Mercurial > repos > azomics > check_fcs_header

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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
author azomics
date Wed, 24 Jun 2020 17:36:27 -0400
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2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
azomics
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1 <tool id="get_fcs_headers" name="Get list of markers" version="2.0+galaxy0">
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
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2 <description>in FCS files.</description>
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
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3 <requirements>
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
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4 <requirement type="package" version="1.42.0">bioconductor-flowcore</requirement>
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
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5 </requirements>
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
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6 <stdio>
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
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7 <exit_code range="10" level="warning" description="Not all files are valid FCS files, see output for details." />
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
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8 </stdio>
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
azomics
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9 <command><![CDATA[
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
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10 Rscript '$__tool_directory__/getFCSheader.R' '${output_file}'
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
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11 #for $f in $input
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
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12 '${f}' '${f.name}'
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
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13 #end for
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
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14 ]]>
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
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15 </command>
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16 <inputs>
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17 <param format="fcs" name="input" type="data_collection" collection_type="list" label="FCS files Collection"/>
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
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18 </inputs>
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
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19 <outputs>
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20 <data format="tabular" name="output_file" label="Headers of files in ${input.name}"/>
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
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21 </outputs>
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
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22 <tests>
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
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23 <test>
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
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24 <param name="input">
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
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25 <collection type="list">
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
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26 <element name="input1.fcs" value="input1.fcs"/>
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
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27 <element name="input2.fcs" value="input2.fcs"/>
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
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28 <element name="input3.fcs" value="input3.fcs"/>
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
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29 </collection>
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
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30 </param>
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
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31 <output name="output_file" file="output.tabular" lines_diff="8"/>
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
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32 </test>
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
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33 </tests>
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
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34 <help><![CDATA[
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
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35 This tool returns a table of the headers of a set of FCS files.
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
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36
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37 -----
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
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38
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
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39 **Input files**
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40
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
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41 This tool requires collections of FCS files as input.
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
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42
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
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43 **Output file**
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44
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
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45 The output file is a table listing the markers and channels for each file.
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46
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47 -----
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
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48
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
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49 **Example**
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50
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
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51 *File1*::
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52
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53 Marker1 Marker2 Marker3
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54 34 45 12
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55 33 65 10
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56
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57 *File2*::
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58
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59 Marker4 Marker5 Marker3
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60 19 62 98
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61 12 36 58
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62
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
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63 *Output*::
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64
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
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65 Filename Index 1 2 3
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66 File1 channels Channel1 Channel2 Channel3
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67 File2 channels Channel4 Channel5 Channel3
2227def10ea4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
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68 File1 markers Marker1 Marker2 Marker3
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69 File2 markers Marker4 Marker5 Marker3
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70 ]]>
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71 </help>
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72 </tool>