Mercurial > repos > iuc > mothur_summary_tax

comparison summary.tax.xml @ 2:f7dded265782 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author iuc
date Tue, 20 Mar 2018 22:24:38 -0400
parents 76c27b0fa016
children
comparison
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1:807ebe300c84 2:f7dded265782
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
8 <expand macro="version_command"/> 8 <expand macro="version_command"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10 @SHELL_OPTIONS@ 10 @SHELL_OPTIONS@
11 11
12 ## create symlinks to input datasets 12 ## create symlinks to input datasets
13 ln -s "$tax.taxonomy" tax.taxonomy.dat && 13 ln -s '$tax.taxonomy' tax.taxonomy.dat &&
14 ln -s "$name" name.dat && 14 ln -s '$name' name.dat &&
15 ln -s "$group" group.dat && 15 ln -s '$group' group.dat &&
16 ln -s "$count" count.dat && 16 ln -s '$count' count.dat &&
17 #if $reftax.source2:
18 ln -s "$reftax.reftaxonomy" myreftax.taxonomy &&
19 ln -s "$sum" myreftax.tree.sum &&
20 #end if
21 17
22 echo 'summary.tax( 18 echo 'summary.tax(
23 taxonomy=tax.taxonomy.dat, 19 taxonomy=tax.taxonomy.dat,
24 #if $name: 20 #if $name:
25 name=name.dat, 21 name=name.dat,
26 #end if 22 #end if
27 #if $group: 23 #if $group:
28 group=group.dat, 24 group=group.dat,
29 #end if 25 #end if
30 #if $reftax.source2: 26 #if $count:
31 reftaxonomy=myreftax.taxonomy, 27 count=count.dat,
32 #end if 28 #end if
33 #if $count: 29 relabund=$relabund,
34 count=count.dat, 30 threshold=$threshold,
35 #end if 31 output=$output,
36 relabund=$relabund 32 printlevel=$printlevel
37 )' 33 )'
38 | sed 's/ //g' ## mothur trips over whitespace 34 | sed 's/ //g' ## mothur trips over whitespace
39 | mothur 35 | mothur
40 | tee mothur.out.log 36 | tee mothur.out.log
41 ]]></command> 37 ]]></command>
42 <inputs> 38 <inputs>
43 <conditional name="tax"> 39 <conditional name="tax">
44 <param name="source" type="select" label="Select Taxonomy from" help=""> 40 <param name="source" type="select" label="Select Taxonomy from" help="">
45 <option value="hist">History</option> 41 <option value="hist">History</option>
54 <param name="taxonomy" type="data" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy Reference"/> 50 <param name="taxonomy" type="data" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy Reference"/>
55 </when> 51 </when>
56 </conditional> 52 </conditional>
57 <param name="name" type="data" format="mothur.names" optional="true" label="name - taxonomy sequence names"/> 53 <param name="name" type="data" format="mothur.names" optional="true" label="name - taxonomy sequence names"/>
58 <param name="group" type="data" format="mothur.groups" optional="true" label="group - Groups for summary file"/> 54 <param name="group" type="data" format="mothur.groups" optional="true" label="group - Groups for summary file"/>
59 <conditional name="reftax">
60 <param name="source2" type="select" label="Select Reference Taxonomy used in Summary.seqs from" help="Including the reference taxonomy file used when you classified your sequences keep the rankIDs in the summary file static.">
61 <option value="" selected="true">Selection is Optional</option>
62 <option value="hist">History</option>
63 <option value="ref">Cached Reference</option>
64 </param>
65 <when value="ref">
66 <param name="reftaxonomy" type="select" format="mothur.seq.taxonomy" label="reftaxonomy - Taxonomy Reference used when sequences were classified">
67 <options from_data_table="mothur_taxonomy"/>
68 </param>
69 <param name="sum" type="data" format="tabular" label="tree.sum - summary file produced when sequences were classified" help="run classify.seqs to get this file"/>
70 </when>
71 <when value="hist">
72 <param name="reftaxonomy" type="data" format="mothur.seq.taxonomy" label="reftaxonomy - Taxonomy Reference used when sequences were classified"/>
73 <param name="sum" type="data" format="tabular" label="tree.sum - summary file produced when sequences were classified" help="run classify.seqs to get this file"/>
74 </when>
75 <when value=""/>
76 </conditional>
77 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> 55 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
78 <param name="relabund" type="boolean" falsevalue="false" truevalue="true" checked="false" label="relabund - allows you to indicate that you want the summary files to be relative abundances rather than raw abundances. default=f"/> 56 <param name="relabund" type="boolean" falsevalue="false" truevalue="true" checked="false"
57 label="relabund - allows you to indicate that you want the summary files to be relative abundances rather than raw abundances. default=f"/>
58 <param name="threshold" type="integer" value="0" min="0" label="threshold- specify a cutoff for the taxonomy file"
59 help="Once the classification falls below the threshold the mothur will refer to it as unclassified when calculating the concensus.
