Mercurial > repos > immport-devteam > check_headers

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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
author azomics
date Tue, 14 Jul 2020 09:46:31 -0400
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05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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1 <tool id="get_headers" name="Check headers" version="1.1+galaxy0" profile="18.01">
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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2 <description>of any set of flowtext files</description>
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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3 <requirements>
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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4 <requirement type="package" version="3.8.3">python</requirement>
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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5 </requirements>
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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6 <stdio>
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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7 <exit_code range="1:" />
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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8 </stdio>
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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9 <command><![CDATA[
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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10 python3 '$__tool_directory__/getHeaders.py' -o '${output_file}'
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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11 #for $f in $input
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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12 -i '${f}'
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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13 -n '${f.name}'
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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14 #end for
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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15 ]]>
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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16 </command>
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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17 <inputs>
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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18 <param format="flowtext,tabular,txt" name="input" type="data_collection" collection_type="list" label="Text files Collection"/>
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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19 </inputs>
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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20 <outputs>
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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21 <data format="tabular" name="output_file" label="Headers of files in ${input.name}"/>
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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22 </outputs>
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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23 <tests>
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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24 <test>
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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25 <param name="input">
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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26 <collection type="list">
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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27 <element name="input1.txt" value="input1.txt"/>
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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28 <element name="input2.txt" value="input2.txt"/>
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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29 <element name="input3.txt" value="input3.txt"/>
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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30 </collection>
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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31 </param>
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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32 <output name="output_file" file="output.tabular" lines_diff="4"/>
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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33 </test>
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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34 </tests>
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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35 <help><![CDATA[
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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36 This tool returns a table of the headers of a set of text files.
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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37
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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38 -----
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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39
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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40 **Input files**
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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41
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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42 This tool requires collections of txt, flowtext or tabular files as input.
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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43
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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44 **Output file**
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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45
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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46 The output file is a table listing the headers for each file.
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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47
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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48 -----
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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49
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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50 **Example**
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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51
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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52 *File1*::
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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53
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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54 Marker1 Marker2 Marker3
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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55 34 45 12
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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56 33 65 10
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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57
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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58 *File2*::
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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59
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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60 Marker4 Marker5 Marker3
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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61 19 62 98
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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62 12 36 58
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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63
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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64 *Output*::
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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65
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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66 Index 1 2 3
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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67 File1 Marker1 Marker2 Marker3
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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68 File2 Marker4 Marker5 Marker3
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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69 ]]>
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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70 </help>
05440ef97f8b "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
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71 </tool>