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comparison pick_open_reference_otus.xml @ 0:c9ba18104883 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
author iuc
date Thu, 18 May 2017 09:16:21 -0400
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-1:000000000000 0:c9ba18104883
1 <tool id="pick_open_reference_otus" name="Perform open-reference OTU picking" version="@WRAPPER_VERSION@.0">
2 <description></description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <version_command>pick_open_reference_otus.py --version</version_command>
8 <command detect_errors="aggressive"><![CDATA[
9 pick_open_reference_otus.py
10 --input_fps '$input_fps'
11 -o otus
12 --otu_picking_method '$otu_picking_method'
13 #if str( $ref_sequences.selector ) == 'history'
14 #set $ref = $ref_sequences.reference_fp
15 #else:
16 #set $ref = $ref_sequences.reference_fp.fields.path
17 #end if
18 --reference_fp '$ref'
19 #if str( $prefilter.use_prefilter ) == 'yes'
20 #if str( $prefilter.prefilter_ref_seq.selector ) == 'history'
21 #set $ref = $prefilter.prefilter_ref_seq.prefilter_refseqs_fp
22 #else:
23 #set $ref = $prefilter.prefilter_ref_seq.prefilter_refseqs_fp.fields.path
24 #end if
25 --prefilter_refseqs_fp '$ref'
26 #end if
27 --new_ref_set_id '$new_ref_set_id'
28 $parallel
29 -O "\${GALAXY_SLOTS:-4}"
30 --percent_subsample '$percent_subsample'
31 --prefilter_percent_id '$prefilter_percent_id'
32 #if str($step1_otu_map_fp) != 'None':
33 --step1_otu_map_fp '$step1_otu_map_fp'
34 #end if
35 #if str($step1_failures_fasta_fp) != 'None':
36 --step1_failures_fasta_fp='$step1_failures_fasta_fp'
37 #end if
38 --minimum_failure_threshold '$minimum_failure_threshold'
39 $suppress_step4
40 --min_otu_size '$min_otu_size'
41 $suppress_taxonomy_assignment
42 $suppress_align_and_tree
43
44 #if str( $suppress_align_and_tree ) == ""
45 #if str( $suppress_taxonomy_assignment ) == ""
46 && mv otus/otu_table_mc*_w_tax.biom otus/otu_table_w_tax.biom
47 && mv otus/otu_table_mc*_w_tax_no_pynast_failures.biom otus/tu_table_w_tax_no_pynast_failures
48 #else
49 && mv otus/otu_table_mc*_no_pynast_failures.biom otus/otu_table_no_pynast_failures.biom
50 #end if
51 #end if
52
53 ]]></command>
54 <inputs>
55 <param argument="--input_fps" type="data" format="fasta,fastq" multiple="True" label="Input sequence files"/>
56 <param argument="--otu_picking_method" type="select" label="The OTU picking method to use for reference and de novo steps">
57 <option value="uclust" selected="True">uclust</option>
58 </param>
59 <conditional name="ref_sequences">
60 <param name="selector" type="select" label="Reference sequences to query">
61 <option value="cached" selected="True">Public databases</option>
62 <option value="history">Databases from your history</option>
63 </param>
64 <when value="cached">
65 <param argument="--reference_fp" label="Reference sequences" type="select">
66 <options from_data_table="qiime_rep_set"/>
67 </param>
68 </when>
69 <when value="history">
70 <param argument="--reference_fp" type="data" format="fasta" label="Reference databases"/>
71 </when>
72 </conditional>
73 <conditional name="prefilter">
74 <param name="use_prefilter" type="select" label="Use different reference sequences for the prefilter?">
75 <option value="true">True</option>
76 <option value="false" selected="True">False</option>
77 </param>
78 <when value="true">
79 <conditional name="prefilter_ref_seq">
80 <param name="selector" type="select" label="Reference sequences to query">
81 <option value="cached" selected="True">Public databases</option>
82 <option value="history">Databases from your history</option>
83 </param>
84 <when value="cached">
85 <param argument="--prefilter_refseqs_fp" label="Reference sequences" type="select">
86 <options from_data_table="qiime_rep_set"/>
87 </param>
88 </when>
89 <when value="history">
90 <param argument="--prefilter_refseqs_fp" type="data" format="fasta" label="Reference databases"/>
91 </when>
92 </conditional>
93 </when>
94 <when value="false"/>
95 </conditional>
96 <param argument="--new_ref_set_id" type="text" value="New" label="Unique identifier for OTUs that get created in this ref set" help="This is useful to support combining of reference sets"/>
97 <param argument="--parallel" type="boolean" truevalue="--parallel" falsevalue="" checked="False" label="Run in parallel where available?"/>
98 <param argument="--percent_subsample" type="float" value="0.001" min="0" max="1" label="Percent of failure sequences to include in the subsample to cluster de novo" help="Large numbers should give more comprehensive results but will be slower"/>
99 <param argument="--prefilter_percent_id" type="float" value="0.0" min="0" max="1" label="Percent of sequence pre-cluster against the reference" help="Any reads which fail to hit are discarded (a quality filter)"/>
