Mercurial > repos > iuc > mothur_make_group
comparison make.group.xml @ 2:4f91a75ac701 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author | iuc |
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date | Tue, 20 Mar 2018 22:09:11 -0400 |
parents | 992d380f24ea |
children | 63a75db03ecc |
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1:8c964d119da8 | 2:4f91a75ac701 |
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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 #set fastas = '' | 12 #set fastas = '' |
13 #set groups = '' | 13 #set groups = '' |
14 #set count = 0 | 14 #set count = 0 |
15 | 15 |
16 #if $method.how == 'collection': | 16 #if $method.how == 'collection': |
17 #for $i in $method.fasta_collection: | 17 #for $i in $method.fasta_collection: |
18 ln -s '$i' fasta_${i.element_identifier}.dat && | 18 ln -s '$i' fasta_${i.element_identifier}.dat && |
19 #set fastas+='fasta_'+$i.element_identifier+'.dat-' | 19 #set fastas+='fasta_'+$i.element_identifier+'.dat-' |
20 #set groups+=$i.element_identifier+'-' | 20 #set groups+=$i.element_identifier+'-' |
21 #end for | 21 #end for |
22 #else | 22 #else |
23 #for $i in $method.inputs: | 23 #for $i in $method.inputs: |
24 ln -s '$i.fasta' fasta_${count}.dat && | 24 ln -s '$i.fasta' fasta_${count}.dat && |
25 #set fastas+='fasta_'+str($count)+'.dat-' | 25 #set fastas+='fasta_'+str($count)+'.dat-' |
26 #set groups+=str($i.group)+'-' | 26 #set groups+=str($i.group)+'-' |
27 #set count+=1 | 27 #set count+=1 |
28 #end for | 28 #end for |
29 #end if | 29 #end if |
30 | 30 |
31 echo 'make.group( | 31 echo 'make.group( |
32 fasta=${ str($fastas).rstrip('-') }, | 32 fasta=${ str($fastas).rstrip('-') }, |
33 groups=${ str($groups).rstrip('-') } | 33 groups=${ str($groups).rstrip('-') } |
34 )' | 34 )' |
35 | sed 's/ //g' ## mothur trips over whitespace | 35 | sed 's/ //g' ## mothur trips over whitespace |
36 | mothur | 36 | mothur |
37 | tee mothur.out.log | 37 | tee mothur.out.log |
38 | |
39 ]]></command> | 38 ]]></command> |
40 <inputs> | 39 <inputs> |
41 <conditional name="method"> | 40 <conditional name="method"> |
42 <param name="how" type="select" label="Method to create group file"> | 41 <param name="how" type="select" label="Method to create group file"> |
43 <option value="collection"> Automatically from collection </option> | 42 <option value="collection"> Automatically from collection </option> |
51 <param name="fasta" type="data" format="fasta" label="fasta - Fasta to group"/> | 50 <param name="fasta" type="data" format="fasta" label="fasta - Fasta to group"/> |
52 <param name="group" type="text" label="group - Group name"/> | 51 <param name="group" type="text" label="group - Group name"/> |
53 </repeat> | 52 </repeat> |
54 </when> | 53 </when> |
55 </conditional> | 54 </conditional> |
55 <expand macro="param-savelog"/> | |
56 </inputs> | 56 </inputs> |
57 <outputs> | 57 <outputs> |
58 <expand macro="logfile-output"/> | 58 <expand macro="logfile-output"/> |
59 <data name="output" format="mothur.groups" from_work_dir="*groups" label="${tool.name} on ${on_string}: group"/> | 59 <data name="output" format="mothur.groups" from_work_dir="*groups" label="${tool.name} on ${on_string}: group"/> |
60 </outputs> | 60 </outputs> |
68 <repeat name="inputs"> | 68 <repeat name="inputs"> |
69 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/> | 69 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/> |
70 <param name="group" value="testgroup2"/> | 70 <param name="group" value="testgroup2"/> |
71 </repeat> | 71 </repeat> |
72 <output name="output" file="Mock_S280_L001_R1_001_small.trim.contigs.good.Mock_S280_L001_R1_001_small.trim.contigs.good.groups"/> | 72 <output name="output" file="Mock_S280_L001_R1_001_small.trim.contigs.good.Mock_S280_L001_R1_001_small.trim.contigs.good.groups"/> |
73 <param name="savelog" value="true"/> | |
73 <expand macro="logfile-test"/> | 74 <expand macro="logfile-test"/> |
74 </test> | 75 </test> |
75 <test> <!-- test auto-creation from collection --> | 76 <test> <!-- test auto-creation from collection --> |
76 <param name="how" value="collection"/> | 77 <param name="how" value="collection"/> |
77 <param name="fasta_collection"> | 78 <param name="fasta_collection"> |
79 <element name="testgroup" ftype="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head" /> | 80 <element name="testgroup" ftype="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head" /> |
80 <element name="testgroup2" ftype="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head" /> | 81 <element name="testgroup2" ftype="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head" /> |
81 </collection> | 82 </collection> |
82 </param> | 83 </param> |
83 <output name="output" file="Mock_S280_L001_R1_001_small.trim.contigs.good.Mock_S280_L001_R1_001_small.trim.contigs.good.groups"/> | 84 <output name="output" file="Mock_S280_L001_R1_001_small.trim.contigs.good.Mock_S280_L001_R1_001_small.trim.contigs.good.groups"/> |
84 <expand macro="logfile-test"/> | 85 <param name="savelog" value="true"/> |
86 <expand macro="logfile-test"/> | |
85 </test> | 87 </test> |
86 </tests> | 88 </tests> |
87 <help> | 89 <help><![CDATA[ |
88 <![CDATA[ | |
89 | 90 |
90 @MOTHUR_OVERVIEW@ | 91 @MOTHUR_OVERVIEW@ |
91 | 92 |
92 **Command Documentation** | 93 **Command Documentation** |
93 | 94 |
94 The make.group_ command reads a fasta file or series of fasta files and creates a group_ file. | 95 The make.group_ command reads a fasta file or series of fasta files and creates a group_ file. |
95 | 96 |
96 .. _group: https://www.mothur.org/wiki/Group_file | 97 .. _group: https://www.mothur.org/wiki/Group_file |
97 .. _make.group: https://www.mothur.org/wiki/Make.group | 98 .. _make.group: https://www.mothur.org/wiki/Make.group |
98 | 99 |
99 ]]> | 100 ]]></help> |
100 </help> | |
101 <expand macro="citations"/> | 101 <expand macro="citations"/> |
102 </tool> | 102 </tool> |