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comparison pick_otus.xml @ 5:127947ced93f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
author iuc
date Sat, 05 Aug 2017 07:34:24 -0400
parents f77fff416ea7
children 241c55a65e1f
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4:8d91fd23b326 5:127947ced93f
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"/>