100 <param argument="--step1_otu_map_fp" type="data" format="txt" optional="True" label="Reference OTU picking OTU map to avoid rebuilding if one has already been built (optional)" help="This must be an OTU map generated by this workflow, not (for example) by pick_closed_reference_otus"/>
101 <param argument="--step1_failures_fasta_fp" type="data" format="fasta" optional="True" label="Reference OTU picking failures fasta filepath, to avoid rebuilding if one has already been built (optional)" help="This must be a failures file generated by this workflow, not (for example) by pick_closed_reference_otus"/>
102 <param argument="--minimum_failure_threshold" type="integer" value="100000" label="Minimum number of sequences that must fail to hit the reference for subsampling to be performed" help="If fewer than this number of sequences fail to hit the reference, the de novo clustering step will run serially rather than invoking the subsampled open reference approach to improve performance"/>
103 <param argument="--suppress_step4" type="boolean" truevalue="--suppress_step4" falsevalue="" checked="False" label="Suppress the final de novo OTU picking step?" help="It may be necessary for extremely large data sets"/>
104 <param argument="--min_otu_size" type="integer" value="2" label="Minimum otu size to retain the OTU" help=""/>
105 <param argument="--suppress_taxonomy_assignment" type="boolean" truevalue="--suppress_taxonomy_assignment" falsevalue="" checked="False" label="Skip the taxonomy assignment step?" help="It results in an OTU table without taxonomy"/>
106 <param argument="--suppress_align_and_tree" type="boolean" truevalue="--suppress_align_and_tree" falsevalue="" checked="False" label="Skip the sequence alignment and tree-building steps?" help=""/>
107 </inputs>
108 <outputs>
109 <data name="final_otu_map" format="txt" from_work_dir="otus/final_otu_map.txt" label="${tool.name} on ${on_string}: Final OTU map"/>
110 <data name="final_otu_map_mc" format="txt" from_work_dir="otus/final_otu_map_mc*.txt" label="${tool.name} on ${on_string}: Final OTU map without the OTUs failing the minimum specified OTU size"/>
111 <data name="rep_set" format="fasta" from_work_dir="otus/rep_set.fna" label="${tool.name} on ${on_string}: OTU representative sequences"/>
112 <data name="otu_table_mc" format="biom1" from_work_dir="otus/otu_table_mc*.biom" label="${tool.name} on ${on_string}: OTU table"/>
113 <data name="otu_table_mc_w_tax" format="biom1" from_work_dir="otus/otu_table_w_tax.biom" label="${tool.name} on ${on_string}: OTU table with taxonomic assignment">
114 <filter>suppress_taxonomy_assignment is False</filter>
115 </data>
116 <data name="otu_table_mc_w_tax_no_pynast_failures" format="biom1" from_work_dir="otus/otu_table_w_tax_no_pynast_failures.biom" label="${tool.name} on ${on_string}: OTU table with taxonomic assignment and without sequences failing the alignment to the OTU representative sequences">
117 <filter>suppress_taxonomy_assignment is False and suppress_align_and_tree is False</filter>
118 </data>
119 <data name="otu_table_mc_no_pynast_failures" format="biom1" from_work_dir="otus/otu_table_no_pynast_failures.biom" label="${tool.name} on ${on_string}: OTU table without sequences failing the alignment to the OTU representative sequences">
120 <filter>suppress_taxonomy_assignment is True and suppress_align_and_tree is False</filter>
121 </data>
122 <data name="rep_set_tree" format="txt" from_work_dir="otus/rep_set.tre" label="${tool.name} on ${on_string}: Representative set tree">
123 <filter>suppress_align_and_tree is False</filter>
124 </data>
125 <data name="new_refseqs" format="fasta" from_work_dir="otus/new_refseqs.fna" label="${tool.name} on ${on_string}: New reference sequences (OTU + input reference sequences)"/>
126 </outputs>
127 <tests>
128 <test>
129 <param name="input_fps" value="pick_open_reference_otus/sequences.fasta"/>
130 <param name="otu_picking_method" value="uclust"/>
131 <conditional name="ref_sequences">
132 <param name="selector" value="history"/>
133 <param name="reference_fp" value="pick_open_reference_otus/gg_13_8_79_otus.fasta"/>
134 </conditional>
135 <conditional name="prefilter">
136 <param name="use_prefilter" value="false"/>
137 </conditional>
138 <param name="new_ref_set_id" value="New"/>
139 <param name="parallel" value="--parallel"/>
140 <param name="percent_subsample" value="0.001"/>
141 <param name="prefilter_percent_id" value="0.0"/>
142 <param name="minimum_failure_threshold" value="100000"/>
143 <param name="suppress_step4" value=""/>
144 <param name="min_otu_size" value="2"/>
145 <param name="suppress_taxonomy_assignment" value=""/>
