Mercurial > repos > iuc > mothur_merge_files

comparison merge.files.xml @ 2:669032cdc951 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author iuc
date Tue, 20 Mar 2018 22:18:51 -0400
parents 28a135978ed0
children
comparison
equal deleted inserted replaced
1:a70b25374a23 2:669032cdc951
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 #for $i in $merge.inputs: 13 #for $i in $merge.inputs:
14 ln -s "$i" input${merge.inputs.index($i)}.dat && 14 ln -s '$i' input${merge.inputs.index($i)}.dat &&
15 #end for 15 #end for
16 16
17 echo 'merge.files( 17 echo 'merge.files(
18 input=#for $i in $merge.inputs#input${merge.inputs.index($i)}.dat-#end for#, 18 input=#for $i in $merge.inputs#input${merge.inputs.index($i)}.dat-#end for#,
19 output=$output 19 output=$output
20 )' 20 )'
21 | sed 's/ //g' ## mothur trips over whitespace 21 | sed 's/ //g' ## mothur trips over whitespace
22 | sed 's/-,/,/g' 22 | sed 's/-,/,/g'
23 | mothur 23 | mothur
24 | tee mothur.out.log 24 | tee mothur.out.log
25 ]]></command> 25 ]]></command>
26 <inputs> 26 <inputs>
27 <conditional name="merge"> 27 <conditional name="merge">
28 <param name="type" type="select" format="fasta,qual,mothur.groups,mothur.names,mothur.accnos" label="Merge"> 28 <param name="type" type="select" format="fasta,qual,mothur.groups,mothur.names,mothur.accnos" label="Merge">
29 <option value="fasta">fasta files</option> 29 <option value="fasta">fasta files</option>
46 </when> <!-- names --> 46 </when> <!-- names -->
47 <when value="accnos"> 47 <when value="accnos">
48 <param name="inputs" type="data" format="mothur.accnos" multiple="true" label="inputs - accnos"/> 48 <param name="inputs" type="data" format="mothur.accnos" multiple="true" label="inputs - accnos"/>
49 </when> <!-- fasta --> 49 </when> <!-- fasta -->
50 </conditional> <!-- merge --> 50 </conditional> <!-- merge -->
51 <expand macro="param-savelog"/>
51 </inputs> 52 </inputs>
52 <outputs> 53 <outputs>
53 <expand macro="logfile-output"/> 54 <expand macro="logfile-output"/>
54 <data format_source="inputs" name="output" label="${tool.name} on ${on_string}: ${merge.type}"/> 55 <data format_source="inputs" name="output" label="${tool.name} on ${on_string}: ${merge.type}"/>
55 </outputs> 56 </outputs>
56 <tests> 57 <tests>
57 <test> 58 <test>
58 <param name="type" value="fasta"/> 59 <param name="type" value="fasta"/>
59 <param name="inputs" value="sample1.fa,sample2.fa,sample3.fa" ftype="fasta"/> 60 <param name="inputs" value="sample1.fa,sample2.fa,sample3.fa" ftype="fasta"/>
60 <output name="output" file="output.fa" ftype="fasta"/> 61 <output name="output" file="output.fa" ftype="fasta"/>
62 <param name="savelog" value="true"/>
61 <expand macro="logfile-test"/> 63 <expand macro="logfile-test"/>
62 </test> 64 </test>
63 </tests> 65 </tests>
64 <help> 66 <help><![CDATA[
65 @MOTHUR_OVERVIEW@ 67 @MOTHUR_OVERVIEW@
66 68
67 **Command Documentation** 69 **Command Documentation**
68 70
69 The merge.files_ command merge inputs into a single output. 71 The merge.files_ command merge inputs into a single output.
70 72
71 .. _merge.files: https://www.mothur.org/wiki/Merge.files 73 .. _merge.files: https://www.mothur.org/wiki/Merge.files
72 74
73 75
74 </help> 76 ]]></help>
75 <expand macro="citations"/> 77 <expand macro="citations"/>
76 </tool> 78 </tool>