60 This feature is similar to adjusting the cutoff in classify.seqs"/>
61 <expand macro="param-output"/>
62 <expand macro="param-printlevel"/>
63 <expand macro="param-savelog"/>
79 </inputs> 64 </inputs>
80 <outputs> 65 <outputs>
81 <expand macro="logfile-output"/> 66 <expand macro="logfile-output"/>
82 <data name="taxsummary" format="mothur.summary" from_work_dir="tax.taxonomy*.tax.summary" label="${tool.name} on ${on_string}: summary"/> 67 <data name="taxsummary" format="mothur.tax.summary" from_work_dir="tax.taxonomy*.tax.summary" label="${tool.name} on ${on_string}: summary"/>
83 </outputs> 68 </outputs>
84 <tests> 69 <tests>
85 <test> 70 <test>
86 <param name="source" value="hist"/> 71 <param name="source" value="hist"/>
87 <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/> 72 <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
88 <output name="taxsummary" md5="1019aae0e68b2ee102565c535a8e03cf" ftype="mothur.summary"/> 73 <output name="taxsummary" ftype="mothur.tax.summary">
74 <assert_contents>
75 <expand macro="test-taxsummary-format"/>
76 <has_text text="Root"/>
77 <has_text text="Bifidobacterium"/>
78 </assert_contents>
79 </output>
80 <param name="savelog" value="true"/>
89 <expand macro="logfile-test"/> 81 <expand macro="logfile-test"/>
90 </test> 82 </test>
91 <test> 83 <test>
92 <param name="source" value="hist"/> 84 <param name="source" value="hist"/>
93 <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/> 85 <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
94 <param name="source2" value="hist"/> 86 <output name="taxsummary" ftype="mothur.tax.summary">
95 <param name="reftaxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/> 87 <assert_contents>
96 <param name="sum" value="abrecovery.pds.wang.tree.sum"/> 88 <expand macro="test-taxsummary-format"/>
97 <output name="taxsummary" md5="1019aae0e68b2ee102565c535a8e03cf" ftype="mothur.summary"/> 89 <has_text text="Root"/>
90 <has_text text="Bifidobacterium"/>
91 </assert_contents>
92 </output>
93 <param name="savelog" value="true"/>
98 <expand macro="logfile-test"/> 94 <expand macro="logfile-test"/>
99 </test> 95 </test>
100 </tests> 96 </tests>
101 <help> 97 <help><![CDATA[
102 <![CDATA[
103 98
104 @MOTHUR_OVERVIEW@ 99 @MOTHUR_OVERVIEW@
105 100
106 **Command Documentation** 101 **Command Documentation**
107 102
108 The summary.tax_ command reads a taxonomy file and an optional name and or group file, and summarizes the taxonomy information. 103 The summary.tax_ command reads a taxonomy file and an optional name and or group file, and summarizes the taxonomy information.
109 104
110 .. _summary.tax: https://www.mothur.org/wiki/Summary.tax 105 .. _summary.tax: https://www.mothur.org/wiki/Summary.tax
111 ]]> 106
112 </help> 107 ]]></help>
113 <expand macro="citations"/> 108 <expand macro="citations"/>
114 </tool> 109 </tool>