Mercurial > repos > azomics > metacyto_checkpanel

annotate metacyto_checkpanel.xml @ 0:67d79ba0f7aa draft default tip

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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
author azomics
date Tue, 27 Jul 2021 21:47:56 +0000
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67d79ba0f7aa "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
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1 <tool id="metacyto_checkpanel" name="Check markers in analysis panels" version="1.0+galaxy0" profile="18.01">
67d79ba0f7aa "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
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2 <description>for MetaCyto</description>
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3 <requirements>
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4 <requirement type="package" version="1.4.0">bioconductor-metacyto</requirement>
67d79ba0f7aa "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
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5 </requirements>
67d79ba0f7aa "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
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6 <stdio>
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7 <exit_code range="1:9" />
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8 <exit_code range="10" level="fatal" description="The input file cannot be used. Please check input format." />
67d79ba0f7aa "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
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9 <exit_code range="11:" />
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10 </stdio>
67d79ba0f7aa "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
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11 <command><![CDATA[
67d79ba0f7aa "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
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12 Rscript --slave --vanilla '$__tool_directory__/metacyto_checkpanel.R' '${input_file}' '${output_file}';
67d79ba0f7aa "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
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13 #if $graph=="TRUE"
67d79ba0f7aa "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
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14 mv panel_summary.pdf '${pdf_out}'
67d79ba0f7aa "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
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15 #end if
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16 ]]>
67d79ba0f7aa "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
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17 </command>
67d79ba0f7aa "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
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18 <inputs>
67d79ba0f7aa "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
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19 <param format="metacyto_summary.txt" name="input_file" type="data" label="MetaCyto preprocessing summary"/>
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20 <param name="graph" type="boolean" label="Output visual summary?" checked="false" truevalue="TRUE" falsevalue="FALSE" />
67d79ba0f7aa "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
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21 </inputs>
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22 <outputs>
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23 <data format="tabular" name="output_file" label="Panel Summary of ${input_file.name}"/>
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24 <data format="pdf" name="pdf_out" label="Visual Panel Summary of ${input_file.name}">
67d79ba0f7aa "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
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25 <filter>(graph)</filter>
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26 </data>
67d79ba0f7aa "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
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27 </outputs>
67d79ba0f7aa "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
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28 <tests>
67d79ba0f7aa "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
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29 <test>
67d79ba0f7aa "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
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30 <param name="input_file" value="mc_preprocesss_summary.metacyto_summary.txt"/>
67d79ba0f7aa "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
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31 <param name="graph" value="True"/>
67d79ba0f7aa "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
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32 <output name="output_file" ftype="tabular">
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33 <assert_contents>
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34 <has_n_columns n="3" />
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35 <has_text text="CD95" />
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36 <has_n_lines n="14" />
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37 </assert_contents>
67d79ba0f7aa "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
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38 </output>
67d79ba0f7aa "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
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39 <output name="pdf_out" ftype="pdf">
67d79ba0f7aa "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
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40 <assert_contents>
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41 <has_size value="4569" delta="500" />
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42 </assert_contents>
67d79ba0f7aa "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
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43 </output>
67d79ba0f7aa "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
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44 </test>
67d79ba0f7aa "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
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45 </tests>
67d79ba0f7aa "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
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46 <help><![CDATA[
67d79ba0f7aa "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
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47 Metacyto Check Markers in analysis panels
67d79ba0f7aa "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
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48 -----------------------------------------
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49
67d79ba0f7aa "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
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50 This tool uses MetaCyto's panel summary function to compare marker names between groups of FCS files.
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51
67d79ba0f7aa "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
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52 **Input**
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53 This tool requires the MetaCyto pre-processing Summary as input.
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54
67d79ba0f7aa "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
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55 **Output**
67d79ba0f7aa "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
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56 This tool generates a table and an optional visual representation in PDF of how markers are distributed in the FCS file sets.
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57
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58
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59 **Example**
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60
67d79ba0f7aa "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
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61 *Input* - Summary Table::
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62
67d79ba0f7aa "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
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63 study_id antibodies filenames
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64 group1 Marker1|Marker2|Marker3|... file1.fcs
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65 group2 Marker1|Marker2|Marker3|... file2.fcs
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66 ... ... ...
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67
67d79ba0f7aa "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
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68 *Output* - Panel Summary::
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69
67d79ba0f7aa "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
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70 Markers group1 group2 ...
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71 Marker1 1 1 ...
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72 Marker2 1 1 ...
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73 Marker3 0 1 ...
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74 ... ... ... ...
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75
67d79ba0f7aa "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
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76 *Graphical output*
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77
67d79ba0f7aa "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
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78 .. image:: ./images/checkpanel.png
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79 ]]>
67d79ba0f7aa "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
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80 </help>
67d79ba0f7aa "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14b2e4d834a9856236affb7b77debecca360c542"
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81 </tool>