppress_uclust_stable_sort | |
90 $method.suppress_prefilter_exact_match | |
91 #end if | |
92 | |
93 #if str($prefix_prefilter_length) != '' | |
94 --prefix_prefilter_length '$prefix_prefilter_length' | |
95 #end if | |
96 $trie_prefilter | |
97 --non_chimeras_retention '$non_chimeras_retention' | |
98 | |
99 #if $method.otu_picking_method == "sortmerna" | |
100 && | |
101 rm pick_otus/sortmerna_otus.log | |
102 #end if | |
103 ]]></command> | 103 ]]></command> |
104 <inputs> | 104 <inputs> |
105 <param argument="--input_seqs_filepath" type="data" format="fasta" label="Input sequences file"/> | 105 <param argument="--input_seqs_filepath" type="data" format="fasta" label="Input sequences file"/> |
106 <conditional name="method"> | 106 <conditional name="method"> |
107 <param argument="--otu_picking_method" type="select" label="Method for picking OTUs"> | 107 <param argument="--otu_picking_method" type="select" label="Method for picking OTUs"> |
124 <param argument="test" type="select" label="Output alignments in the Blast tabular format with two additional columns including the CIGAR string and the percent query coverage?"> | 124 <param argument="test" type="select" label="Output alignments in the Blast tabular format with two additional columns including the CIGAR string and the percent query coverage?"> |
125 <option value="yes">Yes</option> | 125 <option value="yes">Yes</option> |
126 <option value="no" selected="true">No</option> | 126 <option value="no" selected="true">No</option> |
127 </param> | 127 </param> |
128 <when value="yes"> | 128 <when value="yes"> |
129 <param argument="--sortmerna_best_N_alignments" type="integer" value="1" label="how many alignments per read will be written"/> | 129 <param argument="--sortmerna_best_N_alignments" type="integer" value="1" label="How many alignments per read will be written"/> |
130 </when> | 130 </when> |
131 <when value="no"/> | 131 <when value="no"/> |
132 </conditional> | 132 </conditional> |
133 <param argument="--sortmerna_max_pos" type="integer" value="10000" label="Maximum number of positions per seed to store in the indexed database"/> | 133 <param argument="--sortmerna_max_pos" type="integer" value="10000" label="Maximum number of positions per seed to store in the indexed database"/> |
134 <expand macro="pick_otus_similarity"/> | 134 <expand macro="pick_otus_similarity"/> |