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comparison merge.xml @ 4:25136a2b0cfe draft

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planemo upload commit 0340e76ceab90331dab96f4a6b8a9b7df5b8c1c2
author nml
date Fri, 10 Mar 2017 16:12:32 -0500
parents c0c988378838
children 33151a38533a
comparison
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3:c0c988378838 4:25136a2b0cfe
1 <tool id="collapse_dataset" name="Collapse Collection" version="3.0"> 1 <tool id="collapse_dataset" name="Collapse Collection" version="4.0">
2 <description>Collapse collection into single dataset in order of the collection</description> 2 <description>into single dataset in order of the collection</description>
3 <command> 3 <command>
4 <![CDATA[ 4 <![CDATA[
5 5
6 ( 6 (
7 #if $one_header:
8 #if $filename.add_name:
9 awk '{if (NR==1) {print "Sample\t"$0}}' "$input_list[0]";
10 #else:
11 awk '{if (NR==1) {print}}' "$input_list[0]";
12 #end if
13 #end if
14
7 #for $f in $input_list# 15 #for $f in $input_list#
8 #if $filename.add_name: 16 #if $filename.add_name:
9 #if str($filename.place_name) == "same_once": 17 #if str($filename.place_name) == "same_once":
18 #if $one_header:
19 printf "$f.element_identifier\t"; tail -q -n +2 "$f";
20 #else:
10 printf "$f.element_identifier\t"; cat "$f"; 21 printf "$f.element_identifier\t"; cat "$f";
22 #end if
11 #elif str($filename.place_name) == "same_multiple": 23 #elif str($filename.place_name) == "same_multiple":
24 #if $one_header:
25 awk '{if (NR!=1) {print "$f.element_identifier\t"$0}}' "$f";
26 #else:
12 awk '{print "$f.element_identifier\t"$0}' "$f"; 27 awk '{print "$f.element_identifier\t"$0}' "$f";
28 #end if
13 #elif str($filename.place_name) == "above": 29 #elif str($filename.place_name) == "above":
30 #if $one_header:
31 printf "$f.element_identifier\n"; tail -q -n +2 "$f";
32 #else:
14 printf "$f.element_identifier\n"; cat "$f"; 33 printf "$f.element_identifier\n"; cat "$f";
34 #end if
15 #end if 35 #end if
16 #else: 36 #else:
17 cat "$f" ; 37 #if $one_header:
38 awk '{if (NR!=1) {print}}' "$f";
39 #else:
40 cat "$f" ;
41 #end if
18 #end if 42 #end if
19 43
20 #end for# 44 #end for#
21 ) 45 )
22 > $output 46 > $output
23 47
24 ]]> 48 ]]>
25 49
26 </command> 50 </command>
27 <inputs> 51 <inputs>
28 <param name="input_list" type="data" format="data" label="Collection of files to collapse into single dataset" help="" optional="false" multiple="true" /> 52 <param name="input_list" type="data" format="data" label="Collection of files to collapse into single dataset" help="" optional="false" multiple="true" />
53 <param name="one_header" type="boolean" display="checkboxes" label="Keep one header line" help="Combine first line of each file as the header for the final dataset. Useful when same header line is found in all files."/>
29 <conditional name="filename"> 54 <conditional name="filename">
55
30 <param name="add_name" type="boolean" display="checkboxes" label="Append File name"/> 56 <param name="add_name" type="boolean" display="checkboxes" label="Append File name"/>
31 <when value="true"> 57 <when value="true">
32 <param name="place_name" type="select" label="Where to add dataset name"> 58 <param name="place_name" type="select" label="Where to add dataset name">
33 <option value="same_once">Same line and only once per dataset</option> 59 <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> 60 <option value="same_multiple">Same line and each line in dataset</option>
42 <outputs> 68 <outputs>
43 <data name="output" format_source="input_list" ></data> 69 <data name="output" format_source="input_list" ></data>
44 </outputs> 70 </outputs>
45 <tests> 71 <tests>
46 <test> 72 <test>
47 <param name="input_list"> 73 <param name="input_list" value="input1,input2"/>
48 <collection type="list">
49 <element name="input1" value="input1" />
50 <element name="input2" value="input2" />
51 </collection>
52 </param>
53 <output name="output" file="answer.txt"/> 74 <output name="output" file="answer.txt"/>
54 </test> 75 </test>
76 <test>
77 <param name="input_list" value="strain1.tsv,strain2.tsv"/>
78 <param name="one_header" value="True"/>
79 <param name="add_name" value="True"/>
80 <param name="place_name" value="same_multiple"/>
81 <output name="output" file="answer2.tsv"/>
82 </test>
83 <test>
84 <param name="input_list" value="strain1.tsv,strain2.tsv"/>
85 <param name="one_header" value="True"/>
86 <output name="output" file="answer3.tsv"/>
87 </test>
88
55 </tests> 89 </tests>
56 <help> 90 <help>
57 Combines a list collection into a single file dataset with option to include dataset names. 91 Combines a list collection into a single file dataset with option to include dataset names or merge common header line.
58 </help> 92 </help>
59 <citations> 93 <citations>
60 </citations> 94 </citations>
61 </tool> 95 </tool>