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comparison merge.xml @ 3:c0c988378838 draft

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planemo upload commit 6bde05f38465311441e89cfa070f03d3b6edad1b
author nml
date Mon, 24 Oct 2016 16:23:11 -0400
parents 4263967e8d40
children 25136a2b0cfe
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2:4263967e8d40 3:c0c988378838
1 <tool id="collapse_dataset" name="Collapse Collection" version="2.1"> 1 <tool id="collapse_dataset" name="Collapse Collection" version="3.0">
2 <description>Collapse collection into single dataset in order of the collection</description> 2 <description>Collapse collection into single dataset in order of the collection</description>
3 <command> 3 <command>
4 <![CDATA[ 4 <![CDATA[
5 5
6 ( 6 (
7 #for $f in $input_list# 7 #for $f in $input_list#
8 #if $filename.add_name: 8 #if $filename.add_name:
9 #if str($filename.place_name) == "same": 9 #if str($filename.place_name) == "same_once":
10 printf "$f.element_identifier\t" ; 10 printf "$f.element_identifier\t"; cat "$f";
11 #else 11 #elif str($filename.place_name) == "same_multiple":
12 printf "$f.element_identifier\n" ; 12 awk '{print "$f.element_identifier\t"$0}' "$f";
13 #elif str($filename.place_name) == "above":
14 printf "$f.element_identifier\n"; cat "$f";
13 #end if 15 #end if
16 #else:
17 cat "$f" ;
14 #end if 18 #end if
15 cat "$f" ; 19
16 #end for# 20 #end for#
17 ) 21 )
18 > $output 22 > $output
19 23
20 ]]> 24 ]]>
21 25
22 </command> 26 </command>
23 <inputs> 27 <inputs>
24 <param name="input_list" type="data" label="Collection of files to collapse into single dataset" help="" optional="false" multiple="true" /> 28 <param name="input_list" type="data" format="data" label="Collection of files to collapse into single dataset" help="" optional="false" multiple="true" />
25 <conditional name="filename"> 29 <conditional name="filename">
26 <param name="add_name" type="boolean" display="checkboxes" label="Append File name"/> 30 <param name="add_name" type="boolean" display="checkboxes" label="Append File name"/>
27 <when value="true"> 31 <when value="true">
28 <param name="place_name" type="select" label="Where to add dataset name"> 32 <param name="place_name" type="select" label="Where to add dataset name">
29 <option value="same">Same line</option> 33 <option value="same_once">Same line and only once per dataset</option>
34 <option value="same_multiple">Same line and each line in dataset</option>
30 <option value="above">Line Above</option> 35 <option value="above">Line Above</option>
31 </param> 36 </param>
32 </when> 37 </when>
33 <when value='false'> 38 <when value='false'>
34 </when> 39 </when>
36 </inputs> 41 </inputs>
37 <outputs> 42 <outputs>
38 <data name="output" format_source="input_list" ></data> 43 <data name="output" format_source="input_list" ></data>
39 </outputs> 44 </outputs>
40 <tests> 45 <tests>
41 <test> 46 <test>
42 <param name="input_list"> 47 <param name="input_list">
43 <collection type="list"> 48 <collection type="list">
44 <element name="input1" value="input1" /> 49 <element name="input1" value="input1" />
45 <element name="input2" value="input2" /> 50 <element name="input2" value="input2" />
46 </collection> 51 </collection>
47 </param> 52 </param>
48 <output name="output" file="answer.txt"/> 53 <output name="output" file="answer.txt"/>
49 </test> 54 </test>
50 </tests> 55 </tests>
51 <help> 56 <help>
52 Combines a list collection into a single file dataset with option to include dataset names. 57 Combines a list collection into a single file dataset with option to include dataset names.
53
54
55 </help> 58 </help>
56 <citations> 59 <citations>
57 </citations> 60 </citations>
58 </tool> 61 </tool>