Mercurial > repos > iuc > qiime_pick_closed_reference_otus

comparison pick_closed_reference_otus.xml @ 3:935abbf93f99 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 07:30:47 -0400
parents 2b6d3067087a
children 5307c6be95df
comparison
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2:11314ea5d8ac 3:935abbf93f99
1 <tool id="qiime_pick_closed_reference_otus" name="Perform closed-reference OTU picking" version="@WRAPPER_VERSION@.0"> 1 <tool id="qiime_pick_closed_reference_otus" name="Closed-reference OTU picking" version="@WRAPPER_VERSION@.0">
2 <description></description> 2 <description> Shotgun UniFrac workflow (pick_closed_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_closed_reference_otus.py --version</version_command> 7 <version_command>pick_closed_reference_otus.py --version</version_command>
8 <command detect_errors="aggressive"><![CDATA[ 8 <command detect_errors="aggressive"><![CDATA[
9 pick_closed_reference_otus.py 9 pick_closed_reference_otus.py
10 --input_fp '$input_fp' 10 --input_fp '$input_fp'
11 --output_dir otus 11 --output_dir otus
12 #if str( $ref_seq.selector ) == 'history' 12 #if str( $ref_seq.selector ) == 'history'
13 #set $ref = $ref_seq.reference_fp 13 #set $ref = $ref_seq.reference_fp
14 #else 14 #else
15 #set $ref = $ref_seq.reference_fp.fields.path 15 #set $ref = $ref_seq.reference_fp.fields.path
16 #end if 16 #end if
17 --reference_fp '$ref' 17 --reference_fp '$ref'
18 #if str( $taxonomy.selector ) == 'taxonomy_map' 18 #if str( $taxonomy.selector ) == 'taxonomy_map'
19 #if str( $taxonomy.taxo_map.selector ) == 'history' 19 #if str( $taxonomy.taxo_map.selector ) == 'history'
20 #set $taxonomy = $taxonomy.taxo_map.taxonomy_fp 20 #set $taxonomy = $taxonomy.taxo_map.taxonomy_fp
21 #else 21 #else
22 #set $taxonomy = $taxonomy.taxo_map.taxonomy_fp.fields.path 22 #set $taxonomy = $taxonomy.taxo_map.taxonomy_fp.fields.path
23 #end if 23 #end if
24 --taxonomy_fp '$taxonomy' 24 --taxonomy_fp '$taxonomy'
25 #else if str( $taxonomy.selector ) == 'assign_taxonomy' 25 #else if str( $taxonomy.selector ) == 'assign_taxonomy'
26 --assign_taxonomy 26 --assign_taxonomy
27 #else if str( $taxonomy.selector ) == 'suppress_taxonomy_assignment' 27 #else if str( $taxonomy.selector ) == 'suppress_taxonomy_assignment'
28 --suppress_taxonomy_assignment 28 --suppress_taxonomy_assignment
29 #end if 29 #end if
30 #if $parameter_fp 30 #if $parameter_fp
31 --parameter_fp '$parameter_fp' 31 --parameter_fp '$parameter_fp'
32 #end if 32 #end if
33 $parallel 33 $parallel
34 -O "\${GALAXY_SLOTS:-4}" 34 -O "\${GALAXY_SLOTS:-4}"
35 ]]></command> 35 ]]></command>
36 <inputs> 36 <inputs>
37 <param argument="--input_fp" type="data" format="fasta" label="Input sequence file"/> 37 <param argument="--input_fp" type="data" format="fasta" label="Input sequence file"/>
38 <conditional name="ref_seq"> 38 <conditional name="ref_seq">
39 <param name="selector" type="select" label="Reference sequences to query"> 39 <param name="selector" type="select" label="Reference sequences to query">
40 <option value="cached" selected="True">Public databases</option> 40 <option value="cached" selected="true">Public databases</option>
41 <option value="history">Databases from your history</option> 41 <option value="history">Databases from your history</option>
42 </param> 42 </param>
43 <when value="cached"> 43 <when value="cached">
44 <param argument="--reference_fp" label="Reference sequences" type="select"> 44 <param argument="--reference_fp" label="Reference sequences" type="select">
45 <options from_data_table="qiime_rep_set"/> 45 <options from_data_table="qiime_rep_set"/>
48 <when value="history"> 48 <when value="history">
49 <param argument="--reference_fp" type="data" format="fasta" label="Reference databases"/> 49 <param argument="--reference_fp" type="data" format="fasta" label="Reference databases"/>
50 </when> 50 </when>
51 </conditional> 51 </conditional>
52 <conditional name="taxonomy"> 52 <conditional name="taxonomy">
53 <param name="selector" type="select" label="Assign taxonomy?"> 53 <param name="selector" type="select" label="Assign taxonomy?">
54 <option value="taxonomy_map" selected="True">Assign taxonomy using a taxonomy map</option> 54 <option value="taxonomy_map" selected="true">Assign taxonomy using a taxonomy map</option>
55 <option value="assign_taxonomy">Assign taxonomy to each sequence using assign_taxonomy.py</option> 55 <option value="assign_taxonomy">Assign taxonomy to each sequence using assign_taxonomy.py</option>
56 <option value="suppress_taxonomy_assignment">Skip the taxonomy assignment step</option> 56 <option value="suppress_taxonomy_assignment">Skip the taxonomy assignment step</option>
57 </param> 57 </param>
58 <when value="taxonomy_map"> 58 <when value="taxonomy_map">
59 <conditional name="taxo_map"> 59 <conditional name="taxo_map">
73 </when> 73 </when>
74 <when value="assign_taxonomy"/> 74 <when value="assign_taxonomy"/>
75 <when value="suppress_taxonomy_assignment"/> 75 <when value="suppress_taxonomy_assignment"/>
76 </conditional> 76 </conditional>
77 <param argument="--parameter_fp" type="data" format="txt" optional="true" label="Parameter file" help="It specifies changes to the default behavior"/> 77 <param argument="--parameter_fp" type="data" format="txt" optional="true" label="Parameter file" help="It specifies changes to the default behavior"/>
78 <param argument="--parallel" type="boolean" truevalue="--parallel" falsevalue="" checked="True" label="Run in parallel where available?"/> 78 <param argument="--parallel" type="boolean" truevalue="--parallel" falsevalue="" checked="true" label="Run in parallel where available?"/>
79 </inputs> 79 </inputs>
80 <outputs> 80 <outputs>
81 <data name="otu_table" format="biom1" from_work_dir="otus/otu_table.biom" label="${tool.name} on ${on_string}: OTU table"/> 81 <data name="otu_table" format="biom1" from_work_dir="otus/otu_table.biom" label="${tool.name} on ${on_string}: OTU table"/>
82 </outputs> 82 </outputs>
83 <tests> 83 <tests>