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comparison bundle_collection.xml @ 1:cd6da887a5f4 draft

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planemo upload commit 44ee87b603c444f0ae5f73dea57d4ed2f589a4eb
author nml
date Fri, 04 Aug 2017 12:04:09 -0400
parents bae199dc511f
children 705ebd286b57
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0:bae199dc511f 1:cd6da887a5f4
1 <tool id="bundle_collection" name="Bundle Collection" version="1.0.1"> 1 <tool id="bundle_collection" name="Bundle Collection" version="1.2.1">
2 <description>Download a collection of files</description> 2 <description>Download a collection of files</description>
3 <stdio>
4 <exit_code range="1:" level="fatal" description="Unknown error has occurred"/>
5 </stdio>
3 <command interpreter="perl">bundle_collection.pl -h $html_file -p $html_file.files_path 6 <command interpreter="perl">bundle_collection.pl -h $html_file -p $html_file.files_path
4 #for $f in $input.keys 7
5 -i "$f,$input[$f].ext=$input[$f]" 8 #if $singles_or_list.type == "list":
6 #if $input[$f].metadata.bam_index and $input[$f].metadata.bam_index != "None" 9
7 #set $bamind = $f+","+$input[$f].ext+".bai="+$input[$f].metadata.bam_index 10 #if $singles_or_list.input:
8 -i "$bamind" 11 #for $f in $singles_or_list.input.keys
9 #end if 12 -i "$f,$singles_or_list.input[$f].ext=$singles_or_list.input[$f]"
10 #end for 13 #if $singles_or_list.input[$f].metadata.bam_index and $singles_or_list.input[$f].metadata.bam_index != "None"
14 #set $bamind = $f+","+$singles_or_list.input[$f].ext+".bai="+$singles_or_list.input[$f].metadata.bam_index
15 -i "$bamind"
16 #end if
17 #end for
18 #end if
19 #elif $singles_or_list.type == "singles":
20 #for $dataset in $singles_or_list.single_files
21 #if $dataset.single_file:
22 -i "$dataset.single_file.name,$dataset.single_file.ext=$dataset.single_file"
23 #end if
24
25 #if $dataset.single_file.metadata.bam_index and $dataset.single_file.metadata.bam_index != "None"
26 #set $bamind = $dataset.single_file.name+","+$dataset.single_file.ext+".bai="+$dataset.single_file.metadata.bam_index
27 -i "$bamind"
28 #end if
29
30 #end for
31 #end if
11 </command> 32 </command>
12 33
13 <inputs> 34 <inputs>
14 <param name="input" type="data_collection" label="Data Collection" collection_type="list"/> 35 <conditional name="singles_or_list">
36 <param name="type" type="select" label="Bundle type">
37 <option value="singles">Individual datasets</option>
38 <option value="list">List Collection </option>
39 </param>
40 <when value="singles">
41 <repeat name='single_files' title='Single dataset(s)'>
42 <param name="single_file" label="Dataset to add the bundle" type="data" format='data' optional='False'/>
43 </repeat>
44 </when>
45 <when value="list">
46 <param name="input" type="data_collection" label="Data Collection" collection_type="list" optional='False'/>
47 </when>
48 </conditional>
15 </inputs> 49 </inputs>
16 50
17 <outputs> 51 <outputs>
18 <data name="html_file" format="html" label="Bundled Collection" /> 52 <data name="html_file" format="html" label="Bundled Collection" />
19 </outputs> 53 </outputs>
54 <tests>
55 <test>
56 <output/>
57 </test>
58 </tests>
59
20 <help> 60 <help>
21 ***What it does** 61 ***What it does**
22 62
23 This tool will bundle up files in a list collection into a downloadable zip file 63 This tool will bundle up files in a list collection into a downloadable zip file
24 64
25 Author: Mariam Iskander and Jen Cabral 65 Author: Mariam Iskander and Jen Cabral
26 </help> 66 </help>
27 67
68 <citations>
69 </citations>
70
28 </tool> 71 </tool>