Mercurial > repos > iuc > mothur_count_seqs

comparison count.seqs.xml @ 2:0cd054e2876d 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 22:17:19 -0400
parents b6f7f17203ad
children
comparison
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1:ecbd9ed733e6 2:0cd054e2876d
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 "$name" name.dat && 13 ln -s '$name' name.dat &&
14 #if $grouping.use == "yes": 14 #if $grouping.use == "yes":
15 ln -s "$grouping.group" grouping.group.dat && 15 ln -s '$grouping.group' grouping.group.dat &&
16 #end if
17
18 echo 'count.seqs(
19 #if $grouping.use == "yes":
20 group=grouping.group.dat,
21 #if $grouping.groups:
22 groups=${ str($grouping.groups).replace(",","-") },
16 #end if 23 #end if
17 24 #end if
18 echo 'count.seqs( 25 name=name.dat
19 name=name.dat, 26 )'
20 #if $grouping.use == "yes": 27 | sed 's/ //g' ## mothur trips over whitespace
21 group=grouping.group.dat, 28 | mothur
22 #if $grouping.groups: 29 | tee mothur.out.log
23 groups=${ str($grouping.groups).replace(",","-") },
24 #end if
25 #end if
26 large=$large
27 )'
28 | sed 's/ //g' ## mothur trips over whitespace
29 | mothur
30 | tee mothur.out.log
31 ]]></command> 30 ]]></command>
32 <inputs> 31 <inputs>
33 <param name="name" type="data" format="mothur.names" label="name - Sequences Name reference"/> 32 <param name="name" type="data" format="mothur.names" label="name - Sequences Name reference"/>
34 <conditional name="grouping"> 33 <conditional name="grouping">
35 <param name="use" type="select" label="Use a Group file to include counts for groups"> 34 <param name="use" type="select" label="Use a Group file to include counts for groups">
45 </options> 44 </options>
46 </param> 45 </param>
47 </when> 46 </when>
48 <when value="no"/> 47 <when value="no"/>
49 </conditional> 48 </conditional>
50 <param name="large" type="boolean" checked="false" truevalue="true" falsevalue="false" label="large - Datasets are large and may not fit in RAM"/> 49 <expand macro="param-savelog"/>
51 </inputs> 50 </inputs>
52 <outputs> 51 <outputs>
53 <expand macro="logfile-output"/> 52 <expand macro="logfile-output"/>
54 <data name="seq_count" format="mothur.count_table" from_work_dir="name*.count_table" label="${tool.name} on ${on_string}: count_table"/> 53 <data name="seq_count" format="mothur.count_table" from_work_dir="name*.count_table" label="${tool.name} on ${on_string}: count_table"/>
55 </outputs> 54 </outputs>
56 <tests> 55 <tests>
57 <test><!-- test default params --> 56 <test><!-- test default params -->
58 <param name="name" value="amazon.names"/> 57 <param name="name" value="amazon.names"/>
59 <output name="seq_count" file="amazon.count_table" ftype="mothur.count_table"/> 58 <output name="seq_count" file="amazon.count_table" ftype="mothur.count_table"/>
59 <param name="savelog" value="true"/>
60 <expand macro="logfile-test"/> 60 <expand macro="logfile-test"/>
61 </test> 61 </test>
62 <test><!-- test with group file --> 62 <test><!-- test with group file -->
63 <param name="name" value="amazon.names"/> 63 <param name="name" value="amazon.names"/>
64 <param name="use" value="yes"/> 64 <param name="use" value="yes"/>
65 <param name="group" value="amazon.groups"/> 65 <param name="group" value="amazon.groups"/>
66 <output name="seq_count" file="amazon_withgroups.count_table" ftype="mothur.count_table"/> 66 <output name="seq_count" file="amazon_withgroups.count_table" ftype="mothur.count_table"/>
67 <param name="savelog" value="true"/>
67 <expand macro="logfile-test"/> 68 <expand macro="logfile-test"/>
68 </test> 69 </test>
69 <test> <!-- test with group file and subset of groups --> 70 <test> <!-- test with group file and subset of groups -->
70 <param name="name" value="amazon.names"/> 71 <param name="name" value="amazon.names"/>
71 <param name="use" value="yes"/> 72 <param name="use" value="yes"/>
72 <param name="group" value="amazon.groups" ftype="mothur.groups"/> 73 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
73 <param name="groups" value="pasture"/> 74 <param name="groups" value="pasture"/>
74 <output name="seq_count" file="amazon_withgroups_pasture.count_table" ftype="mothur.count_table"/> 75 <output name="seq_count" file="amazon_withgroups_pasture.count_table" ftype="mothur.count_table"/>
76 <param name="savelog" value="true"/>
75 <expand macro="logfile-test"/> 77 <expand macro="logfile-test"/>
76 </test> 78 </test>
77 <test> <!-- test with group file and multiple groups --> 79 <test> <!-- test with group file and multiple groups -->
78 <param name="name" value="amazon.names"/> 80 <param name="name" value="amazon.names"/>
79 <param name="use" value="yes"/> 81 <param name="use" value="yes"/>
80 <param name="group" value="amazon.groups" ftype="mothur.groups"/> 82 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
81 <param name="groups" value="pasture,forest"/> 83 <param name="groups" value="pasture,forest"/>
82 <output name="seq_count" md5="b18c03aee561cd24a36b00ad9b22255a" ftype="mothur.count_table"/> 84 <output name="seq_count" md5="b18c03aee561cd24a36b00ad9b22255a" ftype="mothur.count_table"/>
85 <param name="savelog" value="true"/>
83 <expand macro="logfile-test"/> 86 <expand macro="logfile-test"/>
84 </test> 87 </test>
85 </tests> 88 </tests>
86 <help> 89 <help><![CDATA[
87 <![CDATA[
88 90
89 @MOTHUR_OVERVIEW@ 91 @MOTHUR_OVERVIEW@
90 92
91 **Command Documentation** 93 **Command Documentation**
92 94
96 .. _group: https://www.mothur.org/wiki/Group_file 98 .. _group: https://www.mothur.org/wiki/Group_file
97 .. _count.seqs: https://www.mothur.org/wiki/Count.seqs 99 .. _count.seqs: https://www.mothur.org/wiki/Count.seqs
98 .. _count_table: https://www.mothur.org/wiki/Count_File 100 .. _count_table: https://www.mothur.org/wiki/Count_File
99 101
100 v.1.21.0: Updated to Mothur 1.33 102 v.1.21.0: Updated to Mothur 1.33
101 ]]> 103
102 </help> 104 ]]></help>
103 <expand macro="citations"/> 105 <expand macro="citations"/>
104 </tool> 106 </tool>