Mercurial > repos > iuc > mothur_count_groups

comparison count.groups.xml @ 3:ed773c45b3d6 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 09:50:47 -0500
parents 13a947a26f7a
children 2b127e170db5
comparison
equal deleted inserted replaced
2:43a38d83495b 3:ed773c45b3d6
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 "$group" group.dat && 13 ln -s '$group' group.dat &&
14 #if $groupnames.source == "accnos": 14 #if $groupnames.source == "accnos":
15 ln -s "$groupnames.accnos" groupnames.accnos.dat && 15 ln -s '$groupnames.accnos' groupnames.accnos.dat &&
16 #end if
17
18 echo 'count.groups(
19 #if $group.is_of_type("mothur.shared"):
20 shared=group.dat
21 #elif $group.is_of_type("mothur.count_table"):
22 count=group.dat
23 #else:
24 group=group.dat
25 #end if
26 #if $groupnames.source == "groups":
27 #if $groupnames.groups:
28 ,groups=${ str($groupnames.groups).replace(",","-") }
16 #end if 29 #end if
30 #elif $groupnames.source == "accnos":
31 #if $groupnames.accnos:
32 ,accnos=groupnames.accnos.dat
33 #end if
34 #end if
35 )'
36 | sed 's/ //g' ## mothur trips over whitespace
37 | mothur
38 | tee mothur.out.log &&
17 39
18 echo 'count.groups( 40 ## parse relevant tool output from logfile to file
19 #if $group.is_of_type("mothur.shared"): 41 cat mothur.*.logfile
20 shared=group.dat 42 | head -n-7
21 #elif $group.is_of_type("mothur.count_table"): 43 | sed '1,30d'
22 count=group.dat 44 > '$grp_count'
23 #else:
24 group=group.dat
25 #end if
26 #if $groupnames.source == "groups":
27 #if $groupnames.groups:
28 ,groups=$groupnames.groups
29 #end if
30 #elif $groupnames.source == "accnos":
31 #if $groupnames.accnos:
32 ,accnos=groupnames.accnos.dat
33 #end if
34 #end if
35 )'
36 | sed 's/ //g' ## mothur trips over whitespace
37 | mothur
38 | tee mothur.out.log &&
39
40 ## parse relevant tool output from logfile to file
41 cat mothur.*.logfile
42 | head -n-7
43 | sed '1,29d'
44 > "$grp_count"
45 ]]></command> 45 ]]></command>
46 <inputs> 46 <inputs>
47 <param name="group" type="data" format="mothur.groups,mothur.shared,mothur.count_table" label="group, shared, or count_table - Group file for sequence count"/> 47 <param name="group" type="data" format="mothur.groups,mothur.shared,mothur.count_table" label="group, shared, or count_table - Group file for sequence count"/>
48 <conditional name="groupnames"> 48 <conditional name="groupnames">
49 <param name="source" type="select" label="Filter group names"> 49 <param name="source" type="select" label="Filter group names">
71 <data name="summary" format="tabular" from_work_dir="group*.summary" label="${tool.name} on ${on_string}: summary"/> 71 <data name="summary" format="tabular" from_work_dir="group*.summary" label="${tool.name} on ${on_string}: summary"/>
72 </outputs> 72 </outputs>
73 <tests> 73 <tests>
74 <test> 74 <test>
75 <param name="group" value="amazon.an.shared" ftype="mothur.shared"/> 75 <param name="group" value="amazon.an.shared" ftype="mothur.shared"/>
76 <output name="summary" md5="58508af98ed02e00a707f0f7812c2359"/>
77 <output name="grp_count" md5="34ea2b8be163cf6c9c68d624d92fc73d"/>
78 <expand macro="logfile-test"/>
79 </test>
80 <test>
81 <param name="group" value="amazon.an.shared" ftype="mothur.shared"/>
82 <param name="source" value="groups"/>
76 <param name="groups" value="forest,pasture"/> 83 <param name="groups" value="forest,pasture"/>
77 <output name="summary" md5="58508af98ed02e00a707f0f7812c2359"/> 84 <output name="summary" md5="58508af98ed02e00a707f0f7812c2359"/>
78 <output name="grp_count" md5="34ea2b8be163cf6c9c68d624d92fc73d"/> 85 <output name="grp_count" md5="34ea2b8be163cf6c9c68d624d92fc73d"/>
79 <expand macro="logfile-test"/> 86 <expand macro="logfile-test"/>
80 </test> 87 </test>
81 </tests> 88 </tests>
82 <help> 89 <help><![CDATA[
83 <![CDATA[
84 90
85 @MOTHUR_OVERVIEW@ 91 @MOTHUR_OVERVIEW@
86 92
87 **Command Documentation** 93 **Command Documentation**
88 94
89 The count.groups_ command counts sequences from a specific group or set of groups from a group_ or shared_ file. 95 The count.groups_ command counts sequences from a specific group or set of groups from a group_ or shared_ file.
90 96
91 .. _shared: https://www.mothur.org/wiki/Shared_file 97 .. _shared: https://www.mothur.org/wiki/Shared_file
92 .. _group: https://www.mothur.org/wiki/Group_file 98 .. _group: https://www.mothur.org/wiki/Group_file
93 .. _count.groups: https://www.mothur.org/wiki/Count.groups 99 .. _count.groups: https://www.mothur.org/wiki/Count.groups
94 ]]> 100
95 </help> 101 ]]></help>
96 <expand macro="citations"/> 102 <expand macro="citations"/>
97 </tool> 103 </tool>