146 <param name="suppress_align_and_tree" value=""/>
147 <output name="final_otu_map" value="pick_open_reference_otus/1_final_otu_map.txt"/>
148 <output name="final_otu_map_mc" value="pick_open_reference_otus/1_final_otu_map_mc.txt"/>
149 <output name="rep_set">
150 <assert_contents>
151 <has_line line=">4374484 L1S8_76"></has_line>
152 <has_text text=">New.CleanUp.ReferenceOTU6 L1S208_7"></has_text>
153 </assert_contents>
154 </output>
155 <output name="rep_set_tree" value="pick_open_reference_otus/1_rep_set_tree.tre"/>
156 <output name="new_refseqs">
157 <assert_contents>
158 <has_line line=">1109493"></has_line>
159 <has_text text=">945028"></has_text>
160 <has_text text=">4437874"></has_text>
161 <has_text text=">New.CleanUp.ReferenceOTU6 L1S208_7"></has_text>
162 </assert_contents>
163 </output>
164 </test>
165 <test>
166 <param name="input_fps" value="pick_open_reference_otus/sequences.fasta"/>
167 <param name="otu_picking_method" value="uclust"/>
168 <conditional name="ref_sequences">
169 <param name="selector" value="history"/>
170 <param name="reference_fp" value="pick_open_reference_otus/gg_13_8_79_otus.fasta"/>
171 </conditional>
172 <conditional name="prefilter">
173 <param name="use_prefilter" value="false"/>
174 </conditional>
175 <param name="new_ref_set_id" value="New"/>
176 <param name="parallel" value="--parallel"/>
177 <param name="percent_subsample" value="0.001"/>
178 <param name="prefilter_percent_id" value="0.0"/>
179 <param name="minimum_failure_threshold" value="100000"/>
180 <param name="suppress_step4" value=""/>
181 <param name="min_otu_size" value="3"/>
182 <param name="suppress_taxonomy_assignment" value="--suppress_taxonomy_assignment"/>
183 <param name="suppress_align_and_tree" value="--suppress_align_and_tree"/>
184 <output name="final_otu_map" value="pick_open_reference_otus/2_final_otu_map.txt"/>
185 <output name="final_otu_map_mc" value="pick_open_reference_otus/2_final_otu_map_mc.txt"/>
186 <output name="rep_set">
187 <assert_contents>
188 <has_line line=">4374484 L1S8_76"></has_line>
189 <has_text text=">New.CleanUp.ReferenceOTU6 L1S208_7"></has_text>
190 </assert_contents>
191 </output>
192 <output name="new_refseqs">
193 <assert_contents>
194 <has_line line=">1109493"></has_line>
195 <has_text text=">945028"></has_text>
196 <has_text text=">4437874"></has_text>
197 <has_text text=">New.CleanUp.ReferenceOTU6 L1S208_7"></has_text>
198 </assert_contents>
199 </output>
200 </test>
201 <test>
202 <param name="input_fps" value="pick_open_reference_otus/sequences.fasta"/>
203 <param name="otu_picking_method" value="uclust"/>
204 <conditional name="ref_sequences">
205 <param name="selector" value="history"/>
206 <param name="reference_fp" value="pick_open_reference_otus/gg_13_8_79_otus.fasta"/>
207 </conditional>
208 <conditional name="prefilter">
209 <param name="use_prefilter" value="false"/>
210 </conditional>
211 <param name="new_ref_set_id" value="New"/>
212 <param name="parallel" value="--parallel"/>
213 <param name="percent_subsample" value="0.001"/>
214 <param name="prefilter_percent_id" value="0.0"/>
215 <param name="minimum_failure_threshold" value="100000"/>
216 <param name="suppress_step4" value=""/>
217 <param name="min_otu_size" value="10"/>
218 <param name="suppress_taxonomy_assignment" value="--suppress_taxonomy_assignment"/>
219 <param name="suppress_align_and_tree" value=""/>
220 <output name="final_otu_map" value="pick_open_reference_otus/3_final_otu_map.txt"/>
221 <output name="final_otu_map_mc" value="pick_open_reference_otus/3_final_otu_map_mc.txt"/>
222 <output name="rep_set">
223 <assert_contents>
224 <has_line line=">New.CleanUp.ReferenceOTU20 L1S8_4"></has_line>
225 <has_text text=">New.CleanUp.ReferenceOTU21 L1S140_45"></has_text>
226 <has_text text=">New.CleanUp.ReferenceOTU22 L1S208_15"></has_text>
227 </assert_contents>
228 </output>
229 <output name="rep_set_tree" value="pick_open_reference_otus/3_rep_set_tree.tre"/>
230 <output name="new_refseqs">
231 <assert_contents>
232 <has_line line=">1109493"></has_line>
233 <has_text text=">945028"></has_text>
234 <has_text text=">4431138"></has_text>
235 <has_text text=">New.CleanUp.ReferenceOTU22 L1S208_15"></has_text>
236 </assert_contents>
237 </output>
238 </test>
239 </tests>
240 <help><![CDATA[
241 **What it does**
242
243 This tool performs open-reference OTU picking from sequences.
244
245 This script is broken down into 4 possible OTU picking steps, and 2 steps
246 involving the creation of OTU tables and trees.
247
248 More information about this tool is available on
249 `QIIME documentation <http://qiime.org/scripts/pick_open_reference_otus.html>`_.
250 ]]></help>
251 <citations>
252 <expand macro="citations"/>
253 </citations>
254 </tool>