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comparison pick_open_reference_otus.xml @ 3:41482ca21d31 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 07:24:40 -0400
parents f668a753bcfc
children bf3348cc35d5
comparison
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2:845b4664b98a 3:41482ca21d31
1 <tool id="qiime_pick_open_reference_otus" name="Perform open-reference OTU picking" version="@WRAPPER_VERSION@.0"> 1 <tool id="qiime_pick_open_reference_otus" name="Perform open-reference OTU picking" version="@WRAPPER_VERSION@.0">
2 <description></description> 2 <description>(pick_open_reference_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 <version_command>pick_open_reference_otus.py --version</version_command> 7 <version_command>pick_open_reference_otus.py --version</version_command>
8 <command detect_errors="aggressive"><![CDATA[ 8 <command detect_errors="aggressive"><![CDATA[
9 pick_open_reference_otus.py 9 pick_open_reference_otus.py
10 --input_fps '$input_fps' 10 --input_fps '$input_fps'
11 -o otus 11 -o otus
12 --otu_picking_method '$otu_picking_method' 12 --otu_picking_method '$otu_picking_method'
13 #if str( $ref_sequences.selector ) == 'history' 13 #if str( $ref_sequences.selector ) == 'history'
14 #set $ref = $ref_sequences.reference_fp 14 #set $ref = $ref_sequences.reference_fp
15 #else: 15 #else:
16 #set $ref = $ref_sequences.reference_fp.fields.path 16 #set $ref = $ref_sequences.reference_fp.fields.path
17 #end if 17 #end if
18 --reference_fp '$ref' 18 --reference_fp '$ref'
19 #if str( $prefilter.use_prefilter ) == 'yes' 19 #if str( $prefilter.use_prefilter ) == 'yes'
20 #if str( $prefilter.prefilter_ref_seq.selector ) == 'history' 20 #if str( $prefilter.prefilter_ref_seq.selector ) == 'history'
21 #set $ref = $prefilter.prefilter_ref_seq.prefilter_refseqs_fp 21 #set $ref = $prefilter.prefilter_ref_seq.prefilter_refseqs_fp
22 #else: 22 #else:
23 #set $ref = $prefilter.prefilter_ref_seq.prefilter_refseqs_fp.fields.path 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( $suppress_taxonomy_assignment ) == ""
46 && mv otus/otu_table_mc*_w_tax.biom otus/otu_table_w_tax.biom
47 && mv otus/otu_table_mc*_w_tax_no_pynast_failures.biom otus/tu_table_w_tax_no_pynast_failures
48 #else
49 && mv otus/otu_table_mc*_no_pynast_failures.biom otus/otu_table_no_pynast_failures.biom
50 #end if
51 #end if 24 #end if
52 25 --prefilter_refseqs_fp '$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
53 ]]></command> 52 ]]></command>
54 <inputs> 53 <inputs>
55 <param argument="--input_fps" type="data" format="fasta,fastq" multiple="True" label="Input sequence files"/> 54 <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"> 55 <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> 56 <option value="uclust" selected="true">uclust</option>
58 </param> 57 </param>
59 <conditional name="ref_sequences"> 58 <conditional name="ref_sequences">
60 <param name="selector" type="select" label="Reference sequences to query"> 59 <param name="selector" type="select" label="Reference sequences to query">
61 <option value="cached" selected="True">Public databases</option> 60 <option value="cached" selected="true">Public databases</option>
62 <option value="history">Databases from your history</option> 61 <option value="history">Databases from your history</option>
63 </param> 62 </param>
64 <when value="cached"> 63 <when value="cached">
65 <param argument="--reference_fp" label="Reference sequences" type="select"> 64 <param argument="--reference_fp" label="Reference sequences" type="select">
66 <options from_data_table="qiime_rep_set"/> 65 <options from_data_table="qiime_rep_set"/>
71 </when> 70 </when>
72 </conditional> 71 </conditional>
73 <conditional name="prefilter"> 72 <conditional name="prefilter">
74 <param name="use_prefilter" type="select" label="Use different reference sequences for the prefilter?"> 73 <param name="use_prefilter" type="select" label="Use different reference sequences for the prefilter?">
75 <option value="true">True</option> 74 <option value="true">True</option>
76 <option value="false" selected="True">False</option> 75 <option value="false" selected="true">False</option>
77 </param> 76 </param>
78 <when value="true"> 77 <when value="true">
79 <conditional name="prefilter_ref_seq"> 78 <conditional name="prefilter_ref_seq">
80 <param name="selector" type="select" label="Reference sequences to query"> 79 <param name="selector" type="select" label="Reference sequences to query">
81 <option value="cached" selected="True">Public databases</option> 80 <option value="cached" selected="true">Public databases</option>
82 <option value="history">Databases from your history</option> 81 <option value="history">Databases from your history</option>
83 </param> 82 </param>
84 <when value="cached"> 83 <when value="cached">
85 <param argument="--prefilter_refseqs_fp" label="Reference sequences" type="select"> 84 <param argument="--prefilter_refseqs_fp" label="Reference sequences" type="select">
86 <options from_data_table="qiime_rep_set"/> 85 <options from_data_table="qiime_rep_set"/>
92 </conditional> 91 </conditional>
93 </when> 92 </when>
94 <when value="false"/> 93 <when value="false"/>
95 </conditional> 94 </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"/> 95 <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?"/> 96 <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"/> 97 <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)"/> 98 <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"/> 99 <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"/> 100 <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"/> 101 <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"/> 102 <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=""/> 103 <param argument="--min_otu_size" type="integer" value="2" label="Minimum otu size to retain the OTU"/>
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"/> 104 <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=""/> 105 <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?"/>
107 </inputs> 106 </inputs>
108 <outputs> 107 <outputs>
109 <data name="final_otu_map" format="txt" from_work_dir="otus/final_otu_map.txt" label="${tool.name} on ${on_string}: Final OTU map"/> 108 <data name="final_otu_map" format="txt" from_work_dir="otus/final_otu_map.txt" label="${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 ${on_string}: Final OTU map without the OTUs failing the minimum specified OTU size"/> 109 <data name="final_otu_map_mc" format="txt" from_work_dir="otus/final_otu_map_mc*.txt" label="${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 ${on_string}: OTU representative sequences"/> 110 <data name="rep_set" format="fasta" from_work_dir="otus/rep_set.fna" label="${tool.name} on ${on_string}: OTU representative sequences"/>