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"planemo upload commit a4a44618ffd955909c0d21d12d73659e9086bdb9"
author nml
date Thu, 13 Aug 2020 16:46:16 -0400
parents 830961c48e42
children
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1 <tool id="collapse_dataset" name="Collapse Collection" version="5.1.0" profile="16.04">
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2 <description>into single dataset in order of the collection</description>
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3 <requirements>
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4 <requirement type="package" version="5.1.0">gawk</requirement>
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5 </requirements>
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6 <command>
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7 <![CDATA[
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8
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9 (
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10 #if $one_header:
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11 #if $filename.add_name:
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12 awk '{if (NR==1) {print "Sample\t"$0}}' "$input_list[0]";
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13 #else:
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14 awk '{if (NR==1) {print}}' "$input_list[0]";
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15 #end if
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16 #end if
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17
1
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18 #for $f in $input_list#
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19 #if $filename.add_name:
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20 #if str($filename.place_name) == "same_once":
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21 #if $one_header:
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22 printf "$f.element_identifier\t"; tail -q -n +2 "$f";
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23 #else:
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24 printf "$f.element_identifier\t"; awk '{ print $0 } END { if (NR == 0 && NF == 0) { print "" } }' "$f";
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25 #end if
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26 #elif str($filename.place_name) == "same_multiple":
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27 #if $one_header:
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28 awk '{if (NR!=1) {print "$f.element_identifier\t"$0}}' "$f";
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29 #else:
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30 awk '{print "$f.element_identifier\t"$0} END { if (NR == 0 && NF == 0) { print "$f.element_identifier\t" } }' "$f";
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31 #end if
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32 #elif str($filename.place_name) == "above":
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33 #if $one_header:
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34 printf "$f.element_identifier\n"; tail -q -n +2 "$f";
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35 #else:
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36 printf "$f.element_identifier\n"; cat "$f";
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37 #end if
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38 #end if
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39 #else:
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40 #if $one_header:
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41 awk '{if (NR!=1) {print}}' "$f";
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42 #else:
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43 cat "$f" ;
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44 #end if
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45 #end if
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46
1
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47 #end for#
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48 )
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49 > $output
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50
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51 ]]>
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52
0
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53 </command>
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54 <inputs>
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55 <param name="input_list" type="data" format="data" label="Collection of files to collapse into single dataset" help="" optional="false" multiple="true" />
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56 <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."/>
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57 <conditional name="filename">
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58 <param name="add_name" type="boolean" display="checkboxes" label="Prepend File name"/>
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59 <when value="true">
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60 <param name="place_name" type="select" label="Where to add dataset name">
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61 <option value="same_once">Same line and only once per dataset</option>
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62 <option value="same_multiple">Same line and each line in dataset</option>
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63 <option value="above">Line Above</option>
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64 </param>
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65 </when>
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66 <when value='false'>
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67 </when>
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68 </conditional>
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69 </inputs>
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70 <outputs>
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71 <data name="output" format_source="input_list" ></data>
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72 </outputs>
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73 <tests>
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74 <test>
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75 <param name="input_list" value="input1,input2"/>
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76 <output name="output" file="answer.txt"/>
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77 </test>
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78 <test>
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79 <param name="input_list" value="strain1.tsv,strain2.tsv"/>
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80 <param name="one_header" value="True"/>
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81 <param name="add_name" value="True"/>
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82 <param name="place_name" value="same_multiple"/>
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83 <output name="output" file="answer2.tsv"/>
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84 </test>
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85 <test>
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86 <param name="input_list" value="strain1.tsv,strain2.tsv"/>
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87 <param name="one_header" value="True"/>
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88 <output name="output" file="answer3.tsv"/>
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89 </test>
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90
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91 </tests>
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92 <help>
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93 Combines a list collection into a single file dataset with option to include dataset names or merge common header line.
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94 </help>
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95 <citations>
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96 </citations>
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97 </tool>