Mercurial > repos > iuc > mothur_count_seqs

comparison count.seqs.xml @ 3:448f43db98c4 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
author iuc
date Wed, 14 Feb 2018 09:52:51 -0500
parents cb4e005b8e8d
children 4649b8f719a2
comparison
equal deleted inserted replaced
2:b9fbf6640324 3:448f43db98c4
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"/>
51 </inputs> 49 </inputs>
52 <outputs> 50 <outputs>
53 <expand macro="logfile-output"/> 51 <expand macro="logfile-output"/>
54 <data name="seq_count" format="mothur.count_table" from_work_dir="name*.count_table" label="${tool.name} on ${on_string}: count_table"/> 52 <data name="seq_count" format="mothur.count_table" from_work_dir="name*.count_table" label="${tool.name} on ${on_string}: count_table"/>
55 </outputs> 53 </outputs>
81 <param name="groups" value="pasture,forest"/> 79 <param name="groups" value="pasture,forest"/>
82 <output name="seq_count" md5="b18c03aee561cd24a36b00ad9b22255a" ftype="mothur.count_table"/> 80 <output name="seq_count" md5="b18c03aee561cd24a36b00ad9b22255a" ftype="mothur.count_table"/>
83 <expand macro="logfile-test"/> 81 <expand macro="logfile-test"/>
84 </test> 82 </test>
85 </tests> 83 </tests>
86 <help> 84 <help><![CDATA[
87 <![CDATA[
88 85
89 @MOTHUR_OVERVIEW@ 86 @MOTHUR_OVERVIEW@
90 87
91 **Command Documentation** 88 **Command Documentation**
92 89
96 .. _group: https://www.mothur.org/wiki/Group_file 93 .. _group: https://www.mothur.org/wiki/Group_file
97 .. _count.seqs: https://www.mothur.org/wiki/Count.seqs 94 .. _count.seqs: https://www.mothur.org/wiki/Count.seqs
98 .. _count_table: https://www.mothur.org/wiki/Count_File 95 .. _count_table: https://www.mothur.org/wiki/Count_File
99 96
100 v.1.21.0: Updated to Mothur 1.33 97 v.1.21.0: Updated to Mothur 1.33
101 ]]> 98
102 </help> 99 ]]></help>
103 <expand macro="citations"/> 100 <expand macro="citations"/>
104 </tool> 101 </tool>