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comparison merge.files.xml @ 0:28a135978ed0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 05:10:40 -0400
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1 <tool profile="16.07" id="mothur_merge_files" name="Merge.files" version="@WRAPPER_VERSION@.0">
2 <description>Merge data</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
8 <expand macro="version_command"/>
9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
12 ## create symlinks to input datasets
13 #for $i in $merge.inputs:
14 ln -s "$i" input${merge.inputs.index($i)}.dat &&
15 #end for
16
17 echo 'merge.files(
18 input=#for $i in $merge.inputs#input${merge.inputs.index($i)}.dat-#end for#,
19 output=$output
20 )'
21 | sed 's/ //g' ## mothur trips over whitespace
22 | sed 's/-,/,/g'
23 | mothur
24 | tee mothur.out.log
25 ]]></command>
26 <inputs>
27 <conditional name="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>
30 <option value="qual">qual files</option>
31 <option value="groups">group files</option>
32 <option value="names">name files</option>
33 <option value="accnos">accnos files</option>
34 </param>
35 <when value="fasta">
36 <param name="inputs" type="data" format="fasta" multiple="true" label="inputs - fasta"/>
37 </when> <!-- fasta -->
38 <when value="qual">
39 <param name="inputs" type="data" format="qual" multiple="true" label="inputs - qual"/>
40 </when> <!-- qual -->
41 <when value="groups">
42 <param name="inputs" type="data" format="mothur.groups" multiple="true" label="inputs - groups"/>
43 </when> <!-- groups -->
44 <when value="names">
45 <param name="inputs" type="data" format="mothur.names" multiple="true" label="inputs - names"/>
46 </when> <!-- names -->
47 <when value="accnos">
48 <param name="inputs" type="data" format="mothur.accnos" multiple="true" label="inputs - accnos"/>
49 </when> <!-- fasta -->
50 </conditional> <!-- merge -->
51 </inputs>
52 <outputs>
53 <expand macro="logfile-output"/>
54 <data format_source="inputs" name="output" label="${tool.name} on ${on_string}: ${merge.type}"/>
55 </outputs>
56 <tests>
57 <test>
58 <param name="type" value="fasta"/>
59 <param name="inputs" value="sample1.fa,sample2.fa,sample3.fa" ftype="fasta"/>
60 <output name="output" file="output.fa" ftype="fasta"/>
61 <expand macro="logfile-test"/>
62 </test>
63 </tests>
64 <help>
65 @MOTHUR_OVERVIEW@
66
67 **Command Documentation**
68
69 The merge.files_ command merge inputs into a single output.
70
71 .. _merge.files: https://www.mothur.org/wiki/Merge.files
72
73
74 </help>
75 <expand macro="citations"/>
76 </tool>