Mercurial > repos > iuc > mothur_make_group

comparison make.group.xml @ 4:63a75db03ecc draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit be5c8af076296a53959fc3ed2b82d92dc7607eeb
author iuc
date Mon, 23 Apr 2018 09:42:15 -0400
parents 4f91a75ac701
children
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3:43f7c6cfc023 4:63a75db03ecc
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 #import re
13
12 #set fastas = '' 14 #set fastas = ''
13 #set groups = '' 15 #set groups = ''
14 #set count = 0 16 #set count = 0
15 17
16 #if $method.how == 'collection': 18 #if $method.how == 'collection':
17 #for $i in $method.fasta_collection: 19 #for $i in $method.fasta_collection:
18 ln -s '$i' fasta_${i.element_identifier}.dat && 20 #set $identifier=re.sub('[^\w_]', '_', str($i.element_identifier))
19 #set fastas+='fasta_'+$i.element_identifier+'.dat-' 21 ln -s '$i' 'fasta_${identifier}.dat' &&
20 #set groups+=$i.element_identifier+'-' 22 #set fastas+='fasta_'+$identifier+'.dat-'
23 #set groups+=$identifier+'-'
21 #end for 24 #end for
22 #else 25 #else
23 #for $i in $method.inputs: 26 #for $i in $method.inputs:
24 ln -s '$i.fasta' fasta_${count}.dat && 27 ln -s '$i.fasta' fasta_${count}.dat &&
25 #set fastas+='fasta_'+str($count)+'.dat-' 28 #set fastas+='fasta_'+str($count)+'.dat-'
41 <param name="how" type="select" label="Method to create group file"> 44 <param name="how" type="select" label="Method to create group file">
42 <option value="collection"> Automatically from collection </option> 45 <option value="collection"> Automatically from collection </option>
43 <option value="manually"> Manually specify fasta files and group names</option> 46 <option value="manually"> Manually specify fasta files and group names</option>
44 </param> 47 </param>
45 <when value="collection"> 48 <when value="collection">
46 <param name="fasta_collection" type="data_collection" collection_type="list" format="fasta" label="Collection with fasta files to group" help="group names will be named after the collection element names"/> 49 <param name="fasta_collection" type="data_collection" collection_type="list" format="fasta" label="Collection with fasta files to group"
50 help="group names will be derived from the dataset names of the collection elements, please make sure these are meaningful names"/>
47 </when> 51 </when>
48 <when value="manually"> 52 <when value="manually">
49 <repeat name="inputs" title="Additional"> 53 <repeat name="inputs" title="Additional">
50 <param name="fasta" type="data" format="fasta" label="fasta - Fasta to group"/> 54 <param name="fasta" type="data" format="fasta" label="fasta - Fasta to group"/>
51 <param name="group" type="text" label="group - Group name"/> 55 <param name="group" type="text" label="group - Group name"/>
83 </param> 87 </param>
84 <output name="output" file="Mock_S280_L001_R1_001_small.trim.contigs.good.Mock_S280_L001_R1_001_small.trim.contigs.good.groups"/> 88 <output name="output" file="Mock_S280_L001_R1_001_small.trim.contigs.good.Mock_S280_L001_R1_001_small.trim.contigs.good.groups"/>
85 <param name="savelog" value="true"/> 89 <param name="savelog" value="true"/>
86 <expand macro="logfile-test"/> 90 <expand macro="logfile-test"/>
87 </test> 91 </test>
92 <test> <!-- test with spaces or hyphens in element identifier -->
93 <param name="how" value="collection"/>
94 <param name="fasta_collection">
95 <collection type="list">
96 <element name="test group" ftype="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head" />
97 <element name="test-group2" ftype="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head" />
98 </collection>
99 </param>
100 <output name="output" file="make_group_collection.groups"/>
101 <param name="savelog" value="true"/>
102 <expand macro="logfile-test"/>
103 </test>
88 </tests> 104 </tests>
89 <help><![CDATA[ 105 <help><![CDATA[
90 106
91 @MOTHUR_OVERVIEW@ 107 @MOTHUR_OVERVIEW@
92 108